[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/11541492/KIRC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/KIRC-TP/11549172/transformed.cor.cli.txt"

nPatients in clinical file=525, in cluster file=528, common to both=516
[1] "Reduce the number of clustering variables from 80 to 79."
[1]  79 516
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               24               492 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               24               492 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               51               465 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               51               465 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               75               441 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               75               441 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               77               439 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               77               439 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               19               497 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               19               497 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               60               456 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               60               456 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               13               503 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               13               503 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               13               503 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               13               503 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              191               325 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              191               325 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
              204               312 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
              204               312 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               11               505 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               11               505 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                9               507 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                9               507 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              170               346 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              170               346 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              171               345 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              171               345 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               30               486 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               30               486 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               61               455 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               61               455 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               13               503 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               13               503 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               12               504 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               12               504 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                17                499 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                17                499 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                12                504 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                12                504 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                31                485 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                31                485 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                29                487 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                29                487 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               119                397 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               119                397 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               120                396 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               120                396 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                22                494 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                22                494 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                16                500 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                16                500 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                26                490 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                26                490 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
               105                411 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
               105                411 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                97                419 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                97                419 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                25                491 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                25                491 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                32                484 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                32                484 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                25                491 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                25                491 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                25                491 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                25                491 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                51                465 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                51                465 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                57                459 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                57                459 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               110                406 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               110                406 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               113                403 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               113                403 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                49                467 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                49                467 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                40                476 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                40                476 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               30               486 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               30               486 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               55               461 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               55               461 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               36               480 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               36               480 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               14               502 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               14               502 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               14               502 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               14               502 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              371               145 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              371               145 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               97               419 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               97               419 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               72               444 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               72               444 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               65               451 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               65               451 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                7               509 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                7               509 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                6               510 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                6               510 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
              100               416 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
              100               416 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              128               388 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              128               388 
[1] "7Q LOSS MUTATION ANALYSIS"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                3               513 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                3               513 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              135               381 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              135               381 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               63               453 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               63               453 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              147               369 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              147               369 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              148               368 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              148               368 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                65                451 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                65                451 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                87                429 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                87                429 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                18                498 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                18                498 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                23                493 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                23                493 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 3                513 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 3                513 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 4                512 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 4                512 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                70                446 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                70                446 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               213                303 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               213                303 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                35                481 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                35                481 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 9                507 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 9                507 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                14                502 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                14                502 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                45                471 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                45                471 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                28                488 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                28                488 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                92                424 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                92                424 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                94                422 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                94                422 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                11                505 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                11                505 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 4                512 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 4                512 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 8                508 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 8                508 
[1] "20Q LOSS MUTATION ANALYSIS"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 3                513 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 3                513 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                54                462 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                54                462 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                39                477 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                39                477 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               46               470 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               46               470 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDISEASE"                  
 [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 516 columns.

[1] "Batch" "22"   
[1] "Last Follow UP"
TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 
         267         1120         1436           16           NA          735 
TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 
        1493         1491         1130         1508         1478         1106 
TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 
        1186          751         1137         1485          665         1043 
TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 
         945           NA         1610         1385          910           NA 
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-A6NJ TCGA-A3-A6NL TCGA-A3-A8CQ TCGA-A3-A8OX TCGA-AK-3425 TCGA-AK-3426 
          NA           NA            3           NA         3343           NA 
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-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 
        2087         2044         1745         1423         1471         1280 
TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 
        1217         1779         1481         1397          874           NA 
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-B0-4688 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 
          43           NA           NA           NA           NA           NA 
TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 
          NA           NA           NA          110           NA           NA 
TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 
          NA           26           NA           96           NA           NA 
TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 
          NA          616           NA           NA           18           NA 
TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 
          NA           NA           NA           NA          183           NA 
TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 
          NA           NA           NA           NA           NA           NA 
TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 
          NA           NA           NA           NA           NA           NA 
TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 
          NA           NA           NA           NA           NA           NA 
TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 
          NA           NA           NA           NA           NA           NA 
TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 
          NA           NA           NA           NA           NA           NA 
TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 
          NA           NA           NA          665           NA           NA 
TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 
          NA           NA           NA           NA           NA          911 
TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 
          NA         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-B0-5694 TCGA-B0-5695 
        2408         3431         1487         3076           NA         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-B8-4143 
          16          141          166           11            7           NA 
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-A54E 
         434           15         1046          435          830          909 
TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 
         519           53          256          150          528          110 
TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 
          24         3377           NA         2881         2746         3074 
TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 
        2839           NA         3037           13         2718          701 
TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 
          NA         1893         1879         1955         1670         2964 
TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 
        1625           NA          845         1888           NA         1133 
TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 
         645          461           NA         2859           NA           NA 
TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
          NA           NA         1666           NA         1367          372 
TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 
         970           NA           NA           NA           NA          374 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 
        2208         2372         2361          182           NA           NA 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 
        2184         1462          400         1876           NA           NA 
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-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 
        1854           NA         1489           NA          620         1107 
TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 
          NA           NA         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-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 
        1502         1384           NA         1433         1632          454 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 
          NA         1014         1413           NA          785         1124 
TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 
          NA          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-5009 TCGA-BP-5010 TCGA-BP-5168 
         840         1140         1071           NA           NA           NA 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 
         193         2412           NA         2257          932           NA 
TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 
         293           NA         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-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
        1924           NA           NA         2308         1998           NA 
TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
        1628         1793           NA          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-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 
          NA           NA         1946         2085           NA         1521 
TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 
         750          841           NA         1808         1528           NA 
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-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 
        1531         1657           NA         1373           NA           NA 
TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 
          NA         1943           NA         2430         2575           NA 
TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
          NA           NA           NA          552         1883         1889 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 
        2231         2038           NA         1855           NA           NA 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
        1906         2548           NA           NA         2799         2489 
TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 
          NA         2609         2226         2017         2378         2271 
TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 
          NA         3222         2552         3146           NA          774 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 
        1404           18           NA         1943         1787           NA 
TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 
          NA         1843         1928         2830           NA         1868 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 
        1929         1789           25           NA           NA         1712 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 
        1683         1732         1683         1430          330           NA 
TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 
         662         1740         1446          685           NA           59 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
          NA          386         2439         2067         1997          373 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 
          NA          693         1905         1329         1398         1470 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 
         370          355         1130         2016         1729           NA 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 
         551          119          206          127           NA          305 
TCGA-G6-A8L7 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC 
        1727           61          591          607          337          330 
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=341,	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=55,	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=8,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'YEAROFTOBACCOSMOKINGONSET':	nDistinctValues=4,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
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=15,	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 516 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 
258  69 178  11 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
258  69 178  11 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
 T1  T2  T3  T4 
258  69 178  11 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
258  69 178  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=8, 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    11   2
  1P GAIN WILD-TYPE 336  22
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               13               358 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                2                22 
$`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 
TCGA-MM-A564 
         607 

$`1P GAIN WILD-TYPE`
TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3317 
         267         1120         1436           16          735         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-A3-3382 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-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-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E 
         194          434         1046          435          830          909 
TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 
         519           53          256          150          528          110 
TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
          24         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-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 
         372          970         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-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-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-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-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6088 TCGA-CW-6093 
        2226         2017         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-4866 TCGA-CZ-5451 TCGA-CZ-5453 TCGA-CZ-5456 TCGA-CZ-5457 
        2830         1868         1929           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-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
        1997          373          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         2016         1729 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A8L6 TCGA-G6-A8L7 
         551          119          206          127          305         1727 
TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A84U TCGA-MW-A4EC 
          61          591          337          330 

  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 
             1416              1273 
[1] "15.0 - 2552.0 (1416.0)" "3.0 - 3668.0 (1273.0)" 
[1] "hr=" "2.6"
D1V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  1P GAIN MUTATED         7        4         8        5
  1P GAIN WILD-TYPE     246       53       118       75
D1V3, multiclass
           clus
vv          1P GAIN MUTATED 1P GAIN WILD-TYPE
  STAGE I                 7               246
  STAGE II                4                53
  STAGE III               8               118
  STAGE IV                5                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
  1P GAIN MUTATED     8   4  12   0
  1P GAIN WILD-TYPE 250  65 166  11
D1V4, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  T1               8               250
  T2               4                65
  T3              12               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"
D1V5, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    10   2
  1P GAIN WILD-TYPE 221  16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     10    2
  1P GAIN WILD-TYPE  221   16
   clus
vv  1P GAIN MUTATED 1P GAIN WILD-TYPE
  0              10               221
  1               2                16
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  1P GAIN MUTATED    18   5   1
  1P GAIN WILD-TYPE 399  73  18
D1V6, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  M0              18               399
  M1               5                73
  MX               1                18
[1] 3 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  16
  1P GAIN WILD-TYPE 178 314
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      8   16
  1P GAIN WILD-TYPE  178  314
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE               8               178
  MALE                16               314
[1] 2 2
[1] FALSE
D1V8, continuous
D1V9, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1P GAIN MUTATED       1                         2    21
  1P GAIN WILD-TYPE     7                        42   436
D1V10, multiclass
                           clus
vv                          1P GAIN MUTATED 1P GAIN WILD-TYPE
  ASIAN                                   1                 7
  BLACK OR AFRICAN AMERICAN               2                42
  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  15
  1P GAIN WILD-TYPE  25 323
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      1   15
  1P GAIN WILD-TYPE   25  323
                        clus
vv                       1P GAIN MUTATED 1P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                25
  NOT HISPANIC OR LATINO              15               323
[1] 2 2
[1] FALSE

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                 0   1
  1Q GAIN MUTATED    28   3
  1Q GAIN WILD-TYPE 319  21
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               31               340 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                3                21 
$`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 
TCGA-MM-A564 
         607 

$`1Q GAIN WILD-TYPE`
TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3317 
         267         1120         1436           16          735         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-A3-3347 TCGA-A3-3349 TCGA-A3-3351 
        1137         1485          665         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-3429 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 
        2566         2223         2017         1853         2192         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-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-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 
        1092          359          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-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 
        2741         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-B4-5844 
           7           38           16          141          166            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-A54E TCGA-B8-A54F 
         434         1046          435          830          909          519 
TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ 
          53          256          150          528          110           24 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 
        3377         2881         3074         2839         3037           13 
TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4173 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 
        2718          701         1893         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-4758 TCGA-BP-4759 
        1666         1367          372          970         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-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-4636 TCGA-CJ-4639 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 
        1820         1924         2308         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-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-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-5671 TCGA-CJ-5676 TCGA-CJ-5681 TCGA-CJ-5682 
        1531         1657         1943         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-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6088 
        2489         2609         2017         2378         2271         3222 
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-4866 TCGA-CZ-5451 TCGA-CZ-5453 TCGA-CZ-5456 TCGA-CZ-5457 
        2830         1868         1929           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-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
        1997          373          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         2016         1729 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A8L6 TCGA-G6-A8L7 
         551          119          206          127          305         1727 
TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A84U TCGA-MW-A4EC 
          61          591          337          330 

  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 
           1732.0            1194.5 
[1] "11.0 - 2746.0 (1732.0)" "3.0 - 3668.0 (1194.5)" 
[1] "hr=" "1.4"
D2V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  1Q GAIN MUTATED        17        9        17        8
  1Q GAIN WILD-TYPE     236       48       109       72
D2V3, multiclass
           clus
vv          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  STAGE I                17               236
  STAGE II                9                48
  STAGE III              17               109
  STAGE IV                8                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
  1Q GAIN MUTATED    19  11  21   0
  1Q GAIN WILD-TYPE 239  58 157  11
D2V4, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T1              19               239
  T2              11                58
  T3              21               157
  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 207  15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     24    3
  1Q GAIN WILD-TYPE  207   15
   clus
vv  1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  0              24               207
  1               3                15
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  1Q GAIN MUTATED    41   9   1
  1Q GAIN WILD-TYPE 376  69  18
D2V6, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  M0              41               376
  M1               9                69
  MX               1                18
[1] 3 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  35
  1Q GAIN WILD-TYPE 170 295
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     16   35
  1Q GAIN WILD-TYPE  170  295
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE              16               170
  MALE                35               295
[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                11 
       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-A54E        TCGA-B8-A54F        TCGA-B8-A54G 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-B8-A8YJ        TCGA-G6-A8L7        TCGA-MM-A563 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1Q GAIN MUTATED       1                         4    46
  1Q GAIN WILD-TYPE     7                        40   411
D2V10, multiclass
                           clus
vv                          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  ASIAN                                   1                 7
  BLACK OR AFRICAN AMERICAN               4                40
  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  33
  1Q GAIN WILD-TYPE  23 305
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      3   33
  1Q GAIN WILD-TYPE   23  305
                        clus
vv                       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                23
  NOT HISPANIC OR LATINO              33               305
[1] 2 2
[1] FALSE

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                 0   1
  2P GAIN MUTATED    53   5
  2P GAIN WILD-TYPE 294  19
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               58               313 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                5                19 
$`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-5984 TCGA-EU-5905 
        1430          330         2067          119 

$`2P GAIN WILD-TYPE`
TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 
         267         1120         1436           16          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-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 
        1610         1385          910         2688         1307         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-A3-3374 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-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3431 TCGA-AK-3433 
         617         3343         2566         2223         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-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H 
         435          830          909          519           53          256 
TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 
         528          110           24         3377         2881         2746 
TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4173 TCGA-BP-4176 
        2839         3037         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-4349 TCGA-BP-4758 TCGA-BP-4759 
         645          461         1666          372         2208         2372 
TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4765 TCGA-BP-4769 TCGA-BP-4774 TCGA-BP-4776 
        2361          182         2184         1876         1885          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-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 
        1124          204          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-4991 
         454         1014         1413          785         1124         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-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-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-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 
        2283         2353         2186         2014         1883         1759 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4894 
        2125         1952         1946         2085         1521          841 
TCGA-CJ-4899 TCGA-CJ-4902 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 
        1528         1520         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-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5589 
        1855         1906         2799         2489         2609         2378 
TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4862 
        3222         2552         3146          774           18         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-5458 TCGA-CZ-5459 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 
        1732         1683          662         1740         1446          685 
TCGA-CZ-5468 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5988 
          59          386         2439         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-5906 TCGA-EU-5907 
        1130         2016         1729          551          206          127 
TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U 
         305         1727           61          591          607          337 
TCGA-MW-A4EC 
         330 

  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 
             1440              1217 
[1] "3.0 - 3074.0 (1440.0)" "7.0 - 3668.0 (1217.0)"
[1] "hr=" "1.5"
D3V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  2P GAIN MUTATED        32        9        26        8
  2P GAIN WILD-TYPE     221       48       100       72
D3V3, multiclass
           clus
vv          2P GAIN MUTATED 2P GAIN WILD-TYPE
  STAGE I                32               221
  STAGE II                9                48
  STAGE III              26               100
  STAGE IV                8                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
  2P GAIN MUTATED    33   9  31   2
  2P GAIN WILD-TYPE 225  60 147   9
D3V4, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  T1              33               225
  T2               9                60
  T3              31               147
  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 196  15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     35    3
  2P GAIN WILD-TYPE  196   15
   clus
vv  2P GAIN MUTATED 2P GAIN WILD-TYPE
  0              35               196
  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  17
D3V6, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  M0              65               352
  M1               8                70
  MX               2                17
[1] 3 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 159 282
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     27   48
  2P GAIN WILD-TYPE  159  282
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE              27               159
  MALE                48               282
[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                11 
       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-A54E        TCGA-B8-A54F        TCGA-B8-A54G        TCGA-B8-A8YJ 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-G6-A5PC        TCGA-G6-A8L7        TCGA-MM-A563 
"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                        41   386
D3V10, multiclass
                           clus
vv                          2P GAIN MUTATED 2P GAIN WILD-TYPE
  ASIAN                                   1                 7
  BLACK OR AFRICAN AMERICAN               3                41
  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  22 295
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      4   43
  2P GAIN WILD-TYPE   22  295
                        clus
vv                       2P GAIN MUTATED 2P GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                22
  NOT HISPANIC OR LATINO              43               295
[1] 2 2
[1] FALSE

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                 0   1
  2Q GAIN MUTATED    54   4
  2Q GAIN WILD-TYPE 293  20
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               58               313 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                4                20 
$`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-EU-5905 
        1683         1430          330          119 

$`2Q GAIN WILD-TYPE`
TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 
         267         1120         1436           16          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-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 
        1610         1385          910         2688         1307         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-A3-3374 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-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3430 TCGA-AK-3431 
         617         3343         2566         2223          480         1853 
TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 
        2192         2087         2044         1745         1423         1280 
TCGA-AK-3447 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3456 TCGA-AK-3458 
        1217         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-B0-4819 TCGA-B0-5097 TCGA-B0-5108 TCGA-B0-5110 
          26          616          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-B0-5703 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-B2-3923 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-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
          16          141            7          511          826          838 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 
         762          750          523          788          700          636 
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-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G 
        1046          435          830          909          519           53 
TCGA-B8-A54H TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4160 
         256          528          110           24         3377         2881 
TCGA-BP-4161 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4173 
        2746         2839         3037         2718          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-4349 TCGA-BP-4758 
        1133          645          461         1666          372         2208 
TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4765 TCGA-BP-4769 TCGA-BP-4774 
        2372         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-4803 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 
        1107         1124          204          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-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-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 
        1266          563         1126          840         1140         1071 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5175 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5181 
         193         2412          932          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-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-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 
         603         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-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
        2353         2186         2014         1883         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-4904 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4916 
        1520         1792         1496         1531         1657         1373 
TCGA-CJ-5675 TCGA-CJ-5681 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 
        2430          552         1889         2231         2038         1855 
TCGA-CJ-6031 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5589 TCGA-CW-6088 
        1906         2799         2489         2609         2378         3222 
TCGA-CW-6090 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4863 
        2552         3146          774           18         1843         1928 
TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5458 
        2830         1868         1929         1789           25         1732 
TCGA-CZ-5459 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5468 
        1683          662         1740         1446          685           59 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5988 
         386         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-5906 TCGA-EU-5907 
        1130         2016         1729          551          206          127 
TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U 
         305         1727           61          591          607          337 
TCGA-MW-A4EC 
         330 

  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 
             1440              1217 
[1] "3.0 - 3074.0 (1440.0)" "7.0 - 3668.0 (1217.0)"
[1] "hr=" "1.1"
D4V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  2Q GAIN MUTATED        34        9        25        9
  2Q GAIN WILD-TYPE     219       48       101       71
D4V3, multiclass
           clus
vv          2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  STAGE I                34               219
  STAGE II                9                48
  STAGE III              25               101
  STAGE IV                9                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
  2Q GAIN MUTATED    35   9  31   2
  2Q GAIN WILD-TYPE 223  60 147   9
D4V4, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  T1              35               223
  T2               9                60
  T3              31               147
  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 195  16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     36    2
  2Q GAIN WILD-TYPE  195   16
   clus
vv  2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  0              36               195
  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  17
D4V6, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  M0              66               351
  M1               9                69
  MX               2                17
[1] 3 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 155 284
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     31   46
  2Q GAIN WILD-TYPE  155  284
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE              31               155
  MALE                46               284
[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                11 
       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-A54E        TCGA-B8-A54F        TCGA-B8-A54G        TCGA-B8-A8YJ 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-G6-A5PC        TCGA-G6-A8L7        TCGA-MM-A563 
"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                        41   384
D4V10, multiclass
                           clus
vv                          2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  ASIAN                                   1                 7
  BLACK OR AFRICAN AMERICAN               3                41
  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  21 294
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      5   44
  2Q GAIN WILD-TYPE   21  294
                        clus
vv                       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   5                21
  NOT HISPANIC OR LATINO              44               294
[1] 2 2
[1] FALSE

Clustering(5) Variable = 3P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                 0   1
  3P GAIN MUTATED    10   1
  3P GAIN WILD-TYPE 337  23
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               11               360 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                1                23 
$`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 
        1308          932          603         1808         1712 

$`3P GAIN WILD-TYPE`
TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 
         267         1120         1436           16          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-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 
        1610         1385          910         2688         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-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 
        1621         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-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-B0-5113 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-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 
          38          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-A54E TCGA-B8-A54F 
          15         1046          435          830          909          519 
TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ 
          53          256          150          528          110           24 
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-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-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-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-5199 TCGA-BP-5200 
         714          408          749         1018         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-4899 
        1946         2085         1521          750          841         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-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-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         2016 
TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A8L6 
        1729          551          119          206          127          305 
TCGA-G6-A8L7 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC 
        1727           61          591          607          337          330 

  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 
             1314              1252 
[1] "16.0 - 1808.0 (1314.0)" "3.0 - 3668.0 (1252.0)" 
[1] "hr=" "1.6"
D5V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  3P GAIN MUTATED         6        3         4        6
  3P GAIN WILD-TYPE     247       54       122       74
D5V3, multiclass
           clus
vv          3P GAIN MUTATED 3P GAIN WILD-TYPE
  STAGE I                 6               247
  STAGE II                3                54
  STAGE III               4               122
  STAGE IV                6                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
  3P GAIN MUTATED     6   3   9   1
  3P GAIN WILD-TYPE 252  66 169  10
D5V4, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  T1               6               252
  T2               3                66
  T3               9               169
  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 222  15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      9    3
  3P GAIN WILD-TYPE  222   15
   clus
vv  3P GAIN MUTATED 3P GAIN WILD-TYPE
  0               9               222
  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  19
D5V6, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  M0              13               404
  M1               6                72
  MX               0                19
[1] 3 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 177 320
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      9   10
  3P GAIN WILD-TYPE  177  320
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE               9               177
  MALE                10               320
[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                        43   439
D5V10, multiclass
                           clus
vv                          3P GAIN MUTATED 3P GAIN WILD-TYPE
  ASIAN                                   0                 8
  BLACK OR AFRICAN AMERICAN               1                43
  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  25 325
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      1   13
  3P GAIN WILD-TYPE   25  325
                        clus
vv                       3P GAIN MUTATED 3P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                25
  NOT HISPANIC OR LATINO              13               325
[1] 2 2
[1] FALSE

Clustering(6) Variable = 3Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                 0   1
  3Q GAIN MUTATED    36   3
  3Q GAIN WILD-TYPE 311  21
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               39               332 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                3                21 
$`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 
        1430         1740         1446 

$`3Q GAIN WILD-TYPE`
TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 
         267         1120         1436           16          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-A3-3326 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-3443 TCGA-AK-3444 TCGA-AK-3445 
         480         1853         2192         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-B0-4706 
         951          853          369         1238           43           26 
TCGA-B0-4710 TCGA-B0-4718 TCGA-B0-4813 TCGA-B0-4819 TCGA-B0-5108 TCGA-B0-5110 
          96          616           18          183          911         1092 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
         359          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-B0-5711 
        1605         1203         3668         2414         3117         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-B8-4622 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-B8-5550 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F 
         434         1046          435          830          909          519 
TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ 
          53          256          150          528          110           24 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4165 TCGA-BP-4166 
        3377         2881         2746         3074         3037           13 
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-4330 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4344 
        1625         1888         1133          645          461         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-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 
         211         2660         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-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-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-5199 TCGA-BP-5200 TCGA-BP-5201 
         408          749         1018         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-4872 TCGA-CJ-4873 
        1793          646         2554         1498         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-4903 TCGA-CJ-4904 TCGA-CJ-4905 
         841         1528         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-6088 TCGA-CW-6090 TCGA-CW-6093 
        2226         2017         2378         3222         2552         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-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5457 
        2830         1868         1929         1789           25         1683 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5466 TCGA-CZ-5468 
        1732         1683          330          662          685           59 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5988 
         386         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         2016         1729          551          119          206 
TCGA-EU-5907 TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 
         127          305         1727           61          591          607 
TCGA-MM-A84U TCGA-MW-A4EC 
         337          330 

  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 
           1446.0            1194.5 
[1] "15.0 - 2859.0 (1446.0)" "3.0 - 3668.0 (1194.5)" 
[1] "hr=" "1.1"
D6V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  3Q GAIN MUTATED        17        5        21       17
  3Q GAIN WILD-TYPE     236       52       105       63
D6V3, multiclass
           clus
vv          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  STAGE I                17               236
  STAGE II                5                52
  STAGE III              21               105
  STAGE IV               17                63
[1] 4 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 241  63 145   7
D6V4, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  T1              17               241
  T2               6                63
  T3              33               145
  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 201  11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     30    7
  3Q GAIN WILD-TYPE  201   11
   clus
vv  3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  0              30               201
  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  19
D6V6, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  M0              43               374
  M1              17                61
  MX               0                19
[1] 3 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 166 290
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     20   40
  3Q GAIN WILD-TYPE  166  290
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE              20               166
  MALE                40               290
[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                11 
       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-A54E        TCGA-B8-A54F        TCGA-B8-A54G        TCGA-B8-A8YJ 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G6-A5PC        TCGA-G6-A8L7        TCGA-MM-A563 
"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                        41   401
D6V10, multiclass
                           clus
vv                          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  ASIAN                                   0                 8
  BLACK OR AFRICAN AMERICAN               3                41
  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  23 299
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      3   39
  3Q GAIN WILD-TYPE   23  299
                        clus
vv                       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                23
  NOT HISPANIC OR LATINO              39               299
[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 340  22
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                9               362 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                2                22 
$`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-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 
         267         1120         1436           16          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-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 
        1610         1385          910         2688         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-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 
        1621         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-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3444 
        2017         1853         2087         2044         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-B0-4819 
          43          110           26           96          616          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-A54E TCGA-B8-A54F 
          15         1046          435          830          909          519 
TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ 
          53          256          150          528          110           24 
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-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-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-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-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-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5988 
         386         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         2016         1729          551          119          206 
TCGA-EU-5907 TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 
         127          305         1727           61          591          607 
TCGA-MM-A84U TCGA-MW-A4EC 
         337          330 

  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 
            480.0            1285.5 
[1] "13.0 - 2192.0 (480.0)" "3.0 - 3668.0 (1285.5)"
[1] "hr=" "5.5"
D7V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  4P GAIN MUTATED         4        2         5        2
  4P GAIN WILD-TYPE     249       55       121       78
D7V3, multiclass
           clus
vv          4P GAIN MUTATED 4P GAIN WILD-TYPE
  STAGE I                 4               249
  STAGE II                2                55
  STAGE III               5               121
  STAGE IV                2                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
  4P GAIN MUTATED     4   2   6   1
  4P GAIN WILD-TYPE 254  67 172  10
D7V4, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  T1               4               254
  T2               2                67
  T3               6               172
  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 223  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      8    1
  4P GAIN WILD-TYPE  223   17
   clus
vv  4P GAIN MUTATED 4P GAIN WILD-TYPE
  0               8               223
  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  19
D7V6, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  M0              11               406
  M1               2                76
  MX               0                19
[1] 3 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 183 320
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      3   10
  4P GAIN WILD-TYPE  183  320
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE               3               183
  MALE                10               320
[1] 2 2
[1] FALSE
D7V8, continuous
[1] "Remove cluster labels:" "4P GAIN MUTATED"       
clus
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                1                40 
       TCGA-A3-A6NJ        TCGA-A3-A6NL        TCGA-A3-A8CQ        TCGA-AK-3426 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B0-4838        TCGA-B2-5639        TCGA-B4-5377        TCGA-B4-5378 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B4-5832        TCGA-B4-5834        TCGA-B4-5835        TCGA-B4-5836 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B4-5838        TCGA-B4-5843        TCGA-B4-5844        TCGA-CZ-4854 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CZ-4856        TCGA-CZ-4858        TCGA-CZ-4860        TCGA-CZ-4861 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CZ-4862        TCGA-CZ-5456        TCGA-CZ-5457        TCGA-CZ-5465 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CZ-5469        TCGA-CZ-5982        TCGA-DV-5565        TCGA-DV-5566 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DV-5567        TCGA-DV-5568        TCGA-DV-5569        TCGA-DV-5573 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DV-5574        TCGA-DV-5575        TCGA-DV-5576        TCGA-EU-5904 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EU-5905        TCGA-EU-5907        TCGA-G6-A8L6        TCGA-G6-A8L7 
"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                        43   445
D7V10, multiclass
                           clus
vv                          4P GAIN MUTATED 4P GAIN WILD-TYPE
  ASIAN                                   0                 8
  BLACK OR AFRICAN AMERICAN               1                43
  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  26 330
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      0    8
  4P GAIN WILD-TYPE   26  330
                        clus
vv                       4P GAIN MUTATED 4P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                26
  NOT HISPANIC OR LATINO               8               330
[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 339  22
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               10               361 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                2                22 
$`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-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 
         267         1120         1436           16          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-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 
        1610         1385          910         2688         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-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 
        1621         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-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3444 
        2017         1853         2087         2044         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-B0-4819 
          43          110           26           96          616          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-A54E TCGA-B8-A54F 
          15         1046          435          830          909          519 
TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ 
          53          256          150          528          110           24 
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-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-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-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-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-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-5470 
         662         1740         1446          685           59          386 
TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5988 TCGA-CZ-5989 
        2439         2067         1997          373          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 
        2016         1729          551          119          206          127 
TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U 
         305         1727           61          591          607          337 
TCGA-MW-A4EC 
         330 

  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              1291 
[1] "13.0 - 2192.0 (467.0)" "3.0 - 3668.0 (1291.0)"
[1] "hr=" "5.3"
D8V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  4Q GAIN MUTATED         5        2         5        1
  4Q GAIN WILD-TYPE     248       55       121       79
D8V3, multiclass
           clus
vv          4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  STAGE I                 5               248
  STAGE II                2                55
  STAGE III               5               121
  STAGE IV                1                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
  4Q GAIN MUTATED     5   2   6   0
  4Q GAIN WILD-TYPE 253  67 172  11
D8V4, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  T1               5               253
  T2               2                67
  T3               6               172
  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 224  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      7    1
  4Q GAIN WILD-TYPE  224   17
   clus
vv  4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  0               7               224
  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  19
D8V6, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  M0              12               405
  M1               1                77
  MX               0                19
[1] 3 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 182 321
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      4    9
  4Q GAIN WILD-TYPE  182  321
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE               4               182
  MALE                 9               321
[1] 2 2
[1] FALSE
D8V8, continuous
[1] "Remove cluster labels:" "4Q GAIN MUTATED"       
clus
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                1                40 
       TCGA-A3-A6NJ        TCGA-A3-A6NL        TCGA-A3-A8CQ        TCGA-AK-3426 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B0-4838        TCGA-B2-5639        TCGA-B4-5377        TCGA-B4-5378 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B4-5832        TCGA-B4-5834        TCGA-B4-5835        TCGA-B4-5836 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B4-5838        TCGA-B4-5843        TCGA-B4-5844        TCGA-CZ-4854 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CZ-4856        TCGA-CZ-4858        TCGA-CZ-4860        TCGA-CZ-4861 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CZ-4862        TCGA-CZ-5456        TCGA-CZ-5457        TCGA-CZ-5465 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CZ-5469        TCGA-CZ-5982        TCGA-DV-5565        TCGA-DV-5566 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DV-5567        TCGA-DV-5568        TCGA-DV-5569        TCGA-DV-5573 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DV-5574        TCGA-DV-5575        TCGA-DV-5576        TCGA-EU-5904 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EU-5905        TCGA-EU-5907        TCGA-G6-A8L6        TCGA-G6-A8L7 
"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                        43   445
D8V10, multiclass
                           clus
vv                          4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  ASIAN                                   0                 8
  BLACK OR AFRICAN AMERICAN               1                43
  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  26 331
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      0    7
  4Q GAIN WILD-TYPE   26  331
                        clus
vv                       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                26
  NOT HISPANIC OR LATINO               7               331
[1] 2 2
[1] FALSE

Clustering(9) Variable = 5P GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                 0   1
  5P GAIN MUTATED   136   7
  5P GAIN WILD-TYPE 211  17
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              143               228 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                7                17 
$`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         2016          119 
TCGA-EU-5907 TCGA-G6-A8L6 TCGA-GK-A6C7 TCGA-MM-A564 TCGA-MW-A4EC 
         127          305           61          607          330 

$`5P GAIN WILD-TYPE`
TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3317 
         267         1120         1436           16          735         1491 
TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3335 TCGA-A3-3343 
        1130         1508         1106         1137          665          945 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
        1385          910         2504         1559          319          873 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 
        2270         2274         1621         1070          630          567 
TCGA-A3-3383 TCGA-A3-3387 TCGA-A3-A8CQ TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 
         861          617            3         3343         2566         2223 
TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3447 
        1853         2192         2087         1423         1471         1217 
TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3465 TCGA-AS-3777 
        1779          874         1143         1168          369         1238 
TCGA-AS-3778 TCGA-B0-4699 TCGA-B0-4706 TCGA-B0-4718 TCGA-B0-4813 TCGA-B0-5097 
          43          110           26          616           18          665 
TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 
         911         1092          657          535           59          493 
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-B0-5710 TCGA-B0-5711 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-4098 
        3117         1459         2931         2963          992           51 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR 
         374          648          358          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-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5162 
         750          523          788          700          636           36 
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-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54J TCGA-B8-A7U6 
         830          909          519           53          528          110 
TCGA-B8-A8YJ TCGA-BP-4161 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4167 TCGA-BP-4169 
          24         2746         2839         3037         2718          701 
TCGA-BP-4173 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 
        1893         2964         1625          845         1888         1133 
TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4349 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 
         645          461          372          374         2208         2372 
TCGA-BP-4760 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4774 TCGA-BP-4775 
        2361         2184         1462         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-4803 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4963 
        1124          204          211         2660         2172         1834 
TCGA-BP-4970 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4982 
         433         1502         1384         1433          454         1014 
TCGA-BP-4987 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 
        1124          177         1371          932          563         1177 
TCGA-BP-5006 TCGA-BP-5008 TCGA-BP-5169 TCGA-BP-5174 TCGA-BP-5180 TCGA-BP-5181 
         840         1071          193         2257         2263         1495 
TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5189 TCGA-BP-5190 
        1165         1291         1133          693          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-CJ-4634 TCGA-CJ-4640 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4870 
        1820         1998         1628         1793          646         1498 
TCGA-CJ-4872 TCGA-CJ-4874 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4882 TCGA-CJ-4884 
        1435         2283         1955         2186         1883         1759 
TCGA-CJ-4886 TCGA-CJ-4889 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4901 TCGA-CJ-4902 
        1952         1946          750          841         1450         1520 
TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4916 TCGA-CJ-5681 TCGA-CJ-6031 TCGA-CJ-6032 
        1496         1531         1373          552         1906         2548 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5589 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 
        2799         2489         2378         3222         2552         3146 
TCGA-CZ-4856 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-5453 TCGA-CZ-5458 
          18         1943         1787         1843           25         1732 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5465 TCGA-CZ-5982 TCGA-CZ-5985 TCGA-CZ-5988 
        1683         1430         1446         2439         1997          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-5575 TCGA-EU-5904 TCGA-EU-5906 TCGA-G6-A8L7 TCGA-MM-A563 TCGA-MM-A84U 
        1729          551          206         1727          591          337 

  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 
             1481              1127 
[1] "13.0 - 3668.0 (1481.0)" "3.0 - 3431.0 (1127.0)" 
[1] "hr=" "1.7"
D9V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  5P GAIN MUTATED        82       22        57       30
  5P GAIN WILD-TYPE     171       35        69       50
D9V3, multiclass
           clus
vv          5P GAIN MUTATED 5P GAIN WILD-TYPE
  STAGE I                82               171
  STAGE II               22                35
  STAGE III              57                69
  STAGE IV               30                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    84  28  75   4
  5P GAIN WILD-TYPE 174  41 103   7
D9V4, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  T1              84               174
  T2              28                41
  T3              75               103
  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 143  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     88    8
  5P GAIN WILD-TYPE  143   10
   clus
vv  5P GAIN MUTATED 5P GAIN WILD-TYPE
  0              88               143
  1               8                10
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  5P GAIN MUTATED   155  29   7
  5P GAIN WILD-TYPE 262  49  12
D9V6, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  M0             155               262
  M1              29                49
  MX               7                12
[1] 3 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    56 135
  5P GAIN WILD-TYPE 130 195
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     56  135
  5P GAIN WILD-TYPE  130  195
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE              56               130
  MALE               135               195
[1] 2 2
[1] FALSE
D9V8, continuous
D9V9, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5P GAIN MUTATED       3                        10   176
  5P GAIN WILD-TYPE     5                        34   281
D9V10, multiclass
                           clus
vv                          5P GAIN MUTATED 5P GAIN WILD-TYPE
  ASIAN                                   3                 5
  BLACK OR AFRICAN AMERICAN              10                34
  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    10 123
  5P GAIN WILD-TYPE  16 215
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     10  123
  5P GAIN WILD-TYPE   16  215
                        clus
vv                       5P GAIN MUTATED 5P GAIN WILD-TYPE
  HISPANIC OR LATINO                  10                16
  NOT HISPANIC OR LATINO             123               215
[1] 2 2
[1] FALSE

Clustering(10) Variable = 5Q GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                 0   1
  5Q GAIN MUTATED   145   7
  5Q GAIN WILD-TYPE 202  17
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
              152               219 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                7                17 
$`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-G6-A8L6 TCGA-GK-A6C7 
        1130         2016          119          127          305           61 
TCGA-MM-A564 TCGA-MW-A4EC 
         607          330 

$`5Q GAIN WILD-TYPE`
TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3317 
         267         1120         1436           16          735         1491 
TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3335 TCGA-A3-3343 
        1130         1508         1106         1137          665          945 
TCGA-A3-3349 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 
        1385         1559          319          873         2270         2274 
TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3387 
        1621         1070          630          567          861          617 
TCGA-A3-A8CQ TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3431 TCGA-AK-3433 
           3         3343         2566         2223         1853         2192 
TCGA-AK-3434 TCGA-AK-3443 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3456 
        2087         1423         1217         1779          874         1143 
TCGA-AK-3458 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4699 TCGA-B0-4706 
        1168          369         1238           43          110           26 
TCGA-B0-4718 TCGA-B0-4813 TCGA-B0-5097 TCGA-B0-5110 TCGA-B0-5116 TCGA-B0-5117 
         616           18          665         1092          657          535 
TCGA-B0-5119 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 
          59          652         1132          449         2408         3431 
TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5703 
        1487         3076         1420         2583         2741         1203 
TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5711 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-4098 
        2414         3117         2931         2963          992           51 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR 
         374          648          358          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-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
          11            7          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-B8-5545 TCGA-B8-5546 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E 
         522          505         1046          435          830          909 
TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4161 
         519           53          528          110           24         2746 
TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4173 TCGA-BP-4325 
        2839         3037         2718          701         1893         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-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-4782 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4795 TCGA-BP-4801 
        1731          354         1854         1489          620         1124 
TCGA-BP-4803 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4963 TCGA-BP-4970 
         204          211         2660         2172         1834          433 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4982 TCGA-BP-4987 
        1502         1384         1433          454         1014         1124 
TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5006 
         177         1371          932          563         1177          840 
TCGA-BP-5008 TCGA-BP-5169 TCGA-BP-5174 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 
        1071          193         2257         2263         1495         1165 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5192 
        1291         1133          693          822         1011          714 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-CJ-4634 
         408          749         1018          603         1355         1820 
TCGA-CJ-4640 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4870 TCGA-CJ-4872 
        1998         1628         1793          646         1498         1435 
TCGA-CJ-4874 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 
        2283         1955         2186         2014         1883         1759 
TCGA-CJ-4886 TCGA-CJ-4889 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4901 TCGA-CJ-4902 
        1952         1946          750          841         1450         1520 
TCGA-CJ-4905 TCGA-CJ-4916 TCGA-CJ-5681 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CW-5581 
        1496         1373          552         1906         2548         2799 
TCGA-CW-5583 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CZ-4856 TCGA-CZ-4858 
        2489         3222         2552         3146           18         1943 
TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-5453 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5465 
        1787         1843           25         1683         1430         1446 
TCGA-CZ-5982 TCGA-CZ-5985 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
        2439         1997          693         1905         1329         1398 
TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5906 
        1470          370          355         1729          551          206 
TCGA-G6-A8L7 TCGA-MM-A563 TCGA-MM-A84U 
        1727          591          337 

  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 
           1474.5            1124.0 
[1] "13.0 - 3668.0 (1474.5)" "3.0 - 3431.0 (1124.0)" 
[1] "hr=" "1.9"
D10V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  5Q GAIN MUTATED        92       23        58       31
  5Q GAIN WILD-TYPE     161       34        68       49
D10V3, multiclass
           clus
vv          5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  STAGE I                92               161
  STAGE II               23                34
  STAGE III              58                68
  STAGE IV               31                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    94  29  78   3
  5Q GAIN WILD-TYPE 164  40 100   8
D10V4, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T1              94               164
  T2              29                40
  T3              78               100
  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 134  11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     97    7
  5Q GAIN WILD-TYPE  134   11
   clus
vv  5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  0              97               134
  1               7                11
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  5Q GAIN MUTATED   166  31   7
  5Q GAIN WILD-TYPE 251  47  12
D10V6, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  M0             166               251
  M1              31                47
  MX               7                12
[1] 3 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    61 143
  5Q GAIN WILD-TYPE 125 187
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     61  143
  5Q GAIN WILD-TYPE  125  187
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE              61               125
  MALE               143               187
[1] 2 2
[1] FALSE
D10V8, continuous
D10V9, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5Q GAIN MUTATED       3                        10   189
  5Q GAIN WILD-TYPE     5                        34   268
D10V10, multiclass
                           clus
vv                          5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  ASIAN                                   3                 5
  BLACK OR AFRICAN AMERICAN              10                34
  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    11 134
  5Q GAIN WILD-TYPE  15 204
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     11  134
  5Q GAIN WILD-TYPE   15  204
                        clus
vv                       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  HISPANIC OR LATINO                  11                15
  NOT HISPANIC OR LATINO             134               204
[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 340  23
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                8               363 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                1                23 
$`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-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3316 TCGA-A3-3317 
         267         1120         1436           16         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-B0-5115 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-B4-5832 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-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D 
         505          434           15         1046          435          830 
TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J 
         909          519           53          256          150          528 
TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 
         110           24         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-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-5175 TCGA-BP-5180 TCGA-BP-5181 
         193         2412         2257          932         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-4886 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 
        1883         1759         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-5458 
        1868         1929         1789           25         1712         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-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
          59          386         2439         2067         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-5905 
         355         1130         2016         1729          551          119 
TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-GK-A6C7 TCGA-MM-A563 
         206          127          305         1727           61          591 
TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC 
         607          337          330 

  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            1280.0 
[1] "194.0 - 2125.0 (1082.5)" "3.0 - 3668.0 (1280.0)"  
[1] "hr=" "2.2"
D11V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  6P GAIN MUTATED         4        0         5        2
  6P GAIN WILD-TYPE     249       57       121       78
D11V3, multiclass
           clus
vv          6P GAIN MUTATED 6P GAIN WILD-TYPE
  STAGE I                 4               249
  STAGE II                0                57
  STAGE III               5               121
  STAGE IV                2                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
  6P GAIN MUTATED     4   0   7   0
  6P GAIN WILD-TYPE 254  69 171  11
D11V4, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  T1               4               254
  T2               0                69
  T3               7               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"
D11V5, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     6   0
  6P GAIN WILD-TYPE 225  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      6    0
  6P GAIN WILD-TYPE  225   18
   clus
vv  6P GAIN MUTATED 6P GAIN WILD-TYPE
  0               6               225
  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  19
D11V6, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  M0               9               408
  M1               2                76
  MX               0                19
[1] 3 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 184 321
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      2    9
  6P GAIN WILD-TYPE  184  321
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE               2               184
  MALE                 9               321
[1] 2 2
[1] FALSE
D11V8, continuous
[1] "Remove cluster labels:" "6P GAIN MUTATED"       
clus
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                1                40 
       TCGA-A3-A6NJ        TCGA-A3-A6NL        TCGA-A3-A8CQ        TCGA-AK-3426 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AK-3430        TCGA-B0-4838        TCGA-B2-5639        TCGA-B4-5377 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B4-5378        TCGA-B4-5832        TCGA-B4-5834        TCGA-B4-5835 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B4-5836        TCGA-B4-5838        TCGA-B4-5843        TCGA-B4-5844 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CZ-4854        TCGA-CZ-4856        TCGA-CZ-4858        TCGA-CZ-4860 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CZ-4861        TCGA-CZ-4862        TCGA-CZ-5456        TCGA-CZ-5465 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CZ-5469        TCGA-CZ-5982        TCGA-DV-5565        TCGA-DV-5566 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DV-5567        TCGA-DV-5568        TCGA-DV-5569        TCGA-DV-5573 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DV-5574        TCGA-DV-5575        TCGA-DV-5576        TCGA-EU-5904 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EU-5905        TCGA-EU-5907        TCGA-G6-A8L6        TCGA-G6-A8L7 
"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                        43   447
D11V10, multiclass
                           clus
vv                          6P GAIN MUTATED 6P GAIN WILD-TYPE
  ASIAN                                   0                 8
  BLACK OR AFRICAN AMERICAN               1                43
  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  26 332
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      0    6
  6P GAIN WILD-TYPE   26  332
                        clus
vv                       6P GAIN MUTATED 6P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                26
  NOT HISPANIC OR LATINO               6               332
[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 342  23
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                6               365 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                1                23 
$`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-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3316 TCGA-A3-3317 
         267         1120         1436           16         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-B0-5115 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-B4-5832 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-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D 
         505          434           15         1046          435          830 
TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J 
         909          519           53          256          150          528 
TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 
         110           24         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-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-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-4886 TCGA-CJ-4889 TCGA-CJ-4890 
        2014         1883         1759         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-5470 TCGA-CZ-5982 TCGA-CZ-5984 
        1446          685           59          386         2439         2067 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
        1997          373          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         2016         1729 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A8L6 TCGA-G6-A8L7 
         551          119          206          127          305         1727 
TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC 
          61          591          607          337          330 

  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              1280 
[1] "194.0 - 2125.0 (1209.0)" "3.0 - 3668.0 (1280.0)"  
[1] "hr=" "2.8"
D12V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  6Q GAIN MUTATED         3        0         5        1
  6Q GAIN WILD-TYPE     250       57       121       79
D12V3, multiclass
           clus
vv          6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  STAGE I                 3               250
  STAGE II                0                57
  STAGE III               5               121
  STAGE IV                1                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
  6Q GAIN MUTATED     3   0   6   0
  6Q GAIN WILD-TYPE 255  69 172  11
D12V4, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  T1               3               255
  T2               0                69
  T3               6               172
  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 225  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      6    0
  6Q GAIN WILD-TYPE  225   18
   clus
vv  6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  0               6               225
  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  19
D12V6, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  M0               8               409
  M1               1                77
  MX               0                19
[1] 3 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 185 322
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      1    8
  6Q GAIN WILD-TYPE  185  322
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE               1               185
  MALE                 8               322
[1] 2 2
[1] FALSE
D12V8, continuous
[1] "Remove cluster labels:" "6Q GAIN MUTATED"       
clus
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                1                40 
       TCGA-A3-A6NJ        TCGA-A3-A6NL        TCGA-A3-A8CQ        TCGA-AK-3426 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AK-3430        TCGA-B0-4838        TCGA-B2-5639        TCGA-B4-5377 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B4-5378        TCGA-B4-5832        TCGA-B4-5834        TCGA-B4-5835 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B4-5836        TCGA-B4-5838        TCGA-B4-5843        TCGA-B4-5844 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CZ-4854        TCGA-CZ-4856        TCGA-CZ-4858        TCGA-CZ-4860 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CZ-4861        TCGA-CZ-4862        TCGA-CZ-5456        TCGA-CZ-5465 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CZ-5469        TCGA-CZ-5982        TCGA-DV-5565        TCGA-DV-5566 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DV-5567        TCGA-DV-5568        TCGA-DV-5569        TCGA-DV-5573 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DV-5574        TCGA-DV-5575        TCGA-DV-5576        TCGA-EU-5904 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EU-5905        TCGA-EU-5907        TCGA-G6-A8L6        TCGA-G6-A8L7 
"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                        43   449
D12V10, multiclass
                           clus
vv                          6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  ASIAN                                   0                 8
  BLACK OR AFRICAN AMERICAN               1                43
  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  26 333
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      0    5
  6Q GAIN WILD-TYPE   26  333
                        clus
vv                       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                26
  NOT HISPANIC OR LATINO               5               333
[1] 2 2
[1] FALSE

Clustering(13) Variable = 7P GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                 0   1
  7P GAIN MUTATED   114   8
  7P GAIN WILD-TYPE 233  16
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              122               249 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                8                16 
$`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-A54E TCGA-B8-A54I TCGA-BP-4158 TCGA-BP-4162 TCGA-BP-4166 
         434          909          150         3377         3074           13 
TCGA-BP-4167 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4325 TCGA-BP-4332 
        2718         1893         1879         1955         2964         1133 
TCGA-BP-4335 TCGA-BP-4338 TCGA-BP-4351 TCGA-BP-4759 TCGA-BP-4766 TCGA-BP-4768 
         461         2859          970         2372         1462          400 
TCGA-BP-4775 TCGA-BP-4781 TCGA-BP-4797 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 
        1843         2080         1107          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-5001 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5177 TCGA-BP-5198 
         932         1177          193         2412          293          603 
TCGA-BP-5200 TCGA-BP-5201 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4871 TCGA-CJ-4872 
        1063          951         1416         1924         2423         1435 
TCGA-CJ-4873 TCGA-CJ-4875 TCGA-CJ-4885 TCGA-CJ-4889 TCGA-CJ-4897 TCGA-CJ-4901 
        2259         2353         2125         1946         1808         1450 
TCGA-CJ-4903 TCGA-CJ-4907 TCGA-CJ-4912 TCGA-CJ-5671 TCGA-CJ-5682 TCGA-CJ-5684 
        1560         1499         1657         1943         1883         2231 
TCGA-CW-5588 TCGA-CW-5591 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4858 TCGA-CZ-4866 
        2017         2271         3146         1404         1943         1868 
TCGA-CZ-5453 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5464 
          25         1712         1683         1430          330         1740 
TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5984 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5574 
         685           59         2067         1905         1329         2016 
TCGA-G6-A8L7 TCGA-MM-A564 
        1727          607 

$`7P GAIN WILD-TYPE`
TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3319 TCGA-A3-3320 
         267         1120         1436           16         1130         1508 
TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3343 TCGA-A3-3349 
        1106         1137         1485          665          945         1385 
TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3365 TCGA-A3-3367 
         910         2688         2504         1559          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-AK-3428 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3447 
        2223         1853         2087         1423         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-B0-4699 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-B0-5399 
         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-B0-5699 TCGA-B0-5702 TCGA-B0-5705 
        1420         1727         1835         2741         1605         3668 
TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5812 
        2414         3117         1459         2931         2722         2963 
TCGA-B2-3923 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5635 
         992           51          374          648          952          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-B4-5836 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-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 
         750          636          722           36          822           26 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5551 TCGA-B8-5552 
         737          522          505          194           15         1046 
TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54J 
         435          830          519           53          256          528 
TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4163 TCGA-BP-4165 
         110           24         2881         2746         2839         3037 
TCGA-BP-4169 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4334 
         701         1670         1625          845         1888          645 
TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4760 
        1666         1367          372          374         2208         2361 
TCGA-BP-4761 TCGA-BP-4765 TCGA-BP-4769 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 
         182         2184         1876         1885          411         1731 
TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4795 TCGA-BP-4801 TCGA-BP-4807 
         354         1854         1489          620         1124          211 
TCGA-BP-4959 TCGA-BP-4961 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4968 TCGA-BP-4970 
        2660         1935         1862         1871         1746          433 
TCGA-BP-4972 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4982 TCGA-BP-4986 TCGA-BP-4991 
        1502         1433         1632         1014          785         1413 
TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5004 TCGA-BP-5006 
         177         1371         1266          563         1126          840 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5180 TCGA-BP-5181 
        1140         1071         2257          932         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-5202 TCGA-CJ-4634 TCGA-CJ-4639 TCGA-CJ-4640 
        1018         1355           29         1820         2308         1998 
TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4874 
        1628         1793          646         2554         1498         2283 
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-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4899 TCGA-CJ-4902 
        2085         1521          750          841         1528         1520 
TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4916 TCGA-CJ-5675 TCGA-CJ-5676 
        1792         1496         1531         1373         2430         2575 
TCGA-CJ-5681 TCGA-CJ-5683 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6031 TCGA-CJ-6032 
         552         1889         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-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4863 
        2552          774           18         1787         1843         1928 
TCGA-CZ-4864 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5463 
        2830         1929         1789         1732         1683          662 
TCGA-CZ-5465 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5988 
        1446          386         2439         1997          373          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-G6-A8L6 TCGA-GK-A6C7 
         551          119          206          127          305           61 
TCGA-MM-A563 TCGA-MM-A84U TCGA-MW-A4EC 
         591          337          330 

  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 
           1432.5            1132.0 
[1] "3.0 - 3377.0 (1432.5)" "7.0 - 3668.0 (1132.0)"
[1] "hr=" "1.1"
D13V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  7P GAIN MUTATED        71       19        46       34
  7P GAIN WILD-TYPE     182       38        80       46
D13V3, multiclass
           clus
vv          7P GAIN MUTATED 7P GAIN WILD-TYPE
  STAGE I                71               182
  STAGE II               19                38
  STAGE III              46                80
  STAGE IV               34                46
[1] 4 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    73  24  69   4
  7P GAIN WILD-TYPE 185  45 109   7
D13V4, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  T1              73               185
  T2              24                45
  T3              69               109
  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    81   8
  7P GAIN WILD-TYPE 150  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     81    8
  7P GAIN WILD-TYPE  150   10
   clus
vv  7P GAIN MUTATED 7P GAIN WILD-TYPE
  0              81               150
  1               8                10
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  7P GAIN MUTATED   130  35   5
  7P GAIN WILD-TYPE 287  43  14
D13V6, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  M0             130               287
  M1              35                43
  MX               5                14
[1] 3 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    46 124
  7P GAIN WILD-TYPE 140 206
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     46  124
  7P GAIN WILD-TYPE  140  206
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE              46               140
  MALE               124               206
[1] 2 2
[1] FALSE
D13V8, continuous
D13V9, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7P GAIN MUTATED       4                         9   155
  7P GAIN WILD-TYPE     4                        35   302
D13V10, multiclass
                           clus
vv                          7P GAIN MUTATED 7P GAIN WILD-TYPE
  ASIAN                                   4                 4
  BLACK OR AFRICAN AMERICAN               9                35
  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     6 103
  7P GAIN WILD-TYPE  20 235
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      6  103
  7P GAIN WILD-TYPE   20  235
                        clus
vv                       7P GAIN MUTATED 7P GAIN WILD-TYPE
  HISPANIC OR LATINO                   6                20
  NOT HISPANIC OR LATINO             103               235
[1] 2 2
[1] FALSE

Clustering(14) Variable = 7Q GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                 0   1
  7Q GAIN MUTATED   111  10
  7Q GAIN WILD-TYPE 236  14
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              121               250 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               10                14 
$`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-A54E TCGA-B8-A54I TCGA-BP-4158 
         788          700          434          909          150         3377 
TCGA-BP-4162 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 
        3074           13         2718         1893         1879         1955 
TCGA-BP-4325 TCGA-BP-4332 TCGA-BP-4335 TCGA-BP-4338 TCGA-BP-4351 TCGA-BP-4759 
        2964         1133          461         2859          970         2372 
TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4775 TCGA-BP-4781 TCGA-BP-4803 TCGA-BP-4804 
        1462          400         1843         2080          204         1459 
TCGA-BP-4960 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4967 TCGA-BP-4969 TCGA-BP-4971 
        2172         1785         1834          205         1794         1487 
TCGA-BP-4973 TCGA-BP-4977 TCGA-BP-4983 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4992 
        1384          454         1413         1124          118          501 
TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5177 TCGA-BP-5198 
        1308          932          193         2412          293          603 
TCGA-BP-5200 TCGA-BP-5201 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4871 TCGA-CJ-4872 
        1063          951         1416         1924         2423         1435 
TCGA-CJ-4873 TCGA-CJ-4875 TCGA-CJ-4885 TCGA-CJ-4889 TCGA-CJ-4897 TCGA-CJ-4901 
        2259         2353         2125         1946         1808         1450 
TCGA-CJ-4903 TCGA-CJ-4907 TCGA-CJ-5671 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
        1560         1499         1943         1883         1889         2231 
TCGA-CW-5588 TCGA-CW-5591 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4858 TCGA-CZ-4866 
        2017         2271         3146         1404         1943         1868 
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-5984 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5574 TCGA-G6-A8L7 
          59         2067         1905         1329         2016         1727 
TCGA-MM-A564 
         607 

$`7Q GAIN WILD-TYPE`
TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3319 TCGA-A3-3320 
         267         1120         1436           16         1130         1508 
TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3343 TCGA-A3-3349 
        1106         1137         1485          665          945         1385 
TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3365 TCGA-A3-3367 
         910         2688         2504         1559          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-AK-3428 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3447 
        2223         1853         2087         1423         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-B0-4699 TCGA-B0-4706 
         853          369         1238           43          110           26 
TCGA-B0-4718 TCGA-B0-4813 TCGA-B0-5097 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5115 
         616           18          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-B2-5633 TCGA-B2-5635 
          51          374          648          952          358          315 
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-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-5158 
           7          826          838          762          750          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-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D 
         505          194           15         1046          435          830 
TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ 
         519           53          256          528          110           24 
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-4797 TCGA-BP-4801 TCGA-BP-4807 TCGA-BP-4959 
        1489          620         1107         1124          211         2660 
TCGA-BP-4961 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4972 
        1935         1862         1871         1746          433         1502 
TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4982 TCGA-BP-4986 TCGA-BP-4991 TCGA-BP-4993 
        1433         1632         1014          785         1413          177 
TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 
        1371         1266          563         1177         1126          840 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5180 TCGA-BP-5181 
        1140         1071         2257          932         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-5202 TCGA-CJ-4634 TCGA-CJ-4639 TCGA-CJ-4640 
        1018         1355           29         1820         2308         1998 
TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4874 
        1628         1793          646         2554         1498         2283 
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-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4899 TCGA-CJ-4902 
        2085         1521          750          841         1528         1520 
TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-5675 
        1792         1496         1531         1657         1373         2430 
TCGA-CJ-5676 TCGA-CJ-5681 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6031 TCGA-CJ-6032 
        2575          552         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-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4863 
        2552          774           18         1787         1843         1928 
TCGA-CZ-4864 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5458 TCGA-CZ-5459 
        2830         1929         1789           25         1732         1683 
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-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 
         693         1398         1470          370          355         1130 
TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A8L6 
        1729          551          119          206          127          305 
TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A84U TCGA-MW-A4EC 
          61          591          337          330 

  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 
           1435.0            1132.5 
[1] "3.0 - 3377.0 (1435.0)" "7.0 - 3668.0 (1132.5)"
[1] "hr=" "1.4"
D14V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  7Q GAIN MUTATED        71       17        46       37
  7Q GAIN WILD-TYPE     182       40        80       43
D14V3, multiclass
           clus
vv          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  STAGE I                71               182
  STAGE II               17                40
  STAGE III              46                80
  STAGE IV               37                43
[1] 4 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    73  22  72   4
  7Q GAIN WILD-TYPE 185  47 106   7
D14V4, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T1              73               185
  T2              22                47
  T3              72               106
  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    79   8
  7Q GAIN WILD-TYPE 152  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     79    8
  7Q GAIN WILD-TYPE  152   10
   clus
vv  7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  0              79               152
  1               8                10
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  7Q GAIN MUTATED   128  38   5
  7Q GAIN WILD-TYPE 289  40  14
D14V6, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  M0             128               289
  M1              38                40
  MX               5                14
[1] 3 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    48 123
  7Q GAIN WILD-TYPE 138 207
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     48  123
  7Q GAIN WILD-TYPE  138  207
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE              48               138
  MALE               123               207
[1] 2 2
[1] FALSE
D14V8, continuous
D14V9, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7Q GAIN MUTATED       4                         9   156
  7Q GAIN WILD-TYPE     4                        35   301
D14V10, multiclass
                           clus
vv                          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  ASIAN                                   4                 4
  BLACK OR AFRICAN AMERICAN               9                35
  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     5 106
  7Q GAIN WILD-TYPE  21 232
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      5  106
  7Q GAIN WILD-TYPE   21  232
                        clus
vv                       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   5                21
  NOT HISPANIC OR LATINO             106               232
[1] 2 2
[1] FALSE

Clustering(15) Variable = 8P GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                 0   1
  8P GAIN MUTATED    19   2
  8P GAIN WILD-TYPE 328  22
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               21               350 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                2                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-5470 TCGA-MM-A564 
        1740          386          607 

$`8P GAIN WILD-TYPE`
TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3317 TCGA-A3-3319 
         267         1120         1436           16         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-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 
         480         1853         2087         2044         1745         1423 
TCGA-AK-3444 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 
        1471         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-B0-5108 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 
         183          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-B4-5838 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-A54E TCGA-B8-A54F TCGA-B8-A54G 
        1046          435          830          909          519           53 
TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 
         256          150          528          110           24         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-4769 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 
        1462         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-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-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-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-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-4872 TCGA-CJ-4873 
        1793          646         2554         1498         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-4902 TCGA-CJ-4903 
         750          841         1808         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-5589 TCGA-CW-6088 TCGA-CW-6090 
        2489         2609         2226         2378         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-5457 
        1928         2830         1929         1789           25         1683 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5465 
        1732         1683         1430          330          662         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-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         2016         1729          551          119 
TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-GK-A6C7 TCGA-MM-A563 
         206          127          305         1727           61          591 
TCGA-MM-A84U TCGA-MW-A4EC 
         337          330 

  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 
             1413              1252 
[1] "7.0 - 2423.0 (1413.0)" "3.0 - 3668.0 (1252.0)"
[1] "hr=" "1.5"
D15V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  8P GAIN MUTATED         6        8         9        7
  8P GAIN WILD-TYPE     247       49       117       73
D15V3, multiclass
           clus
vv          8P GAIN MUTATED 8P GAIN WILD-TYPE
  STAGE I                 6               247
  STAGE II                8                49
  STAGE III               9               117
  STAGE IV                7                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
  8P GAIN MUTATED     6   9  15   0
  8P GAIN WILD-TYPE 252  60 163  11
D15V4, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  T1               6               252
  T2               9                60
  T3              15               163
  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 219  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     12    1
  8P GAIN WILD-TYPE  219   17
   clus
vv  8P GAIN MUTATED 8P GAIN WILD-TYPE
  0              12               219
  1               1                17
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  8P GAIN MUTATED    22   7   1
  8P GAIN WILD-TYPE 395  71  18
D15V6, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  M0              22               395
  M1               7                71
  MX               1                18
[1] 3 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  21
  8P GAIN WILD-TYPE 177 309
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      9   21
  8P GAIN WILD-TYPE  177  309
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE               9               177
  MALE                21               309
[1] 2 2
[1] FALSE
D15V8, continuous
D15V9, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8P GAIN MUTATED       1                         2    26
  8P GAIN WILD-TYPE     7                        42   431
D15V10, multiclass
                           clus
vv                          8P GAIN MUTATED 8P GAIN WILD-TYPE
  ASIAN                                   1                 7
  BLACK OR AFRICAN AMERICAN               2                42
  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  19
  8P GAIN WILD-TYPE  26 319
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      0   19
  8P GAIN WILD-TYPE   26  319
                        clus
vv                       8P GAIN MUTATED 8P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                26
  NOT HISPANIC OR LATINO              19               319
[1] 2 2
[1] FALSE

Clustering(16) Variable = 8Q GAIN MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                 0   1
  8Q GAIN MUTATED    39   4
  8Q GAIN WILD-TYPE 308  20
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               43               328 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                4                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-5470 
        1868         1712         1740          685           59          386 
TCGA-MM-A564 
         607 

$`8Q GAIN WILD-TYPE`
TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3317 TCGA-A3-3320 TCGA-A3-3322 
         267         1120         1436         1491         1508         1478 
TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3343 
        1106         1186         1137         1485          665          945 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 
        1610         1385          910         2688         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-A3-3378 TCGA-A3-3380 TCGA-A3-3382 
        1621         1314         1070          630          567          574 
TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A8CQ TCGA-AK-3427 TCGA-AK-3428 
         861         1993          617            3         2566         2223 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 
        2017          480         1853         2044         1745         1423 
TCGA-AK-3444 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 
        1471         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-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 
         183         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-B8-5159 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-A54E 
         194          434         1046          435          830          909 
TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ 
         519           53          256          528          110           24 
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-4176 TCGA-BP-4177 
          13         2718          701         1893         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-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-4765 TCGA-BP-4766 TCGA-BP-4769 
        2208         2372         2361         2184         1462         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-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-5170 TCGA-BP-5174 
        1126          840         1140         1071         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-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-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-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-4907 TCGA-CJ-4908 TCGA-CJ-4916 TCGA-CJ-5671 
        1792         1496         1499         1531         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-6088 TCGA-CW-6090 TCGA-CW-6093 
        2609         2226         2378         3222         2552         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-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-5465 TCGA-CZ-5982 TCGA-CZ-5984 
        1430          330          662         1446         2439         2067 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
        1997          373          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         2016         1729 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A8L6 TCGA-G6-A8L7 
         551          119          206          127          305         1727 
TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A84U TCGA-MW-A4EC 
          61          591          337          330 

  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 
           1130.0            1307.5 
[1] "7.0 - 3343.0 (1130.0)" "3.0 - 3668.0 (1307.5)"
[1] "hr=" "1.6"
D16V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  8Q GAIN MUTATED        18       11        19       13
  8Q GAIN WILD-TYPE     235       46       107       67
D16V3, multiclass
           clus
vv          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  STAGE I                18               235
  STAGE II               11                46
  STAGE III              19               107
  STAGE IV               13                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
  8Q GAIN MUTATED    19  12  29   1
  8Q GAIN WILD-TYPE 239  57 149  10
D16V4, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T1              19               239
  T2              12                57
  T3              29               149
  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 205  15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     26    3
  8Q GAIN WILD-TYPE  205   15
   clus
vv  8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  0              26               205
  1               3                15
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  8Q GAIN MUTATED    45  14   2
  8Q GAIN WILD-TYPE 372  64  17
D16V6, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  M0              45               372
  M1              14                64
  MX               2                17
[1] 3 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  45
  8Q GAIN WILD-TYPE 170 285
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     16   45
  8Q GAIN WILD-TYPE  170  285
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE              16               170
  MALE                45               285
[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                11 
       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-A54E        TCGA-B8-A54F        TCGA-B8-A54G        TCGA-B8-A8YJ 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-G6-A5PC        TCGA-G6-A8L7        TCGA-MM-A563 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8Q GAIN MUTATED       1                         4    54
  8Q GAIN WILD-TYPE     7                        40   403
D16V10, multiclass
                           clus
vv                          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  ASIAN                                   1                 7
  BLACK OR AFRICAN AMERICAN               4                40
  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  36
  8Q GAIN WILD-TYPE  25 302
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      1   36
  8Q GAIN WILD-TYPE   25  302
                        clus
vv                       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                25
  NOT HISPANIC OR LATINO              36               302
[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 337  24
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               10               361 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                0                24 
$`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-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 
         267         1120         1436           16          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-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 
        1610         1385          910         2688         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-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 
        1621         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-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-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-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E 
         434           15         1046          435          830          909 
TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 
         519           53          256          150          528          110 
TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
          24         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-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-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-5182 
        2412         2257          932          293         2263         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-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 
         646         2554         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-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-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-5988 TCGA-CZ-5989 
        2439         2067         1997          373          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 
        2016         1729          551          119          206          127 
TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U 
         305         1727           61          591          607          337 
TCGA-MW-A4EC 
         330 

  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            1186.0 
[1] "1314.0 - 2192.0 (1769.5)" "3.0 - 3668.0 (1186.0)"   
[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     247       55       123       78
D17V3, multiclass
           clus
vv          9P GAIN MUTATED 9P GAIN WILD-TYPE
  STAGE I                 6               247
  STAGE II                2                55
  STAGE III               3               123
  STAGE IV                2                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
  9P GAIN MUTATED     6   2   3   2
  9P GAIN WILD-TYPE 252  67 175   9
D17V4, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  T1               6               252
  T2               2                67
  T3               3               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"
D17V5, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     5   0
  9P GAIN WILD-TYPE 226  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      5    0
  9P GAIN WILD-TYPE  226   18
   clus
vv  9P GAIN MUTATED 9P GAIN WILD-TYPE
  0               5               226
  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  19
D17V6, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  M0              13               404
  M1               0                78
  MX               0                19
[1] 3 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 177 326
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      9    4
  9P GAIN WILD-TYPE  177  326
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE               9               177
  MALE                 4               326
[1] 2 2
[1] FALSE
D17V8, continuous
[1] "Remove cluster labels:" "9P GAIN MUTATED"       
clus
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                1                40 
       TCGA-A3-A6NJ        TCGA-A3-A6NL        TCGA-A3-A8CQ        TCGA-AK-3426 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AK-3430        TCGA-B0-4838        TCGA-B2-5639        TCGA-B4-5377 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-B4-5378        TCGA-B4-5832        TCGA-B4-5834        TCGA-B4-5835 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-B4-5836        TCGA-B4-5838        TCGA-B4-5843        TCGA-B4-5844 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CZ-4854        TCGA-CZ-4856        TCGA-CZ-4858        TCGA-CZ-4860 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CZ-4861        TCGA-CZ-4862        TCGA-CZ-5456        TCGA-CZ-5465 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CZ-5469        TCGA-CZ-5982        TCGA-DV-5565        TCGA-DV-5566 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DV-5567        TCGA-DV-5568        TCGA-DV-5569        TCGA-DV-5573 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DV-5574        TCGA-DV-5575        TCGA-DV-5576        TCGA-EU-5904 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EU-5905        TCGA-EU-5907        TCGA-G6-A8L6        TCGA-G6-A8L7 
"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                        42   446
D17V10, multiclass
                           clus
vv                          9P GAIN MUTATED 9P GAIN WILD-TYPE
  ASIAN                                   0                 8
  BLACK OR AFRICAN AMERICAN               2                42
  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  25 328
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      1   10
  9P GAIN WILD-TYPE   25  328
                        clus
vv                       9P GAIN MUTATED 9P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                25
  NOT HISPANIC OR LATINO              10               328
[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 339  23
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                9               362 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                1                23 
$`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-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 
         267         1120         1436           16          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-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 
        1610         1385          910         2688         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-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 
        1621         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-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-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-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E 
         434           15         1046          435          830          909 
TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 
         519           53          256          150          528          110 
TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
          24         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-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-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-4899 TCGA-CJ-4901 TCGA-CJ-4902 
        1521          750          841         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-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5456 TCGA-CZ-5458 TCGA-CZ-5459 
        1929         1789           25         1712         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-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5988 
         386         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         2016         1729          551          119          206 
TCGA-EU-5907 TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 
         127          305         1727           61          591          607 
TCGA-MM-A84U TCGA-MW-A4EC 
         337          330 

  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              1210 
[1] "59.0 - 2192.0 (1794.0)" "3.0 - 3668.0 (1210.0)" 
[1] "hr=" "1.4"
D18V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  9Q GAIN MUTATED         4        2         2        4
  9Q GAIN WILD-TYPE     249       55       124       76
D18V3, multiclass
           clus
vv          9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  STAGE I                 4               249
  STAGE II                2                55
  STAGE III               2               124
  STAGE IV                4                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
  9Q GAIN MUTATED     4   2   3   3
  9Q GAIN WILD-TYPE 254  67 175   8
D18V4, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  T1               4               254
  T2               2                67
  T3               3               175
  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 226  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      5    0
  9Q GAIN WILD-TYPE  226   18
   clus
vv  9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  0               5               226
  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  19
D18V6, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  M0              10               407
  M1               2                76
  MX               0                19
[1] 3 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 179 325
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      7    5
  9Q GAIN WILD-TYPE  179  325
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE               7               179
  MALE                 5               325
[1] 2 2
[1] FALSE
D18V8, continuous
[1] "Remove cluster labels:" "9Q GAIN MUTATED"       
clus
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                1                40 
       TCGA-A3-A6NJ        TCGA-A3-A6NL        TCGA-A3-A8CQ        TCGA-AK-3426 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AK-3430        TCGA-B0-4838        TCGA-B2-5639        TCGA-B4-5377 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-B4-5378        TCGA-B4-5832        TCGA-B4-5834        TCGA-B4-5835 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-B4-5836        TCGA-B4-5838        TCGA-B4-5843        TCGA-B4-5844 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CZ-4854        TCGA-CZ-4856        TCGA-CZ-4858        TCGA-CZ-4860 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CZ-4861        TCGA-CZ-4862        TCGA-CZ-5456        TCGA-CZ-5465 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CZ-5469        TCGA-CZ-5982        TCGA-DV-5565        TCGA-DV-5566 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DV-5567        TCGA-DV-5568        TCGA-DV-5569        TCGA-DV-5573 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DV-5574        TCGA-DV-5575        TCGA-DV-5576        TCGA-EU-5904 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EU-5905        TCGA-EU-5907        TCGA-G6-A8L6        TCGA-G6-A8L7 
"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                        43   446
D18V10, multiclass
                           clus
vv                          9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  ASIAN                                   0                 8
  BLACK OR AFRICAN AMERICAN               1                43
  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  25 328
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      1   10
  9Q GAIN WILD-TYPE   25  328
                        clus
vv                       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                25
  NOT HISPANIC OR LATINO              10               328
[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 336  22
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                13                358 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 2                 22 
$`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-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3317 
         267         1120         1436           16          735         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-B4-5843 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-B8-4620 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-A54E 
         434           15         1046          435          830          909 
TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 
         519           53          256          150          528          110 
TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
          24         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-4344 TCGA-BP-4347 TCGA-BP-4349 
        1133          645          461         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-5470 TCGA-CZ-5982 TCGA-CZ-5984 
        1740         1446          685          386         2439         2067 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
        1997          373          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         2016         1729 
TCGA-EU-5904 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-GK-A6C7 
         551          206          127          305         1727           61 
TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC 
         591          607          337          330 

  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               1273 
[1] "7.0 - 2859.0 (1397.0)" "3.0 - 3668.0 (1273.0)"
[1] "hr=" "2.6"
D19V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  10P GAIN MUTATED         7        4         3        3
  10P GAIN WILD-TYPE     246       53       123       77
D19V3, multiclass
           clus
vv          10P GAIN MUTATED 10P GAIN WILD-TYPE
  STAGE I                  7                246
  STAGE II                 4                 53
  STAGE III                3                123
  STAGE IV                 3                 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
  10P GAIN MUTATED     7   5   4   1
  10P GAIN WILD-TYPE 251  64 174  10
D19V4, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  T1                7                251
  T2                5                 64
  T3                4                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"
D19V5, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     6   2
  10P GAIN WILD-TYPE 225  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      6    2
  10P GAIN WILD-TYPE  225   16
   clus
vv  10P GAIN MUTATED 10P GAIN WILD-TYPE
  0                6                225
  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  19
D19V6, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  M0               14                403
  M1                3                 75
  MX                0                 19
[1] 3 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 181 318
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      5   12
  10P GAIN WILD-TYPE  181  318
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE                5                181
  MALE                 12                318
[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                        44   440
D19V10, multiclass
                           clus
vv                          10P GAIN MUTATED 10P GAIN WILD-TYPE
  ASIAN                                    0                  8
  BLACK OR AFRICAN AMERICAN                0                 44
  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  26 328
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      0   10
  10P GAIN WILD-TYPE   26  328
                        clus
vv                       10P GAIN MUTATED 10P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 26
  NOT HISPANIC OR LATINO               10                328
[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 339  22
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                10                361 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 2                 22 
$`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-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 
         267         1120         1436           16          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-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 
        1610         1385          910         2688         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-A3-3378 TCGA-A3-3380 TCGA-A3-3382 
        1621         1314         1070          630          567          574 
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-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 
        2223         2017          480         1853         2192         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-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-B0-4699 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-B4-5834 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-B8-5158 
         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-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I 
         830          909          519           53          256          150 
TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 
         528          110           24         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-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-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5988 
         386         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-5906 TCGA-EU-5907 
        1130         2016         1729          551          206          127 
TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U 
         305         1727           61          591          607          337 
TCGA-MW-A4EC 
         330 

  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             1280.0 
[1] "7.0 - 2080.0 (1164.5)" "3.0 - 3668.0 (1280.0)"
[1] "hr=" "3.8"
D20V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  10Q GAIN MUTATED         6        2         2        2
  10Q GAIN WILD-TYPE     247       55       124       78
D20V3, multiclass
           clus
vv          10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  STAGE I                  6                247
  STAGE II                 2                 55
  STAGE III                2                124
  STAGE IV                 2                 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
  10Q GAIN MUTATED     6   2   4   0
  10Q GAIN WILD-TYPE 252  67 174  11
D20V4, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  T1                6                252
  T2                2                 67
  T3                4                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"
D20V5, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     3   1
  10Q GAIN WILD-TYPE 228  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      3    1
  10Q GAIN WILD-TYPE  228   17
   clus
vv  10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  0                3                228
  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  19
D20V6, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  M0               10                407
  M1                2                 76
  MX                0                 19
[1] 3 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 180 324
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      6    6
  10Q GAIN WILD-TYPE  180  324
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FEMALE                6                180
  MALE                  6                324
[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                        44   445
D20V10, multiclass
                           clus
vv                          10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  ASIAN                                    0                  8
  BLACK OR AFRICAN AMERICAN                0                 44
  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  26 330
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      0    8
  10Q GAIN WILD-TYPE   26  330
                        clus
vv                       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 26
  NOT HISPANIC OR LATINO                8                330
[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 325  21
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                25                346 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 3                 21 
$`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-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3316 TCGA-A3-3317 
         267         1120         1436           16         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-A3-3382 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-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-B0-4718 TCGA-B0-4813 TCGA-B0-4819 TCGA-B0-5097 
         110           26          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-B0-5400 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-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
         750          523          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-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54J TCGA-B8-A7U6 
         909          519           53          256          528          110 
TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
          24         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-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-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-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-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-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-4872 
        1628         1793          646         2554         1498         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-4886 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 
        1883         1759         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-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-5683 TCGA-CJ-5684 
        1943         2430         2575          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-4859 
        2552         3146          774         1404           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-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5461 TCGA-CZ-5463 
        1712         1683         1732         1683          330          662 
TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 
        1740         1446          685          386         2439         2067 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
        1997          373          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         2016         1729 
TCGA-EU-5904 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-GK-A6C7 
         551          206          127          305         1727           61 
TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC 
         591          607          337          330 

  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               1273 
[1] "7.0 - 2718.0 (1308.0)" "3.0 - 3668.0 (1273.0)"
[1] "hr=" "2.1"
D21V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  11P GAIN MUTATED         8        4        11        8
  11P GAIN WILD-TYPE     245       53       115       72
D21V3, multiclass
           clus
vv          11P GAIN MUTATED 11P GAIN WILD-TYPE
  STAGE I                  8                245
  STAGE II                 4                 53
  STAGE III               11                115
  STAGE IV                 8                 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
  11P GAIN MUTATED     8   4  18   1
  11P GAIN WILD-TYPE 250  65 160  10
D21V4, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  T1                8                250
  T2                4                 65
  T3               18                160
  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 221  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     10    0
  11P GAIN WILD-TYPE  221   18
   clus
vv  11P GAIN MUTATED 11P GAIN WILD-TYPE
  0               10                221
  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  18
D21V6, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  M0               22                395
  M1                8                 70
  MX                1                 18
[1] 3 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 176 309
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     10   21
  11P GAIN WILD-TYPE  176  309
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE               10                176
  MALE                 21                309
[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                        42   428
D21V10, multiclass
                           clus
vv                          11P GAIN MUTATED 11P GAIN WILD-TYPE
  ASIAN                                    0                  8
  BLACK OR AFRICAN AMERICAN                2                 42
  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  25 319
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      1   19
  11P GAIN WILD-TYPE   25  319
                        clus
vv                       11P GAIN MUTATED 11P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 25
  NOT HISPANIC OR LATINO               19                319
[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 325  22
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                24                347 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 2                 22 
$`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-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3316 TCGA-A3-3317 
         267         1120         1436           16         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-A3-3382 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-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-B0-4718 TCGA-B0-4813 TCGA-B0-4819 TCGA-B0-5097 
         110           26          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-B0-5400 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-B2-4101 TCGA-B2-4102 
        2963          992         1092           51          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-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
         750          523          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-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54J TCGA-B8-A7U6 
         909          519           53          256          528          110 
TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
          24         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-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-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-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-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-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-4872 
        1628         1793          646         2554         1498         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-4886 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 
        1883         1759         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-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-5683 TCGA-CJ-5684 
        1943         2430         2575          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-4859 
        2552         3146          774         1404           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-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5461 TCGA-CZ-5463 
        1712         1683         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-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         2016 
TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A8L6 TCGA-G6-A8L7 
        1729          551          206          127          305         1727 
TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC 
          61          591          607          337          330 

  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             1266.0 
[1] "96.0 - 2718.0 (1352.5)" "3.0 - 3668.0 (1266.0)" 
[1] "hr=" "1.3"
D22V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  11Q GAIN MUTATED         9        4        10        6
  11Q GAIN WILD-TYPE     244       53       116       74
D22V3, multiclass
           clus
vv          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  STAGE I                  9                244
  STAGE II                 4                 53
  STAGE III               10                116
  STAGE IV                 6                 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 GAIN MUTATED     9   4  16   0
  11Q GAIN WILD-TYPE 249  65 162  11
D22V4, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T1                9                249
  T2                4                 65
  T3               16                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"
D22V5, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     9   0
  11Q GAIN WILD-TYPE 222  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      9    0
  11Q GAIN WILD-TYPE  222   18
   clus
vv  11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  0                9                222
  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  18
D22V6, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  M0               22                395
  M1                6                 72
  MX                1                 18
[1] 3 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 176 311
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     10   19
  11Q GAIN WILD-TYPE  176  311
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE               10                176
  MALE                 19                311
[1] 2 2
[1] FALSE
D22V8, continuous
[1] "Remove cluster labels:" "11Q GAIN MUTATED"      
clus
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 2                 39 
        TCGA-A3-A6NJ         TCGA-A3-A6NL         TCGA-A3-A8CQ 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-AK-3426         TCGA-AK-3430         TCGA-B0-4838 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-B2-5639         TCGA-B4-5377         TCGA-B4-5378 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-B4-5832         TCGA-B4-5834         TCGA-B4-5835 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-B4-5836         TCGA-B4-5838         TCGA-B4-5843 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-B4-5844         TCGA-CZ-4854         TCGA-CZ-4856 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CZ-4860         TCGA-CZ-4861         TCGA-CZ-4862 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CZ-5456         TCGA-CZ-5457         TCGA-CZ-5465 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-CZ-5469         TCGA-CZ-5982         TCGA-DV-5565 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DV-5566         TCGA-DV-5567         TCGA-DV-5568 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DV-5569         TCGA-DV-5573         TCGA-DV-5574 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-DV-5575         TCGA-DV-5576         TCGA-EU-5904 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-EU-5907         TCGA-G6-A8L6         TCGA-G6-A8L7 
"11Q GAIN WILD-TYPE" "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                        42   430
D22V10, multiclass
                           clus
vv                          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  ASIAN                                    0                  8
  BLACK OR AFRICAN AMERICAN                2                 42
  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  25 320
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      1   18
  11Q GAIN WILD-TYPE   25  320
                        clus
vv                       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 25
  NOT HISPANIC OR LATINO               18                320
[1] 2 2
[1] FALSE

Clustering(23) Variable = 12P GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                  0   1
  12P GAIN MUTATED    70   7
  12P GAIN WILD-TYPE 277  17
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                77                294 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 7                 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-5984 TCGA-EU-5905 
        1740          685           59         2067          119 

$`12P GAIN WILD-TYPE`
TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 
         267         1120         1436           16          735         1493 
TCGA-A3-3317 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3326 
        1491         1508         1478         1106         1186         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-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
        2688         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-A3-3385 TCGA-A3-A8CQ TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3431 
        1993            3         2566         2223         2017         1853 
TCGA-AK-3434 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 
        2087         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-B0-4706 TCGA-B0-4718 TCGA-B0-4813 
         369         1238           43           26          616           18 
TCGA-B0-5097 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5115 TCGA-B0-5117 TCGA-B0-5119 
         665          911         1092          797          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-B0-5698 TCGA-B0-5699 
        3431         1487         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-B0-5812 TCGA-B2-3923 TCGA-B2-3924 
        1459         2931         2722         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-B8-5158 
         838          762          750          523          777          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-B8-5549 TCGA-B8-5550 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E 
         194          434         1046          435          830          909 
TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 
          53          256          528          110           24         3377 
TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4169 TCGA-BP-4173 
        2881         2746         3037           13          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-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-4765 TCGA-BP-4766 TCGA-BP-4769 
        2208         2372         2361         2184         1462         1876 
TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4784 
        1885         1843          411         1731         2080         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-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 
        1935         1785         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-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-5195 
         693          406          822         1011          714          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-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-4871 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
        2554         1498         2423         2283         2353         1955 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4889 
        2186         2014         1883         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-4904 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4916 
        1450         1520         1792         1496         1531         1373 
TCGA-CJ-5675 TCGA-CJ-5681 TCGA-CJ-5683 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6031 
        2430          552         1889         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-4858 TCGA-CZ-4859 
        3222         2552         3146          774         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-5460 TCGA-CZ-5463 TCGA-CZ-5465 
        1683         1732         1683         1430          662         1446 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5988 TCGA-CZ-5989 
         386         2439         1997          373          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-G6-A8L6 
        2016         1729          551          206          127          305 
TCGA-G6-A8L7 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC 
        1727           61          591          607          337          330 

  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 
            1314.0             1227.5 
[1] "7.0 - 3343.0 (1314.0)" "3.0 - 3668.0 (1227.5)"
[1] "hr=" "1.6"
D23V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  12P GAIN MUTATED        43        9        39       28
  12P GAIN WILD-TYPE     210       48        87       52
D23V3, multiclass
           clus
vv          12P GAIN MUTATED 12P GAIN WILD-TYPE
  STAGE I                 43                210
  STAGE II                 9                 48
  STAGE III               39                 87
  STAGE IV                28                 52
[1] 4 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 213  56 121   7
D23V4, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  T1               45                213
  T2               13                 56
  T3               57                121
  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 175  10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     56    8
  12P GAIN WILD-TYPE  175   10
   clus
vv  12P GAIN MUTATED 12P GAIN WILD-TYPE
  0               56                175
  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  17
D23V6, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  M0               90                327
  M1               27                 51
  MX                2                 17
[1] 3 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 147 250
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     39   80
  12P GAIN WILD-TYPE  147  250
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE               39                147
  MALE                 80                250
[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                 10 
        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-A54E         TCGA-B8-A54G 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-B8-A8YJ         TCGA-G6-A5PC         TCGA-G6-A8L7 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-MM-A563 
"12P GAIN WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12P GAIN MUTATED       2                         5   110
  12P GAIN WILD-TYPE     6                        39   347
D23V10, multiclass
                           clus
vv                          12P GAIN MUTATED 12P GAIN WILD-TYPE
  ASIAN                                    2                  6
  BLACK OR AFRICAN AMERICAN                5                 39
  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  23 258
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      3   80
  12P GAIN WILD-TYPE   23  258
                        clus
vv                       12P GAIN MUTATED 12P GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                 23
  NOT HISPANIC OR LATINO               80                258
[1] 2 2
[1] FALSE

Clustering(24) Variable = 12Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                  0   1
  12Q GAIN MUTATED    71   7
  12Q GAIN WILD-TYPE 276  17
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                78                293 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 7                 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-5984 TCGA-EU-5905 
         330         1740          685           59         2067          119 

$`12Q GAIN WILD-TYPE`
TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 
         267         1120         1436           16          735         1493 
TCGA-A3-3317 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3326 
        1491         1508         1478         1106         1186         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-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
        2688         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-A3-3385 TCGA-A3-A8CQ TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3431 
        1993            3         2566         2223         2017         1853 
TCGA-AK-3434 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 
        2087         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-B0-4706 TCGA-B0-4718 TCGA-B0-4813 
         369         1238           43           26          616           18 
TCGA-B0-5097 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5115 TCGA-B0-5117 TCGA-B0-5119 
         665          911         1092          797          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-B0-5698 TCGA-B0-5699 
        3431         1487         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-B0-5812 TCGA-B2-3923 TCGA-B2-3924 
        1459         2931         2722         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-B8-5158 
         838          762          750          523          777          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-B8-5549 TCGA-B8-5550 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E 
         194          434         1046          435          830          909 
TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 
          53          256          528          110           24         3377 
TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4169 TCGA-BP-4173 
        2881         2746         3037           13          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-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-4765 TCGA-BP-4766 TCGA-BP-4769 
        2208         2372         2361         2184         1462         1876 
TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4784 
        1885         1843          411         1731         2080         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-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 
        1935         1785         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-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-5195 
         693          406          822         1011          714          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-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-4871 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
        2554         1498         2423         2283         2353         1955 
TCGA-CJ-4878 TCGA-CJ-4882 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4889 TCGA-CJ-4890 
        2186         1883         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-4904 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4916 TCGA-CJ-5675 
        1520         1792         1496         1531         1373         2430 
TCGA-CJ-5681 TCGA-CJ-5683 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6031 TCGA-CJ-6032 
         552         1889         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-4858 TCGA-CZ-4859 TCGA-CZ-4862 
        2552         3146          774         1943         1787         1843 
TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5457 
        1928         2830         1929         1789           25         1683 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5470 
        1732         1683         1430          662         1446          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-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 
        1398         1470          370          355         1130         2016 
TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A8L6 TCGA-G6-A8L7 
        1729          551          206          127          305         1727 
TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC 
          61          591          607          337          330 

  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 
            1355.5             1217.0 
[1] "7.0 - 3343.0 (1355.5)" "3.0 - 3668.0 (1217.0)"
[1] "hr=" "1.6"
D24V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  12Q GAIN MUTATED        43        9        40       28
  12Q GAIN WILD-TYPE     210       48        86       52
D24V3, multiclass
           clus
vv          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  STAGE I                 43                210
  STAGE II                 9                 48
  STAGE III               40                 86
  STAGE IV                28                 52
[1] 4 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 213  56 120   7
D24V4, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T1               45                213
  T2               13                 56
  T3               58                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"
D24V5, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    56   8
  12Q GAIN WILD-TYPE 175  10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     56    8
  12Q GAIN WILD-TYPE  175   10
   clus
vv  12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  0               56                175
  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  17
D24V6, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  M0               91                326
  M1               27                 51
  MX                2                 17
[1] 3 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 147 249
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     39   81
  12Q GAIN WILD-TYPE  147  249
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE               39                147
  MALE                 81                249
[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                 10 
        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-A54E         TCGA-B8-A54G 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-B8-A8YJ         TCGA-G6-A5PC         TCGA-G6-A8L7 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-MM-A563 
"12Q GAIN WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12Q GAIN MUTATED       2                         5   111
  12Q GAIN WILD-TYPE     6                        39   346
D24V10, multiclass
                           clus
vv                          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  ASIAN                                    2                  6
  BLACK OR AFRICAN AMERICAN                5                 39
  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  23 257
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      3   81
  12Q GAIN WILD-TYPE   23  257
                        clus
vv                       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                 23
  NOT HISPANIC OR LATINO               81                257
[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 329  21
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                21                350 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 3                 21 
$`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         2016 

$`13Q GAIN WILD-TYPE`
TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 
         267         1120         1436           16          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-A3-3326 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-B0-4718 TCGA-B0-4813 
         369         1238           43          110          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-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 
        1132          449         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-B2-5641 
         374          648          952          358          315          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-A54E TCGA-B8-A54F TCGA-B8-A54G 
        1046          435          830          909          519           53 
TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 
         256          150          528          110           24         3377 
TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4167 
        2881         2746         3074         2839         3037         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-4334 TCGA-BP-4335 TCGA-BP-4338 
        1625          845         1888          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-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-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-5199 TCGA-BP-5201 TCGA-BP-5202 
         408          749         1018         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-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-4908 TCGA-CJ-4916 TCGA-CJ-5675 
        1520         1560         1792         1531         1373         2430 
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-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-5463 TCGA-CZ-5465 TCGA-CZ-5466 
        1683         1732         1683          662         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-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-5575 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
         355         1130         1729          551          119          206 
TCGA-EU-5907 TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 
         127          305         1727           61          591          607 
TCGA-MM-A84U TCGA-MW-A4EC 
         337          330 

  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 
              1413               1252 
[1] "13.0 - 2575.0 (1413.0)" "3.0 - 3668.0 (1252.0)" 
[1] "hr=" "2.5"
D25V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  13Q GAIN MUTATED         6        3         8        5
  13Q GAIN WILD-TYPE     247       54       118       75
D25V3, multiclass
           clus
vv          13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  STAGE I                  6                247
  STAGE II                 3                 54
  STAGE III                8                118
  STAGE IV                 5                 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
  13Q GAIN MUTATED     7   3  12   0
  13Q GAIN WILD-TYPE 251  66 166  11
D25V4, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  T1                7                251
  T2                3                 66
  T3               12                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"
D25V5, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     4   0
  13Q GAIN WILD-TYPE 227  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      4    0
  13Q GAIN WILD-TYPE  227   18
   clus
vv  13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  0                4                227
  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  19
D25V6, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  M0               17                400
  M1                5                 73
  MX                0                 19
[1] 3 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 181 313
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      5   17
  13Q GAIN WILD-TYPE  181  313
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE                5                181
  MALE                 17                313
[1] 2 2
[1] FALSE
D25V8, continuous
[1] "Remove cluster labels:" "13Q GAIN MUTATED"      
clus
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 2                 39 
        TCGA-A3-A6NJ         TCGA-A3-A6NL         TCGA-A3-A8CQ 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AK-3426         TCGA-AK-3430         TCGA-B0-4838 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-B4-5377         TCGA-B4-5378         TCGA-B4-5832 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-B4-5834         TCGA-B4-5835         TCGA-B4-5836 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-B4-5838         TCGA-B4-5843         TCGA-B4-5844 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CZ-4854         TCGA-CZ-4856         TCGA-CZ-4858 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CZ-4860         TCGA-CZ-4861         TCGA-CZ-4862 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CZ-5456         TCGA-CZ-5457         TCGA-CZ-5465 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CZ-5469         TCGA-CZ-5982         TCGA-DV-5565 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DV-5566         TCGA-DV-5567         TCGA-DV-5568 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DV-5569         TCGA-DV-5573         TCGA-DV-5575 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DV-5576         TCGA-EU-5904         TCGA-EU-5905 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EU-5907         TCGA-G6-A8L6         TCGA-G6-A8L7 
"13Q GAIN WILD-TYPE" "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                        44   436
D25V10, multiclass
                           clus
vv                          13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  ASIAN                                    1                  7
  BLACK OR AFRICAN AMERICAN                0                 44
  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  23 325
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      3   13
  13Q GAIN WILD-TYPE   23  325
                        clus
vv                       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                 23
  NOT HISPANIC OR LATINO               13                325
[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 339  23
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 9                362 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 1                 23 
$`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-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 
         267         1120         1436           16          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-A3-3326 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-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-B0-4706 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-B4-5835 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-A54E TCGA-B8-A54F 
          15         1046          435          830          909          519 
TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ 
          53          256          150          528          110           24 
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-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-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-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-4902 TCGA-CJ-4903 TCGA-CJ-4904 
         841         1808         1528         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-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-5988 
         386         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         2016         1729          551          119          206 
TCGA-EU-5907 TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 
         127          305         1727           61          591          607 
TCGA-MM-A84U TCGA-MW-A4EC 
         337          330 

  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               1252 
[1] "110.0 - 2192.0 (1314.0)" "3.0 - 3668.0 (1252.0)"  
[1] "hr=" "1.7"
D26V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  14Q GAIN MUTATED         5        2         4        5
  14Q GAIN WILD-TYPE     248       55       122       75
D26V3, multiclass
           clus
vv          14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  STAGE I                  5                248
  STAGE II                 2                 55
  STAGE III                4                122
  STAGE IV                 5                 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
  14Q GAIN MUTATED     5   2   6   3
  14Q GAIN WILD-TYPE 253  67 172   8
D26V4, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  T1                5                253
  T2                2                 67
  T3                6                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"
D26V5, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     9   0
  14Q GAIN WILD-TYPE 222  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      9    0
  14Q GAIN WILD-TYPE  222   18
   clus
vv  14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  0                9                222
  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  19
D26V6, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  M0               12                405
  M1                4                 74
  MX                0                 19
[1] 3 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 181 319
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      5   11
  14Q GAIN WILD-TYPE  181  319
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE                5                181
  MALE                 11                319
[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                        43   442
D26V10, multiclass
                           clus
vv                          14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  ASIAN                                    0                  8
  BLACK OR AFRICAN AMERICAN                1                 43
  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  26 327
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      0   11
  14Q GAIN WILD-TYPE   26  327
                        clus
vv                       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 26
  NOT HISPANIC OR LATINO               11                327
[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 327  23
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                21                350 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 1                 23 
$`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-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 
         267         1120         1436           16          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-A3-3326 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-A3-3376 
         319          873         2270         2274         1621         1070 
TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-A8CQ 
         630          567          574          861         1993            3 
TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3431 TCGA-AK-3434 
        3343         2566         2223         2017         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-B0-4710 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-B4-5843 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-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H 
         435          830          909          519           53          256 
TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4160 
         150          528          110           24         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-4176 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 
         701         1893         1955         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-4804 
        1854         1489          620         1107         1124         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-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-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-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-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-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4876 
        2554         1498         1435         2259         2283         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-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-5587 TCGA-CW-5589 
        1906         2548         2799         2489         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-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 
        1929         1789           25         1683         1732         1683 
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-5988 
         386         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         2016         1729          551          119          206 
TCGA-EU-5907 TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 
         127          305         1727           61          591          607 
TCGA-MM-A84U TCGA-MW-A4EC 
         337          330 

  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               1210 
[1] "166.0 - 2609.0 (1670.0)" "3.0 - 3668.0 (1210.0)"  
[1] "hr=" "1.5"
D27V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  15Q GAIN MUTATED        10        4         7        5
  15Q GAIN WILD-TYPE     243       53       119       75
D27V3, multiclass
           clus
vv          15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  STAGE I                 10                243
  STAGE II                 4                 53
  STAGE III                7                119
  STAGE IV                 5                 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
  15Q GAIN MUTATED    10   4  11   1
  15Q GAIN WILD-TYPE 248  65 167  10
D27V4, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  T1               10                248
  T2                4                 65
  T3               11                167
  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 221  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     10    2
  15Q GAIN WILD-TYPE  221   16
   clus
vv  15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  0               10                221
  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  19
D27V6, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  M0               21                396
  M1                5                 73
  MX                0                 19
[1] 3 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 178 312
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      8   18
  15Q GAIN WILD-TYPE  178  312
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE                8                178
  MALE                 18                312
[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                        43   432
D27V10, multiclass
                           clus
vv                          15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  ASIAN                                    0                  8
  BLACK OR AFRICAN AMERICAN                1                 43
  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  25 322
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      1   16
  15Q GAIN WILD-TYPE   25  322
                        clus
vv                       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 25
  NOT HISPANIC OR LATINO               16                322
[1] 2 2
[1] FALSE

Clustering(28) Variable = 16P GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                  0   1
  16P GAIN MUTATED    74   5
  16P GAIN WILD-TYPE 273  19
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                79                292 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 5                 19 
$`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-A54E TCGA-B8-A54I TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4166 
         788          909          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-4995 TCGA-BP-5175 TCGA-BP-5198 TCGA-BP-5200 TCGA-CJ-4636 TCGA-CJ-4871 
        1371          932          603         1063         1924         2423 
TCGA-CJ-4873 TCGA-CJ-4875 TCGA-CJ-4885 TCGA-CJ-4889 TCGA-CJ-4897 TCGA-CJ-4901 
        2259         2353         2125         1946         1808         1450 
TCGA-CJ-4903 TCGA-CJ-4907 TCGA-CJ-5671 TCGA-CJ-5676 TCGA-CJ-5682 TCGA-CJ-5683 
        1560         1499         1943         2575         1883         1889 
TCGA-CW-5581 TCGA-CW-5588 TCGA-CW-5591 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4866 
        2799         2017         2271         1943         1787         1868 
TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5460 TCGA-CZ-5984 TCGA-DV-5568 TCGA-DV-5573 
        1712         1683         1430         2067          370         1130 
TCGA-EU-5905 
         119 

$`16P GAIN WILD-TYPE`
TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3316 TCGA-A3-3317 
         267         1120         1436           16         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-A3-3347 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-A3-3373 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-A8CQ TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 
         861         1993            3         3343         2566         2223 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3443 
        2017          480         1853         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-B0-5115 TCGA-B0-5116 TCGA-B0-5117 
         665          911         1092          797          657          535 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5690 TCGA-B0-5691 
          59          493          554          652         2408         3431 
TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
        3076         1420         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-B2-4099 
        2722         1865         2963          992         1092          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-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 
         291          175          141           11            7          511 
TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4622 
         826          838          762          750          523          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-A54J 
         435          830          519           53          256          528 
TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4165 
         110           24         3377         2881         2746         3037 
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-4347 TCGA-BP-4349 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 
        1367          372         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-4784 TCGA-BP-4789 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4801 
        1731         1854         1489          620         1107         1124 
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-4970 TCGA-BP-4973 TCGA-BP-4975 TCGA-BP-4976 
        1871         1746          433         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-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
         177          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-5199 TCGA-BP-5201 
         714          408          749         1018         1355          951 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4642 
          29         1820         1416         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-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4886 
        1955         2186         2014         1883         1759         1952 
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-4904 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-5675 
        1792         1496         1531         1657         1373         2430 
TCGA-CJ-5681 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6031 TCGA-CJ-6032 
         552         2231         2038         1855         1906         2548 
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-4854 TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4863 
        3146          774         1404           18         1843         1928 
TCGA-CZ-4864 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5458 TCGA-CZ-5459 
        2830         1929         1789           25         1732         1683 
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-5985 TCGA-CZ-5986 TCGA-CZ-5988 TCGA-CZ-5989 
         386         2439         1997          373          693         1905 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 
        1329         1398         1470          355         2016         1729 
TCGA-EU-5904 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-GK-A6C7 
         551          206          127          305         1727           61 
TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC 
         591          607          337          330 

  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 
            1430.0             1194.5 
[1] "7.0 - 3074.0 (1430.0)" "3.0 - 3668.0 (1194.5)"
[1] "hr=" "1"  
D28V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  16P GAIN MUTATED        46        8        33       18
  16P GAIN WILD-TYPE     207       49        93       62
D28V3, multiclass
           clus
vv          16P GAIN MUTATED 16P GAIN WILD-TYPE
  STAGE I                 46                207
  STAGE II                 8                 49
  STAGE III               33                 93
  STAGE IV                18                 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
  16P GAIN MUTATED    46  10  46   3
  16P GAIN WILD-TYPE 212  59 132   8
D28V4, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  T1               46                212
  T2               10                 59
  T3               46                132
  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 181  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     50    1
  16P GAIN WILD-TYPE  181   17
   clus
vv  16P GAIN MUTATED 16P GAIN WILD-TYPE
  0               50                181
  1                1                 17
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  16P GAIN MUTATED    85  18   2
  16P GAIN WILD-TYPE 332  60  17
D28V6, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  M0               85                332
  M1               18                 60
  MX                2                 17
[1] 3 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    36  69
  16P GAIN WILD-TYPE 150 261
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     36   69
  16P GAIN WILD-TYPE  150  261
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE               36                150
  MALE                 69                261
[1] 2 2
[1] FALSE
D28V8, continuous
D28V9, continuous
[1] "Remove cluster labels:" "16P GAIN MUTATED"      
clus
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 2                 10 
        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-B8-A8YJ         TCGA-G6-A5PC         TCGA-G6-A8L7 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-MM-A563 
"16P GAIN WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16P GAIN MUTATED       1                         5    99
  16P GAIN WILD-TYPE     7                        39   358
D28V10, multiclass
                           clus
vv                          16P GAIN MUTATED 16P GAIN WILD-TYPE
  ASIAN                                    1                  7
  BLACK OR AFRICAN AMERICAN                5                 39
  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     5  63
  16P GAIN WILD-TYPE  21 275
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      5   63
  16P GAIN WILD-TYPE   21  275
                        clus
vv                       16P GAIN MUTATED 16P GAIN WILD-TYPE
  HISPANIC OR LATINO                    5                 21
  NOT HISPANIC OR LATINO               63                275
[1] 2 2
[1] FALSE

Clustering(29) Variable = 16Q GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                  0   1
  16Q GAIN MUTATED    69   4
  16Q GAIN WILD-TYPE 278  20
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                73                298 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 4                 20 
$`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-A54E TCGA-B8-A54I TCGA-BP-4162 TCGA-BP-4163 
         777          788          909          150         3074         2839 
TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4174 TCGA-BP-4338 TCGA-BP-4351 TCGA-BP-4756 
          13         2718         1879         2859          970          374 
TCGA-BP-4768 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 
         400         2080          354          204         1459         2172 
TCGA-BP-4967 TCGA-BP-4969 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4977 TCGA-BP-4989 
         205         1794         1487         1502          454          118 
TCGA-BP-4994 TCGA-BP-5175 TCGA-BP-5198 TCGA-BP-5200 TCGA-CJ-4636 TCGA-CJ-4871 
        1308          932          603         1063         1924         2423 
TCGA-CJ-4873 TCGA-CJ-4875 TCGA-CJ-4885 TCGA-CJ-4889 TCGA-CJ-4897 TCGA-CJ-4901 
        2259         2353         2125         1946         1808         1450 
TCGA-CJ-4903 TCGA-CJ-4907 TCGA-CJ-5671 TCGA-CJ-5676 TCGA-CJ-5682 TCGA-CJ-5683 
        1560         1499         1943         2575         1883         1889 
TCGA-CW-5581 TCGA-CW-5588 TCGA-CW-5591 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4866 
        2799         2017         2271         1943         1787         1868 
TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5460 TCGA-CZ-5984 TCGA-DV-5568 TCGA-DV-5573 
        1712         1683         1430         2067          370         1130 
TCGA-EU-5905 
         119 

$`16Q GAIN WILD-TYPE`
TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3316 TCGA-A3-3317 
         267         1120         1436           16         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-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
         910         2688         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-A3-3383 TCGA-A3-3385 TCGA-A3-A8CQ TCGA-AK-3425 
         630          567          861         1993            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-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-B0-4706 TCGA-B0-4710 TCGA-B0-4718 
         369         1238           43           26           96          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-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
         657          535           59          493          554          652 
TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5698 
         449         2408         3431         3076         1420         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-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 
         315          417          656          507          291          175 
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-B8-4622 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          528          110 
TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4165 TCGA-BP-4169 
          24         3377         2881         2746         3037          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-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4765 
         372         2208         2372         2361          182         2184 
TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 
        1462         1876         1885         1843          411         1731 
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-4973 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4982 
        1746          433         1384         1433         1632         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-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-5199 TCGA-BP-5201 
         714          408          749         1018         1355          951 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4642 
          29         1820         1416         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-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4886 
        1955         2186         2014         1883         1759         1952 
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-4904 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-5675 
        1792         1496         1531         1657         1373         2430 
TCGA-CJ-5681 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6031 TCGA-CJ-6032 
         552         2231         2038         1855         1906         2548 
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-4854 TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4863 
        3146          774         1404           18         1843         1928 
TCGA-CZ-4864 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5458 TCGA-CZ-5459 
        2830         1929         1789           25         1732         1683 
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-5985 TCGA-CZ-5986 TCGA-CZ-5988 TCGA-CZ-5989 
         386         2439         1997          373          693         1905 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 
        1329         1398         1470          355         2016         1729 
TCGA-EU-5904 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-GK-A6C7 
         551          206          127          305         1727           61 
TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC 
         591          607          337          330 

  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 
            1487.0             1172.5 
[1] "7.0 - 3074.0 (1487.0)" "3.0 - 3668.0 (1172.5)"
[1] "hr=" "1.3"
D29V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  16Q GAIN MUTATED        43        8        32       14
  16Q GAIN WILD-TYPE     210       49        94       66
D29V3, multiclass
           clus
vv          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  STAGE I                 43                210
  STAGE II                 8                 49
  STAGE III               32                 94
  STAGE IV                14                 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
  16Q GAIN MUTATED    43   8  44   2
  16Q GAIN WILD-TYPE 215  61 134   9
D29V4, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T1               43                215
  T2                8                 61
  T3               44                134
  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 184  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     47    1
  16Q GAIN WILD-TYPE  184   17
   clus
vv  16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  0               47                184
  1                1                 17
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  16Q GAIN MUTATED    80  15   2
  16Q GAIN WILD-TYPE 337  63  17
D29V6, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  M0               80                337
  M1               15                 63
  MX                2                 17
[1] 3 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    35  62
  16Q GAIN WILD-TYPE 151 268
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     35   62
  16Q GAIN WILD-TYPE  151  268
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE               35                151
  MALE                 62                268
[1] 2 2
[1] FALSE
D29V8, continuous
D29V9, continuous
[1] "Remove cluster labels:" "16Q GAIN MUTATED"      
clus
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 2                 10 
        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-B8-A8YJ         TCGA-G6-A5PC         TCGA-G6-A8L7 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-MM-A563 
"16Q GAIN WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16Q GAIN MUTATED       1                         5    91
  16Q GAIN WILD-TYPE     7                        39   366
D29V10, multiclass
                           clus
vv                          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  ASIAN                                    1                  7
  BLACK OR AFRICAN AMERICAN                5                 39
  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     5  57
  16Q GAIN WILD-TYPE  21 281
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      5   57
  16Q GAIN WILD-TYPE   21  281
                        clus
vv                       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    5                 21
  NOT HISPANIC OR LATINO               57                281
[1] 2 2
[1] FALSE

Clustering(30) Variable = 17P GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                  0   1
  17P GAIN MUTATED    18   1
  17P GAIN WILD-TYPE 329  23
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                19                352 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 1                 23 
$`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-EU-5905 
         119 

$`17P GAIN WILD-TYPE`
TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3316 TCGA-A3-3317 
         267         1120         1436           16         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-A3-3365 
         910         2688         1307         2504         1559          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-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-B0-4699 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-B4-5843 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-B8-4622 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-B8-5552 
         737          522          505          194          434         1046 
TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H 
         435          830          909          519           53          256 
TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4160 
         150          528          110           24         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-4325 TCGA-BP-4326 TCGA-BP-4329 
         701         1893         1879         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-4758 TCGA-BP-4759 TCGA-BP-4760 
        1367          372          970         2208         2372         2361 
TCGA-BP-4761 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4774 TCGA-BP-4775 
         182         2184         1462         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-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-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-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
        1997          373          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         2016         1729 
TCGA-EU-5904 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-GK-A6C7 
         551          206          127          305         1727           61 
TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC 
         591          607          337          330 

  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 
              1063               1299 
[1] "15.0 - 2259.0 (1063.0)" "3.0 - 3668.0 (1299.0)" 
[1] "hr=" "1"  
D30V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  17P GAIN MUTATED        14        4         7        0
  17P GAIN WILD-TYPE     239       53       119       80
D30V3, multiclass
           clus
vv          17P GAIN MUTATED 17P GAIN WILD-TYPE
  STAGE I                 14                239
  STAGE II                 4                 53
  STAGE III                7                119
  STAGE IV                 0                 80
[1] 4 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 244  65 171  11
D30V4, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  T1               14                244
  T2                4                 65
  T3                7                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"
D30V5, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    10   2
  17P GAIN WILD-TYPE 221  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     10    2
  17P GAIN WILD-TYPE  221   16
   clus
vv  17P GAIN MUTATED 17P GAIN WILD-TYPE
  0               10                221
  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  19
D30V6, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  M0               25                392
  M1                0                 78
  MX                0                 19
[1] 3 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 178 313
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      8   17
  17P GAIN WILD-TYPE  178  313
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE                8                178
  MALE                 17                313
[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                 11 
        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-A54E         TCGA-B8-A54F 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-B8-A54G         TCGA-B8-A8YJ         TCGA-G6-A5PC 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G6-A8L7         TCGA-MM-A563 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17P GAIN MUTATED       2                         3    20
  17P GAIN WILD-TYPE     6                        41   437
D30V10, multiclass
                           clus
vv                          17P GAIN MUTATED 17P GAIN WILD-TYPE
  ASIAN                                    2                  6
  BLACK OR AFRICAN AMERICAN                3                 41
  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  26 324
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      0   14
  17P GAIN WILD-TYPE   26  324
                        clus
vv                       17P GAIN MUTATED 17P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 26
  NOT HISPANIC OR LATINO               14                324
[1] 2 2
[1] FALSE

Clustering(31) Variable = 17Q GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                  0   1
  17Q GAIN MUTATED    22   1
  17Q GAIN WILD-TYPE 325  23
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                23                348 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 1                 23 
$`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-EU-5905 TCGA-G6-A8L7 
        1450         1499         1868          119         1727 

$`17Q GAIN WILD-TYPE`
TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3316 TCGA-A3-3317 
         267         1120         1436           16         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-A3-3365 
         910         2688         1307         2504         1559          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-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-B0-4699 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-B4-5836 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-B8-4622 
         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-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I 
         830          909          519           53          256          150 
TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 
         528          110           24         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-4325 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 
        1893         1879         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-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4765 
         372          970         2372         2361          182         2184 
TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 
        1462         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-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-5175 
        1140         1071          193         2412         2257          932 
TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 
         293         2263         1495         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-5988 
         386         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-5906 TCGA-EU-5907 
        1130         2016         1729          551          206          127 
TCGA-G6-A8L6 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC 
         305           61          591          607          337          330 

  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 
              1132               1299 
[1] "15.0 - 2259.0 (1132.0)" "3.0 - 3668.0 (1299.0)" 
[1] "hr=" "1.3"
D31V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  17Q GAIN MUTATED        18        4         8        2
  17Q GAIN WILD-TYPE     235       53       118       78
D31V3, multiclass
           clus
vv          17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  STAGE I                 18                235
  STAGE II                 4                 53
  STAGE III                8                118
  STAGE IV                 2                 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
  17Q GAIN MUTATED    18   4   9   1
  17Q GAIN WILD-TYPE 240  65 169  10
D31V4, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T1               18                240
  T2                4                 65
  T3                9                169
  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    14   2
  17Q GAIN WILD-TYPE 217  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     14    2
  17Q GAIN WILD-TYPE  217   16
   clus
vv  17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  0               14                217
  1                2                 16
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  17Q GAIN MUTATED    29   2   1
  17Q GAIN WILD-TYPE 388  76  18
D31V6, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  M0               29                388
  M1                2                 76
  MX                1                 18
[1] 3 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    12  20
  17Q GAIN WILD-TYPE 174 310
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     12   20
  17Q GAIN WILD-TYPE  174  310
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE               12                174
  MALE                 20                310
[1] 2 2
[1] FALSE
D31V8, continuous
D31V9, continuous
[1] "Remove cluster labels:" "17Q GAIN MUTATED"      
clus
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 2                 10 
        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-A54E         TCGA-B8-A54F 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-B8-A54G         TCGA-B8-A8YJ         TCGA-G6-A5PC 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-MM-A563 
"17Q GAIN WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17Q GAIN MUTATED       2                         4    26
  17Q GAIN WILD-TYPE     6                        40   431
D31V10, multiclass
                           clus
vv                          17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  ASIAN                                    2                  6
  BLACK OR AFRICAN AMERICAN                4                 40
  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  18
  17Q GAIN WILD-TYPE  26 320
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      0   18
  17Q GAIN WILD-TYPE   26  320
                        clus
vv                       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 26
  NOT HISPANIC OR LATINO               18                320
[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 325  24
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                22                349 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 0                 24 
$`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-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 
         267         1120         1436          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-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 
        2087         2044         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-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-B0-4718 TCGA-B0-4813 TCGA-B0-4819 TCGA-B0-5097 
         110           26          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-B0-5400 TCGA-B0-5402 TCGA-B0-5690 
         493          554          652         1132          449         2408 
TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 
        3431         1487         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-B2-5635 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-B8-5158 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-A54E 
         434           15         1046          435          830          909 
TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 
         519           53          256          150          528          110 
TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
          24         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-4325 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 
        1955         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-4765 
         374         2208         2372         2361          182         2184 
TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 
        1462         1876         1885         1843          411         1731 
TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4801 
        2080          354         1854          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-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 
         118         1413          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-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-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-4901 TCGA-CJ-4902 
        1521          750          841         1528         1450         1520 
TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4916 
        1560         1792         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-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-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-5988 TCGA-CZ-5989 
        2439         2067         1997          373          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 
        2016         1729          551          119          206          127 
TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U 
         305         1727           61          591          607          337 
TCGA-MW-A4EC 
         330 

  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               1266 
[1] "16.0 - 3076.0 (1365.0)" "3.0 - 3668.0 (1266.0)" 
[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     240       55       118       78
D32V3, multiclass
           clus
vv          18P GAIN MUTATED 18P GAIN WILD-TYPE
  STAGE I                 13                240
  STAGE II                 2                 55
  STAGE III                8                118
  STAGE IV                 2                 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
  18P GAIN MUTATED    13   2  10   0
  18P GAIN WILD-TYPE 245  67 168  11
D32V4, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  T1               13                245
  T2                2                 67
  T3               10                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"
D32V5, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    12   1
  18P GAIN WILD-TYPE 219  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     12    1
  18P GAIN WILD-TYPE  219   17
   clus
vv  18P GAIN MUTATED 18P GAIN WILD-TYPE
  0               12                219
  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  19
D32V6, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  M0               23                394
  M1                2                 76
  MX                0                 19
[1] 3 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 173 318
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     13   12
  18P GAIN WILD-TYPE  173  318
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE               13                173
  MALE                 12                318
[1] 2 2
[1] FALSE
D32V8, continuous
[1] "Remove cluster labels:" "18P GAIN MUTATED"      
clus
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 2                 39 
        TCGA-A3-A6NJ         TCGA-A3-A6NL         TCGA-A3-A8CQ 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AK-3426         TCGA-AK-3430         TCGA-B0-4838 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-B2-5639         TCGA-B4-5377         TCGA-B4-5378 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-B4-5832         TCGA-B4-5834         TCGA-B4-5835 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-B4-5836         TCGA-B4-5843         TCGA-B4-5844 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CZ-4854         TCGA-CZ-4856         TCGA-CZ-4858 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CZ-4860         TCGA-CZ-4861         TCGA-CZ-4862 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CZ-5456         TCGA-CZ-5465         TCGA-CZ-5469 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CZ-5982         TCGA-DV-5565         TCGA-DV-5566 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DV-5567         TCGA-DV-5568         TCGA-DV-5569 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DV-5573         TCGA-DV-5574         TCGA-DV-5575 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DV-5576         TCGA-EU-5904         TCGA-EU-5905 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EU-5907         TCGA-G6-A8L6         TCGA-G6-A8L7 
"18P GAIN WILD-TYPE" "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                        43   433
D32V10, multiclass
                           clus
vv                          18P GAIN MUTATED 18P GAIN WILD-TYPE
  ASIAN                                    0                  8
  BLACK OR AFRICAN AMERICAN                1                 43
  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  24 323
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      2   15
  18P GAIN WILD-TYPE   24  323
                        clus
vv                       18P GAIN MUTATED 18P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                 24
  NOT HISPANIC OR LATINO               15                323
[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 326  24
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                21                350 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 0                 24 
$`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-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 
         267         1120         1436          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-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 
        2087         2044         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-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-B0-4718 TCGA-B0-4813 TCGA-B0-4819 TCGA-B0-5097 
         110           26          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-B0-5400 TCGA-B0-5402 TCGA-B0-5690 
         493          554          652         1132          449         2408 
TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 
        3431         1487         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-B2-5635 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-B8-5158 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-A54E 
         434           15         1046          435          830          909 
TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 
         519           53          256          150          528          110 
TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
          24         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-4325 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 
        1955         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-4765 
         374         2208         2372         2361          182         2184 
TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 
        1462         1876         1885         1843          411         1731 
TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4801 
        2080          354         1854          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-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 
         118         1413          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-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-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-4907 TCGA-CJ-4908 TCGA-CJ-4912 
        1520         1560         1792         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-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6088 
        2799         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-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5988 
         386         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         2016         1729          551          119          206 
TCGA-EU-5907 TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 
         127          305         1727           61          591          607 
TCGA-MM-A84U TCGA-MW-A4EC 
         337          330 

  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               1273 
[1] "16.0 - 3076.0 (1314.0)" "3.0 - 3668.0 (1273.0)" 
[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     241       55       117       78
D33V3, multiclass
           clus
vv          18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  STAGE I                 12                241
  STAGE II                 2                 55
  STAGE III                9                117
  STAGE IV                 2                 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
  18Q GAIN MUTATED    12   2  11   0
  18Q GAIN WILD-TYPE 246  67 167  11
D33V4, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  T1               12                246
  T2                2                 67
  T3               11                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"
D33V5, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    11   1
  18Q GAIN WILD-TYPE 220  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     11    1
  18Q GAIN WILD-TYPE  220   17
   clus
vv  18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  0               11                220
  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  19
D33V6, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  M0               23                394
  M1                2                 76
  MX                0                 19
[1] 3 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 173 318
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     13   12
  18Q GAIN WILD-TYPE  173  318
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE               13                173
  MALE                 12                318
[1] 2 2
[1] FALSE
D33V8, continuous
[1] "Remove cluster labels:" "18Q GAIN MUTATED"      
clus
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 2                 39 
        TCGA-A3-A6NJ         TCGA-A3-A6NL         TCGA-A3-A8CQ 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AK-3426         TCGA-AK-3430         TCGA-B0-4838 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B2-5639         TCGA-B4-5377         TCGA-B4-5378 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B4-5832         TCGA-B4-5834         TCGA-B4-5835 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B4-5836         TCGA-B4-5843         TCGA-B4-5844 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CZ-4854         TCGA-CZ-4856         TCGA-CZ-4858 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CZ-4860         TCGA-CZ-4861         TCGA-CZ-4862 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CZ-5456         TCGA-CZ-5465         TCGA-CZ-5469 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CZ-5982         TCGA-DV-5565         TCGA-DV-5566 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DV-5567         TCGA-DV-5568         TCGA-DV-5569 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DV-5573         TCGA-DV-5574         TCGA-DV-5575 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DV-5576         TCGA-EU-5904         TCGA-EU-5905 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EU-5907         TCGA-G6-A8L6         TCGA-G6-A8L7 
"18Q GAIN WILD-TYPE" "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                        43   433
D33V10, multiclass
                           clus
vv                          18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  ASIAN                                    0                  8
  BLACK OR AFRICAN AMERICAN                1                 43
  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  24 323
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      2   15
  18Q GAIN WILD-TYPE   24  323
                        clus
vv                       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                 24
  NOT HISPANIC OR LATINO               15                323
[1] 2 2
[1] FALSE

Clustering(34) Variable = 19P GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                  0   1
  19P GAIN MUTATED    34   3
  19P GAIN WILD-TYPE 313  21
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                37                334 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 3                 21 
$`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-5984 
        1712         1683         1430          330         1740         2067 
TCGA-EU-5905 
         119 

$`19P GAIN WILD-TYPE`
TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 
         267         1120         1436           16          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-A3-3326 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-A3-3383 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-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-B0-4706 
         951          853          369         1238           43           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-B0-5113 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-B4-5843 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-B8-4620 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-A54E 
         434           15         1046          435          830          909 
TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 
         519           53          256          150          528          110 
TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
          24         3377         2881         2746         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-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-4765 
         374         2208         2372         2361          182         2184 
TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 
        1462         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-4968 
        1935         1785         1834         1862         1871         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-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-4636 
        1018         1355          951           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-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
        1498         1435         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-4908 TCGA-CJ-4912 
        1520         1560         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-5588 TCGA-CW-5589 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 
        2226         2017         2378         3222         2552         3146 
TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4863 
         774           18         1943         1787         1843         1928 
TCGA-CZ-4864 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5458 TCGA-CZ-5459 
        2830         1929         1789           25         1732         1683 
TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5470 TCGA-CZ-5982 
         662         1446          685           59          386         2439 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
        1997          373          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         2016         1729 
TCGA-EU-5904 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-GK-A6C7 
         551          206          127          305         1727           61 
TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC 
         591          607          337          330 

  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 
              1404               1210 
[1] "7.0 - 2575.0 (1404.0)" "3.0 - 3668.0 (1210.0)"
[1] "hr=" "1.4"
D34V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  19P GAIN MUTATED        15        7        14       15
  19P GAIN WILD-TYPE     238       50       112       65
D34V3, multiclass
           clus
vv          19P GAIN MUTATED 19P GAIN WILD-TYPE
  STAGE I                 15                238
  STAGE II                 7                 50
  STAGE III               14                112
  STAGE IV                15                 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
  19P GAIN MUTATED    16   7  26   2
  19P GAIN WILD-TYPE 242  62 152   9
D34V4, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  T1               16                242
  T2                7                 62
  T3               26                152
  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 209  15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     22    3
  19P GAIN WILD-TYPE  209   15
   clus
vv  19P GAIN MUTATED 19P GAIN WILD-TYPE
  0               22                209
  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  19
D34V6, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  M0               36                381
  M1               15                 63
  MX                0                 19
[1] 3 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 172 293
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     14   37
  19P GAIN WILD-TYPE  172  293
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE               14                172
  MALE                 37                293
[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                        43   407
D34V10, multiclass
                           clus
vv                          19P GAIN MUTATED 19P GAIN WILD-TYPE
  ASIAN                                    0                  8
  BLACK OR AFRICAN AMERICAN                1                 43
  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  23 305
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      3   33
  19P GAIN WILD-TYPE   23  305
                        clus
vv                       19P GAIN MUTATED 19P GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                 23
  NOT HISPANIC OR LATINO               33                305
[1] 2 2
[1] FALSE

Clustering(35) Variable = 19Q GAIN MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                  0   1
  19Q GAIN MUTATED    36   3
  19Q GAIN WILD-TYPE 311  21
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                39                332 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 3                 21 
$`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-5984 TCGA-EU-5905 
        1740         2067          119 

$`19Q GAIN WILD-TYPE`
TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 
         267         1120         1436           16          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-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3343 TCGA-A3-3347 TCGA-A3-3349 
        1137         1485          665          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-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 
        2087         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-B0-4706 TCGA-B0-4718 TCGA-B0-4813 
         369         1238           43           26          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-B4-5834 
         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-A54E TCGA-B8-A54F TCGA-B8-A54G 
        1046          435          830          909          519           53 
TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 
         256          150          528          110           24         3377 
TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4167 
        2881         2746         3074         2839         3037         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-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-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-4968 TCGA-BP-4970 TCGA-BP-4971 
        1834         1862         1871         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-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-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-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5199 
         967          714          408          749         1018         1355 
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-4872 
        1628         1793          646         2554         1498         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-4899 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 
         750          841         1528         1450         1520         1560 
TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-5675 
        1792         1496         1531         1657         1373         2430 
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-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-5451 
        1943         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-5466 TCGA-CZ-5468 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5985 TCGA-CZ-5986 
         685           59          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         2016         1729          551          206 
TCGA-EU-5907 TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 
         127          305         1727           61          591          607 
TCGA-MM-A84U TCGA-MW-A4EC 
         337          330 

  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 
              1404               1210 
[1] "7.0 - 2575.0 (1404.0)" "3.0 - 3668.0 (1210.0)"
[1] "hr=" "1.3"
D35V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  19Q GAIN MUTATED        16        7        17       17
  19Q GAIN WILD-TYPE     237       50       109       63
D35V3, multiclass
           clus
vv          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  STAGE I                 16                237
  STAGE II                 7                 50
  STAGE III               17                109
  STAGE IV                17                 63
[1] 4 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 241  60 149   9
D35V4, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  T1               17                241
  T2                9                 60
  T3               29                149
  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 206  15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     25    3
  19Q GAIN WILD-TYPE  206   15
   clus
vv  19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  0               25                206
  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  19
D35V6, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  M0               40                377
  M1               17                 61
  MX                0                 19
[1] 3 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 170 289
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     16   41
  19Q GAIN WILD-TYPE  170  289
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE               16                170
  MALE                 41                289
[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                        43   402
D35V10, multiclass
                           clus
vv                          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  ASIAN                                    1                  7
  BLACK OR AFRICAN AMERICAN                1                 43
  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  23 300
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      3   38
  19Q GAIN WILD-TYPE   23  300
                        clus
vv                       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                 23
  NOT HISPANIC OR LATINO               38                300
[1] 2 2
[1] FALSE

Clustering(36) Variable = 20P GAIN MUTATION ANALYSIS
D36V1, survival
                    sevent
clus2                  0   1
  20P GAIN MUTATED    69   7
  20P GAIN WILD-TYPE 278  17
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                76                295 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 7                 17 
$`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-5984 TCGA-EU-5905 
        1740           59         2067          119 

$`20P GAIN WILD-TYPE`
TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 
         267         1120         1436         1491         1130         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-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3387 
        1621         1070          630          567          861          617 
TCGA-A3-A8CQ TCGA-AK-3425 TCGA-AK-3428 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 
           3         3343         2223          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-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-B0-5097 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5115 TCGA-B0-5117 TCGA-B0-5119 
         665          911         1092          797          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-B4-5843 
         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-B8-5159 TCGA-B8-5162 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
         523          722           36           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-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54J TCGA-B8-A7U6 
         909          519           53          256          528          110 
TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
          24         3377         2881         2746         3074         2839 
TCGA-BP-4165 TCGA-BP-4169 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4177 TCGA-BP-4325 
        3037          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-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-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4774 TCGA-BP-4775 
        2361         2184         1462         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-4797 TCGA-BP-4801 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4961 TCGA-BP-4962 
        1107         1124          211         2660         1935         1785 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 
        1834         1862         1871         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-4986 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4993 TCGA-BP-4995 
         785         1124          118         1413          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-5186 
        2263         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-5199 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4636 
        1018         1355          951           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-4874 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4884 TCGA-CJ-4885 
        1498         2283         1955         2186         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-4904 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4916 
        1528         1792         1496         1531         1657         1373 
TCGA-CJ-5675 TCGA-CJ-5681 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 
        2430          552         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-4856 
        2378         3222         2552         3146          774           18 
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-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5463 TCGA-CZ-5465 
          25         1683         1732         1683          662         1446 
TCGA-CZ-5466 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5988 
         685          386         2439         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-5906 TCGA-EU-5907 
        1130         2016         1729          551          206          127 
TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U 
         305         1727           61          591          607          337 
TCGA-MW-A4EC 
         330 

  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 
            1400.5             1186.0 
[1] "7.0 - 2859.0 (1400.5)" "3.0 - 3668.0 (1186.0)"
[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     220       45        87       54
D36V3, multiclass
           clus
vv          20P GAIN MUTATED 20P GAIN WILD-TYPE
  STAGE I                 33                220
  STAGE II                12                 45
  STAGE III               39                 87
  STAGE IV                26                 54
[1] 4 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 224  56 121   5
D36V4, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  T1               34                224
  T2               13                 56
  T3               57                121
  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 184  13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     47    5
  20P GAIN WILD-TYPE  184   13
   clus
vv  20P GAIN MUTATED 20P GAIN WILD-TYPE
  0               47                184
  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  18
D36V6, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  M0               83                334
  M1               26                 52
  MX                1                 18
[1] 3 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 162 244
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     24   86
  20P GAIN WILD-TYPE  162  244
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE               24                162
  MALE                 86                244
[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                 10 
        TCGA-A3-A8CQ         TCGA-B2-A4SR         TCGA-B8-5164 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-B8-A54E         TCGA-B8-A54F         TCGA-B8-A54G 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-B8-A8YJ         TCGA-G6-A5PC         TCGA-G6-A8L7 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-MM-A563 
"20P GAIN WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20P GAIN MUTATED       1                         6   103
  20P GAIN WILD-TYPE     7                        38   354
D36V10, multiclass
                           clus
vv                          20P GAIN MUTATED 20P GAIN WILD-TYPE
  ASIAN                                    1                  7
  BLACK OR AFRICAN AMERICAN                6                 38
  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  23 269
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      3   69
  20P GAIN WILD-TYPE   23  269
                        clus
vv                       20P GAIN MUTATED 20P GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                 23
  NOT HISPANIC OR LATINO               69                269
[1] 2 2
[1] FALSE

Clustering(37) Variable = 20Q GAIN MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                  0   1
  20Q GAIN MUTATED    70   8
  20Q GAIN WILD-TYPE 277  16
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                78                293 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 8                 16 
$`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-5984 TCGA-EU-5905 
        1430          330         1740           59         2067          119 

$`20Q GAIN WILD-TYPE`
TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3317 TCGA-A3-3320 TCGA-A3-3322 
         267         1120         1436         1491         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-A3-3349 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3359 TCGA-A3-3362 
         945         1385          910         2688         2504         1559 
TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3376 
         319          873         2270         2274         1621         1070 
TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3387 TCGA-A3-A8CQ TCGA-AK-3425 
         630          567          861          617            3         3343 
TCGA-AK-3428 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3443 
        2223          480         1853         2087         2044         1423 
TCGA-AK-3444 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3456 
        1471         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-B0-5097 TCGA-B0-5108 
          26           96          616           18          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-B4-5834 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-B8-5159 
         826          838          762          750          523          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-A54E TCGA-B8-A54F 
         434         1046          435          830          909          519 
TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 
          53          256          528          110           24         3377 
TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4169 
        2881         2746         3074         2839         3037          701 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 
        1893         1879         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-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4765 
         372          374         2208         2372         2361         2184 
TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 
        1462         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-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-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 
        1871         1746          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-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-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5199 
        1011          714          408          749         1018         1355 
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-4874 
        1628         1793          646         2554         1498         2283 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4889 
        1955         2186         1759         2125         1952         1946 
TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4899 TCGA-CJ-4904 
        2085         1521          750          841         1528         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-4856 TCGA-CZ-4859 TCGA-CZ-4862 
        2552         3146          774           18         1787         1843 
TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5457 
        1928         2830         1929         1789           25         1683 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5470 
        1732         1683          662         1446          685          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-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 
        1398         1470          370          355         1130         2016 
TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A8L6 TCGA-G6-A8L7 
        1729          551          206          127          305         1727 
TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC 
          61          591          607          337          330 

  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 
            1400.5             1186.0 
[1] "7.0 - 2859.0 (1400.5)" "3.0 - 3668.0 (1186.0)"
[1] "hr=" "1.9"
D37V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  20Q GAIN MUTATED        34       12        41       26
  20Q GAIN WILD-TYPE     219       45        85       54
D37V3, multiclass
           clus
vv          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  STAGE I                 34                219
  STAGE II                12                 45
  STAGE III               41                 85
  STAGE IV                26                 54
[1] 4 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 222  56 119   6
D37V4, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T1               36                222
  T2               13                 56
  T3               59                119
  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 183  12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     48    6
  20Q GAIN WILD-TYPE  183   12
   clus
vv  20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  0               48                183
  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  18
D37V6, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  M0               86                331
  M1               26                 52
  MX                1                 18
[1] 3 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 159 244
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     27   86
  20Q GAIN WILD-TYPE  159  244
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE               27                159
  MALE                 86                244
[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                 10 
        TCGA-A3-A8CQ         TCGA-B2-A4SR         TCGA-B8-5164 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-B8-A54E         TCGA-B8-A54F         TCGA-B8-A54G 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-B8-A8YJ         TCGA-G6-A5PC         TCGA-G6-A8L7 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-MM-A563 
"20Q GAIN WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20Q GAIN MUTATED       2                         6   105
  20Q GAIN WILD-TYPE     6                        38   352
D37V10, multiclass
                           clus
vv                          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  ASIAN                                    2                  6
  BLACK OR AFRICAN AMERICAN                6                 38
  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  23 267
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      3   71
  20Q GAIN WILD-TYPE   23  267
                        clus
vv                       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                 23
  NOT HISPANIC OR LATINO               71                267
[1] 2 2
[1] FALSE

Clustering(38) Variable = 21Q GAIN MUTATION ANALYSIS
D38V1, survival
                    sevent
clus2                  0   1
  21Q GAIN MUTATED    31   3
  21Q GAIN WILD-TYPE 316  21
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                34                337 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 3                 21 
$`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-DV-5568 TCGA-DV-5573 TCGA-EU-5905 
          59          370         1130          119 

$`21Q GAIN WILD-TYPE`
TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3317 
         267         1120         1436           16          735         1491 
TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 
        1130         1508         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-A3-3383 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-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-3444 TCGA-AK-3447 
        2087         2044         1745         1423         1471         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-B0-4710 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-B0-5117 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-B0-5697 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-B4-5835 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-B8-5164 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-A54E TCGA-B8-A54G 
          15         1046          435          830          909           53 
TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 
         256          150          528          110           24         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-4169 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 
         701         1893         1879         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-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-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-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-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 
         785         1124          118         1413          501          177 
TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
        1308          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-5192 
        1133          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-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-5681 TCGA-CJ-5682 
        1657         1373         1943         2430          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-6088 
        2489         2609         2226         2017         2378         3222 
TCGA-CW-6090 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4858 TCGA-CZ-4859 
        2552         3146          774           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-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5463 TCGA-CZ-5464 
        1712         1683         1732         1683          662         1740 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
        1446          685          386         2439         2067         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-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5906 TCGA-EU-5907 
         355         2016         1729          551          206          127 
TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U 
         305         1727           61          591          607          337 
TCGA-MW-A4EC 
         330 

  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 
            1387.5             1238.0 
[1] "7.0 - 2859.0 (1387.5)" "3.0 - 3668.0 (1238.0)"
[1] "hr=" "1.4"
D38V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  21Q GAIN MUTATED        20        3        17        9
  21Q GAIN WILD-TYPE     233       54       109       71
D38V3, multiclass
           clus
vv          21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  STAGE I                 20                233
  STAGE II                 3                 54
  STAGE III               17                109
  STAGE IV                 9                 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
  21Q GAIN MUTATED    21   3  24   1
  21Q GAIN WILD-TYPE 237  66 154  10
D38V4, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  T1               21                237
  T2                3                 66
  T3               24                154
  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 211  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     20    1
  21Q GAIN WILD-TYPE  211   17
   clus
vv  21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  0               20                211
  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  18
D38V6, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  M0               39                378
  M1                9                 69
  MX                1                 18
[1] 3 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 171 296
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     15   34
  21Q GAIN WILD-TYPE  171  296
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE               15                171
  MALE                 34                296
[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                 11 
        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-A54E 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-B8-A54G         TCGA-B8-A8YJ         TCGA-G6-A5PC 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G6-A8L7         TCGA-MM-A563 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  21Q GAIN MUTATED       0                         1    48
  21Q GAIN WILD-TYPE     8                        43   409
D38V10, multiclass
                           clus
vv                          21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  ASIAN                                    0                  8
  BLACK OR AFRICAN AMERICAN                1                 43
  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  23 308
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      3   30
  21Q GAIN WILD-TYPE   23  308
                        clus
vv                       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                 23
  NOT HISPANIC OR LATINO               30                308
[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 318  23
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                30                341 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 1                 23 
$`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-6D-AA2E TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 
         267         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-A3-3376 
         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-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-B0-4706 
         951          853          369         1238           43           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-B0-5116 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-B0-5692 
         554          652          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-A54E TCGA-B8-A54F 
          15         1046          435          830          909          519 
TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ 
          53          256          150          528          110           24 
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-4167 TCGA-BP-4169 TCGA-BP-4173 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 
        2718          701         1893         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-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4774 
        2361          182         1462          400         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-4976 TCGA-BP-4977 TCGA-BP-4982 TCGA-BP-4983 
        1502         1384         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-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-4904 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 
        1450         1520         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-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-5985 TCGA-CZ-5986 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
        1997          373          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         2016         1729 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A8L6 TCGA-G6-A8L7 
         551          119          206          127          305         1727 
TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC 
          61          591          607          337          330 

  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             1238.0 
[1] "7.0 - 2575.0 (1373.5)" "3.0 - 3668.0 (1238.0)"
[1] "hr=" "2.1"
D39V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  22Q GAIN MUTATED        17        4        12        7
  22Q GAIN WILD-TYPE     236       53       114       73
D39V3, multiclass
           clus
vv          22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  STAGE I                 17                236
  STAGE II                 4                 53
  STAGE III               12                114
  STAGE IV                 7                 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
  22Q GAIN MUTATED    17   4  16   3
  22Q GAIN WILD-TYPE 241  65 162   8
D39V4, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  T1               17                241
  T2                4                 65
  T3               16                162
  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 213  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     18    1
  22Q GAIN WILD-TYPE  213   17
   clus
vv  22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  0               18                213
  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  19
D39V6, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  M0               33                384
  M1                7                 71
  MX                0                 19
[1] 3 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 175 301
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     11   29
  22Q GAIN WILD-TYPE  175  301
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE               11                175
  MALE                 29                301
[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                        43   418
D39V10, multiclass
                           clus
vv                          22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  ASIAN                                    0                  8
  BLACK OR AFRICAN AMERICAN                1                 43
  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  25 317
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      1   21
  22Q GAIN WILD-TYPE   25  317
                        clus
vv                       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 25
  NOT HISPANIC OR LATINO               21                317
[1] 2 2
[1] FALSE

Clustering(40) Variable = XQ GAIN MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                 0   1
  XQ GAIN MUTATED    19   3
  XQ GAIN WILD-TYPE 328  21
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               22               349 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                3                21 
$`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 TCGA-MM-A84U 
        1740           59          119          337 

$`XQ GAIN WILD-TYPE`
TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 
         267         1120         1436           16          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-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 
        1610         1385          910         2688         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-A3-3378 TCGA-A3-3380 TCGA-A3-3382 
        1621         1314         1070          630          567          574 
TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A8CQ TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3430 
        1993          617            3         3343         2566          480 
TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 
        1853         2192         2087         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-B4-5838 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-A54E TCGA-B8-A54F 
          15         1046          435          830          909          519 
TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 
          53          256          528          110           24         3377 
TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 
        2881         2746         2839         3037           13         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-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-4970 
        1834         1862         1871          205         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-4983 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4991 TCGA-BP-4992 
        1014         1413          785         1124         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-4886 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 
        1883         1759         1952         1946         2085         1521 
TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4897 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 
         750          841         1808         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-5682 TCGA-CJ-5683 TCGA-CJ-5684 
        1943         2430         2575         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-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-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
        1928         2830         1868         1929         1789           25 
TCGA-CZ-5457 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5465 
        1683         1683         1430          330          662         1446 
TCGA-CZ-5466 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
         685          386         2439         2067         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         2016         1729          551          206 
TCGA-EU-5907 TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 
         127          305         1727           61          591          607 
TCGA-MW-A4EC 
         330 

  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 
             1722              1203 
[1] "59.0 - 3074.0 (1722.0)" "3.0 - 3668.0 (1203.0)" 
[1] "hr=" "2"  
D40V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  XQ GAIN MUTATED        10        4         7        9
  XQ GAIN WILD-TYPE     243       53       119       71
D40V3, multiclass
           clus
vv          XQ GAIN MUTATED XQ GAIN WILD-TYPE
  STAGE I                10               243
  STAGE II                4                53
  STAGE III               7               119
  STAGE IV                9                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
  XQ GAIN MUTATED    10   5  15   0
  XQ GAIN WILD-TYPE 248  64 163  11
D40V4, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  T1              10               248
  T2               5                64
  T3              15               163
  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 215  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     16    1
  XQ GAIN WILD-TYPE  215   17
   clus
vv  XQ GAIN MUTATED XQ GAIN WILD-TYPE
  0              16               215
  1               1                17
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  XQ GAIN MUTATED    19   9   2
  XQ GAIN WILD-TYPE 398  69  17
D40V6, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  M0              19               398
  M1               9                69
  MX               2                17
[1] 3 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    12  18
  XQ GAIN WILD-TYPE 174 312
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     12   18
  XQ GAIN WILD-TYPE  174  312
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE              12               174
  MALE                18               312
[1] 2 2
[1] FALSE
D40V8, continuous
D40V9, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XQ GAIN MUTATED       1                         2    27
  XQ GAIN WILD-TYPE     7                        42   430
D40V10, multiclass
                           clus
vv                          XQ GAIN MUTATED XQ GAIN WILD-TYPE
  ASIAN                                   1                 7
  BLACK OR AFRICAN AMERICAN               2                42
  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  18
  XQ GAIN WILD-TYPE  26 320
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      0   18
  XQ GAIN WILD-TYPE   26  320
                        clus
vv                       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                26
  NOT HISPANIC OR LATINO              18               320
[1] 2 2
[1] FALSE

Clustering(41) Variable = 1P LOSS MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                 0   1
  1P LOSS MUTATED    35   5
  1P LOSS WILD-TYPE 312  19
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               40               331 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                5                19 
$`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-EU-5907 
        2017         1868         1683          127 

$`1P LOSS WILD-TYPE`
TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3316 TCGA-A3-3317 
         267         1120         1436           16         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-A3-3376 
         319          873         2270         2274          735         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-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 
        3343         2223         2017          480         1853         2087 
TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 
        2044         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-B0-5690 
          59          493          554          652         1132         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-B0-5705 TCGA-B0-5706 
        2583         2741         1732         1605         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-B2-3924 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-B4-5832 
         417          656          507          291          175            7 
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-B8-4620 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-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I 
         830          909          519           53          256          150 
TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 
         528          110           24         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-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 
        1893         1879         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-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-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-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-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5169 
         563         1177          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-5202 TCGA-CJ-4634 
        1018          603         1355         1063           29         1820 
TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4639 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 
        1416         1924         2308         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-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
        2353         2186         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-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-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-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-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-5988 
         386         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         2016         1729          551          119          206 
TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U 
         305         1727           61          591          607          337 
TCGA-MW-A4EC 
         330 

  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 
             1210              1307 
[1] "16.0 - 2566.0 (1210.0)" "3.0 - 3668.0 (1307.0)" 
[1] "hr=" "2.4"
D41V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  1P LOSS MUTATED        29        8        10        8
  1P LOSS WILD-TYPE     224       49       116       72
D41V3, multiclass
           clus
vv          1P LOSS MUTATED 1P LOSS WILD-TYPE
  STAGE I                29               224
  STAGE II                8                49
  STAGE III              10               116
  STAGE IV                8                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
  1P LOSS MUTATED    30   9  12   4
  1P LOSS WILD-TYPE 228  60 166   7
D41V4, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  T1              30               228
  T2               9                60
  T3              12               166
  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 205  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     26    1
  1P LOSS WILD-TYPE  205   17
   clus
vv  1P LOSS MUTATED 1P LOSS WILD-TYPE
  0              26               205
  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  19
D41V6, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  M0              49               368
  M1               6                72
  MX               0                19
[1] 3 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 171 290
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     15   40
  1P LOSS WILD-TYPE  171  290
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE              15               171
  MALE                40               290
[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                        38   410
D41V10, multiclass
                           clus
vv                          1P LOSS MUTATED 1P LOSS WILD-TYPE
  ASIAN                                   1                 7
  BLACK OR AFRICAN AMERICAN               6                38
  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  21 301
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      5   37
  1P LOSS WILD-TYPE   21  301
                        clus
vv                       1P LOSS MUTATED 1P LOSS WILD-TYPE
  HISPANIC OR LATINO                   5                21
  NOT HISPANIC OR LATINO              37               301
[1] 2 2
[1] FALSE

Clustering(42) Variable = 1Q LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                 0   1
  1Q LOSS MUTATED    23   2
  1Q LOSS WILD-TYPE 324  22
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               25               346 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                2                22 
$`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 
        1683 

$`1Q LOSS WILD-TYPE`
TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 
         267         1120         1436           16          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-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 
        1610         1385          910         2688         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-A3-3376 TCGA-A3-3378 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 
        1621         1070          630          574          861         1993 
TCGA-A3-3387 TCGA-A3-A8CQ TCGA-AK-3425 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 
         617            3         3343         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-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-B4-5843 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-B8-4620 TCGA-B8-4621 
         826          838          762          750          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-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
         737          522          505          434           15         1046 
TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H 
         435          830          909          519           53          256 
TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4160 
         150          528          110           24         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-4769 
        2372         2361          182         2184         1462         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-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-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-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-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-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-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-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
         685           59          386         2439         2067         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         2016         1729          551 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-GK-A6C7 
         119          206          127          305         1727           61 
TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC 
         591          607          337          330 

  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 
             1308              1273 
[1] "110.0 - 2566.0 (1308.0)" "3.0 - 3668.0 (1273.0)"  
[1] "hr=" "1.4"
D42V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  1Q LOSS MUTATED        19        5         8        4
  1Q LOSS WILD-TYPE     234       52       118       76
D42V3, multiclass
           clus
vv          1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  STAGE I                19               234
  STAGE II                5                52
  STAGE III               8               118
  STAGE IV                4                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
  1Q LOSS MUTATED    19   5   9   3
  1Q LOSS WILD-TYPE 239  64 169   8
D42V4, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  T1              19               239
  T2               5                64
  T3               9               169
  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 214  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     17    1
  1Q LOSS WILD-TYPE  214   17
   clus
vv  1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  0              17               214
  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  19
D42V6, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  M0              33               384
  M1               3                75
  MX               0                19
[1] 3 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 175 305
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     11   25
  1Q LOSS WILD-TYPE  175  305
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE              11               175
  MALE                25               305
[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                        42   425
D42V10, multiclass
                           clus
vv                          1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  ASIAN                                   1                 7
  BLACK OR AFRICAN AMERICAN               2                42
  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  23 311
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      3   27
  1Q LOSS WILD-TYPE   23  311
                        clus
vv                       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                23
  NOT HISPANIC OR LATINO              27               311
[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 337  21
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               13               358 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                3                21 
$`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-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3316 TCGA-A3-3317 
         267         1120         1436           16         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-A54E 
         434           15         1046          435          830          909 
TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 
         519           53          256          150          528          110 
TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
          24         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-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-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-5177 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 
        2257          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-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-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
         685           59          386         2439         2067         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         2016         1729          551 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-GK-A6C7 
         119          206          127          305         1727           61 
TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC 
         591          607          337          330 

  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              1318 
[1] "110.0 - 2192.0 (992.0)" "3.0 - 3668.0 (1318.0)" 
[1] "hr=" "4.6"
D43V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  2P LOSS MUTATED         8        3         2        1
  2P LOSS WILD-TYPE     245       54       124       79
D43V3, multiclass
           clus
vv          2P LOSS MUTATED 2P LOSS WILD-TYPE
  STAGE I                 8               245
  STAGE II                3                54
  STAGE III               2               124
  STAGE IV                1                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
  2P LOSS MUTATED     8   3   2   1
  2P LOSS WILD-TYPE 250  66 176  10
D43V4, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  T1               8               250
  T2               3                66
  T3               2               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"
D43V5, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     6   0
  2P LOSS WILD-TYPE 225  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      6    0
  2P LOSS WILD-TYPE  225   18
   clus
vv  2P LOSS MUTATED 2P LOSS WILD-TYPE
  0               6               225
  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  19
D43V6, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  M0              13               404
  M1               1                77
  MX               0                19
[1] 3 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 182 320
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      4   10
  2P LOSS WILD-TYPE  182  320
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE               4               182
  MALE                10               320
[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                        41   447
D43V10, multiclass
                           clus
vv                          2P LOSS MUTATED 2P LOSS WILD-TYPE
  ASIAN                                   1                 7
  BLACK OR AFRICAN AMERICAN               3                41
  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  26 328
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      0   10
  2P LOSS WILD-TYPE   26  328
                        clus
vv                       2P LOSS MUTATED 2P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                26
  NOT HISPANIC OR LATINO              10               328
[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 337  22
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               12               359 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                2                22 
$`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-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 
         267         1120         1436           16          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-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 
        1610         1385          910         2688         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-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 
        1621         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-3443 
        2017          480         1853         2087         2044         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-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4706 
        1143         1168          951          853           43           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-B0-5119 TCGA-B0-5120 
        1092          359          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-B0-5696 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-B2-3924 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-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J 
         909          519           53          256          150          528 
TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 
         110           24         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-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-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-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-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-5470 TCGA-CZ-5982 TCGA-CZ-5984 
        1446          685           59          386         2439         2067 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
        1997          373          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         2016         1729 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A8L6 TCGA-G6-A8L7 
         551          119          206          127          305         1727 
TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC 
          61          591          607          337          330 

  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            1307.0 
[1] "110.0 - 2192.0 (1104.5)" "3.0 - 3668.0 (1307.0)"  
[1] "hr=" "3.2"
D44V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  2Q LOSS MUTATED         7        3         3        1
  2Q LOSS WILD-TYPE     246       54       123       79
D44V3, multiclass
           clus
vv          2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  STAGE I                 7               246
  STAGE II                3                54
  STAGE III               3               123
  STAGE IV                1                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
  2Q LOSS MUTATED     7   3   3   1
  2Q LOSS WILD-TYPE 251  66 175  10
D44V4, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  T1               7               251
  T2               3                66
  T3               3               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"
D44V5, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     6   0
  2Q LOSS WILD-TYPE 225  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      6    0
  2Q LOSS WILD-TYPE  225   18
   clus
vv  2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  0               6               225
  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  19
D44V6, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  M0              13               404
  M1               1                77
  MX               0                19
[1] 3 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 182 320
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      4   10
  2Q LOSS WILD-TYPE  182  320
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE               4               182
  MALE                10               320
[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                        42   446
D44V10, multiclass
                           clus
vv                          2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  ASIAN                                   1                 7
  BLACK OR AFRICAN AMERICAN               2                42
  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  26 327
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      0   11
  2Q LOSS WILD-TYPE   26  327
                        clus
vv                       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                26
  NOT HISPANIC OR LATINO              11               327
[1] 2 2
[1] FALSE

Clustering(45) Variable = 3P LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                 0   1
  3P LOSS MUTATED   251  17
  3P LOSS WILD-TYPE  96   7
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              268               103 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               17                 7 
$`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          528 
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-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5573 
         693         1905         1329         1398          370         1130 
TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A8L6 TCGA-GK-A6C7 
        2016         1729          206          127          305           61 
TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC 
         591          607          337          330 

$`3P LOSS WILD-TYPE`
TCGA-6D-AA2E TCGA-A3-3308 TCGA-A3-3326 TCGA-A3-3343 TCGA-A3-3349 TCGA-A3-3362 
         267           16         1137          945         1385         1559 
TCGA-A3-3363 TCGA-A3-3374 TCGA-A3-3385 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3440 
         319         1314         1993         2566         2223         1745 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3447 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3465 
        1423         1471         1217         1397         1143          369 
TCGA-AS-3777 TCGA-B0-4699 TCGA-B0-4718 TCGA-B0-5117 TCGA-B0-5121 TCGA-B0-5400 
        1238          110          616          535          554         1132 
TCGA-B0-5691 TCGA-B0-5705 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-4098 TCGA-B2-4101 
        3431         3668         2963          992           51          648 
TCGA-B2-4102 TCGA-B2-5635 TCGA-B4-5378 TCGA-B4-5835 TCGA-B8-4151 TCGA-B8-4153 
         952          315          175           16          838          762 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4621 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
         750          523          788          737          522          505 
TCGA-B8-5550 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A8YJ TCGA-BP-4161 TCGA-BP-4162 
         434          830          909           24         2746         3074 
TCGA-BP-4165 TCGA-BP-4173 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4334 TCGA-BP-4335 
        3037         1893         1670         1625          645          461 
TCGA-BP-4349 TCGA-BP-4756 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4769 TCGA-BP-4775 
         372          374         2372         2361         1876         1843 
TCGA-BP-4784 TCGA-BP-4795 TCGA-BP-4804 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 
        1854          620         1459          205         1746         1794 
TCGA-BP-4970 TCGA-BP-4976 TCGA-BP-4994 TCGA-BP-5001 TCGA-BP-5007 TCGA-BP-5170 
         433         1632         1308         1177         1140         2412 
TCGA-BP-5175 TCGA-BP-5177 TCGA-BP-5186 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5198 
         932          293          693          967          714          603 
TCGA-CJ-4639 TCGA-CJ-4872 TCGA-CJ-4875 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4889 
        2308         1435         2353         1759         2125         1946 
TCGA-CJ-4890 TCGA-CJ-4897 TCGA-CJ-4912 TCGA-CJ-5681 TCGA-CJ-5686 TCGA-CJ-6031 
        2085         1808         1657          552         2038         1906 
TCGA-CW-5581 TCGA-CW-5585 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4862 TCGA-CZ-4866 
        2799         2609         3146         1404         1843         1868 
TCGA-CZ-5456 TCGA-CZ-5470 TCGA-DV-5567 TCGA-DV-5569 TCGA-EU-5904 TCGA-EU-5905 
        1712          386         1470          355          551          119 
TCGA-G6-A8L7 
        1727 

  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 
             1299              1217 
[1] "3.0 - 3377.0 (1299.0)"  "16.0 - 3668.0 (1217.0)"
[1] "hr=" "1.1"
D45V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  3P LOSS MUTATED       177       42       102       50
  3P LOSS WILD-TYPE      76       15        24       30
D45V3, multiclass
           clus
vv          3P LOSS MUTATED 3P LOSS WILD-TYPE
  STAGE I               177                76
  STAGE II               42                15
  STAGE III             102                24
  STAGE IV               50                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   180  51 136   4
  3P LOSS WILD-TYPE  78  18  42   7
D45V4, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  T1             180                78
  T2              51                18
  T3             136                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  69   6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED    162   12
  3P LOSS WILD-TYPE   69    6
   clus
vv  3P LOSS MUTATED 3P LOSS WILD-TYPE
  0             162                69
  1              12                 6
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  3P LOSS MUTATED   306  50  14
  3P LOSS WILD-TYPE 111  28   5
D45V6, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  M0             306               111
  M1              50                28
  MX              14                 5
[1] 3 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   121 250
  3P LOSS WILD-TYPE  65  80
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED    121  250
  3P LOSS WILD-TYPE   65   80
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE             121                65
  MALE               250                80
[1] 2 2
[1] FALSE
D45V8, continuous
D45V9, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3P LOSS MUTATED       5                        26   334
  3P LOSS WILD-TYPE     3                        18   123
D45V10, multiclass
                           clus
vv                          3P LOSS MUTATED 3P LOSS WILD-TYPE
  ASIAN                                   5                 3
  BLACK OR AFRICAN AMERICAN              26                18
  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    20 239
  3P LOSS WILD-TYPE   6  99
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     20  239
  3P LOSS WILD-TYPE    6   99
                        clus
vv                       3P LOSS MUTATED 3P LOSS WILD-TYPE
  HISPANIC OR LATINO                  20                 6
  NOT HISPANIC OR LATINO             239                99
[1] 2 2
[1] FALSE

Clustering(46) Variable = 3Q LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                 0   1
  3Q LOSS MUTATED    66   8
  3Q LOSS WILD-TYPE 281  16
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               74               297 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                8                16 
$`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-DV-5573 TCGA-DV-5574 TCGA-EU-5907 
          59         2067          373         1130         2016          127 
TCGA-GK-A6C7 TCGA-MM-A564 
          61          607 

$`3Q LOSS WILD-TYPE`
TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3316 TCGA-A3-3319 
         267         1120         1436           16         1493         1130 
TCGA-A3-3320 TCGA-A3-3323 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 
        1508         1106          751         1137         1485          665 
TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3358 TCGA-A3-3359 
        1043          945         1385          910         1307         2504 
TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 
        1559          319         2270         2274         1621         1314 
TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-A8CQ TCGA-AK-3427 
        1070          630          861         1993            3         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-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-3461 
        1481         1397          874         1143         1168          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-B0-5121 TCGA-B0-5399 
         359          657          535           59          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-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-4098 TCGA-B2-4099 
        2931         1865         2963          992           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-B8-4151 TCGA-B8-4153 
         166           11            7          511          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-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
         722           36           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-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54J TCGA-B8-A7U6 
         909          519           53          256          528          110 
TCGA-B8-A8YJ TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 
          24         2881         2746         3074         2839         3037 
TCGA-BP-4167 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 
        2718         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-4349 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 
        2859          372          374         2208         2372         2361 
TCGA-BP-4761 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4774 TCGA-BP-4775 
         182         2184         1462         1876         1885         1843 
TCGA-BP-4776 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4795 TCGA-BP-4804 
         411          354         1854         1489          620         1459 
TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4964 
         211         2660         2172         1935         1785         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-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 
        1124          118         1413          177         1308         1371 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5169 
         563         1177         1126          840         1140          193 
TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5177 TCGA-BP-5181 TCGA-BP-5182 
        2412         2257          932          293         1495         1165 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 
        1291         1133          693         1011          967          714 
TCGA-BP-5194 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 
         408         1018          603          951           29         1820 
TCGA-CJ-4636 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 
        1924         2308         1998         1793          646         2554 
TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
        1498         2423         1435         2353         1955         2186 
TCGA-CJ-4881 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4889 TCGA-CJ-4890 
        2014         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-4905 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4916 
        1520         1560         1496         1531         1657         1373 
TCGA-CJ-5671 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5681 TCGA-CJ-5683 TCGA-CJ-5684 
        1943         2430         2575          552         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-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6088 TCGA-CW-6093 
        2226         2017         2378         2271         3222         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-4866 TCGA-CZ-5453 TCGA-CZ-5456 TCGA-CZ-5458 TCGA-CZ-5460 TCGA-CZ-5464 
        1868           25         1712         1732         1430         1740 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5985 TCGA-CZ-5988 
        1446          685          386         2439         1997          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-5575 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-G6-A8L6 TCGA-G6-A8L7 
        1729          551          119          206          305         1727 
TCGA-MM-A563 TCGA-MM-A84U TCGA-MW-A4EC 
         591          337          330 

  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 
             1127              1314 
[1] "13.0 - 3377.0 (1127.0)" "3.0 - 3668.0 (1314.0)" 
[1] "hr=" "2"  
D46V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  3Q LOSS MUTATED        46       15        23       13
  3Q LOSS WILD-TYPE     207       42       103       67
D46V3, multiclass
           clus
vv          3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  STAGE I                46               207
  STAGE II               15                42
  STAGE III              23               103
  STAGE IV               13                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
  3Q LOSS MUTATED    49  17  31   0
  3Q LOSS WILD-TYPE 209  52 147  11
D46V4, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  T1              49               209
  T2              17                52
  T3              31               147
  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 194  16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     37    2
  3Q LOSS WILD-TYPE  194   16
   clus
vv  3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  0              37               194
  1               2                16
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  3Q LOSS MUTATED    80  14   3
  3Q LOSS WILD-TYPE 337  64  16
D46V6, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  M0              80               337
  M1              14                64
  MX               3                16
[1] 3 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  78
  3Q LOSS WILD-TYPE 167 252
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     19   78
  3Q LOSS WILD-TYPE  167  252
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE              19               167
  MALE                78               252
[1] 2 2
[1] FALSE
D46V8, continuous
D46V9, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3Q LOSS MUTATED       1                         6    88
  3Q LOSS WILD-TYPE     7                        38   369
D46V10, multiclass
                           clus
vv                          3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  ASIAN                                   1                 7
  BLACK OR AFRICAN AMERICAN               6                38
  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  55
  3Q LOSS WILD-TYPE  21 283
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      5   55
  3Q LOSS WILD-TYPE   21  283
                        clus
vv                       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   5                21
  NOT HISPANIC OR LATINO              55               283
[1] 2 2
[1] FALSE

Clustering(47) Variable = 4P LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                 0   1
  4P LOSS MUTATED    34   3
  4P LOSS WILD-TYPE 313  21
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               37               334 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                3                21 
$`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-EU-5907 
        1943         1868         1683          330         1446          127 
TCGA-G6-A8L7 
        1727 

$`4P LOSS WILD-TYPE`
TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3317 
         267         1120         1436           16          735         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-A3-3374 
         319          873         2270         2274          735         1314 
TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3387 TCGA-A3-A8CQ 
        1070          630          574          861          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-B0-5400 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-B4-5836 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-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
         838          762          523          777          788          700 
TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
         722          822           26          737          522          505 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E 
         434           15         1046          435          830          909 
TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 
         519           53          256          150          528          110 
TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 
          24         3377         2881         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-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-4769 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 
        1462         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-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-5184 
         932          293         2263         1495         1165         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-5199 TCGA-BP-5200 TCGA-BP-5201 
         714          408          749         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-4881 
        1435         2259         2283         2353         1955         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-4901 TCGA-CJ-4902 TCGA-CJ-4904 
        1521          750         1528         1450         1520         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-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-5591 TCGA-CW-6088 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4854 
        2378         2271         3222         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-5458 TCGA-CZ-5459 TCGA-CZ-5460 
        1789           25         1712         1732         1683         1430 
TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5470 TCGA-CZ-5982 
         662         1740          685           59          386         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         2016 
TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-G6-A8L6 TCGA-GK-A6C7 
        1729          551          119          206          305           61 
TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC 
         591          607          337          330 

  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 
           1168.0            1293.5 
[1] "16.0 - 2746.0 (1168.0)" "3.0 - 3668.0 (1293.5)" 
[1] "hr=" "1.4"
D47V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  4P LOSS MUTATED        21        6        26       19
  4P LOSS WILD-TYPE     232       51       100       61
D47V3, multiclass
           clus
vv          4P LOSS MUTATED 4P LOSS WILD-TYPE
  STAGE I                21               232
  STAGE II                6                51
  STAGE III              26               100
  STAGE IV               19                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
  4P LOSS MUTATED    22   8  38   4
  4P LOSS WILD-TYPE 236  61 140   7
D47V4, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  T1              22               236
  T2               8                61
  T3              38               140
  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    33   3
  4P LOSS WILD-TYPE 198  15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     33    3
  4P LOSS WILD-TYPE  198   15
   clus
vv  4P LOSS MUTATED 4P LOSS WILD-TYPE
  0              33               198
  1               3                15
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  4P LOSS MUTATED    53  18   1
  4P LOSS WILD-TYPE 364  60  18
D47V6, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  M0              53               364
  M1              18                60
  MX               1                18
[1] 3 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    25  47
  4P LOSS WILD-TYPE 161 283
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     25   47
  4P LOSS WILD-TYPE  161  283
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE              25               161
  MALE                47               283
[1] 2 2
[1] FALSE
D47V8, continuous
D47V9, continuous
[1] "Remove cluster labels:" "4P LOSS MUTATED"       
clus
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                2                10 
       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-A54E        TCGA-B8-A54F        TCGA-B8-A54G        TCGA-B8-A8YJ 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-G6-A5PC        TCGA-MM-A563 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4P LOSS MUTATED       1                         2    67
  4P LOSS WILD-TYPE     7                        42   390
D47V10, multiclass
                           clus
vv                          4P LOSS MUTATED 4P LOSS WILD-TYPE
  ASIAN                                   1                 7
  BLACK OR AFRICAN AMERICAN               2                42
  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  49
  4P LOSS WILD-TYPE  21 289
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      5   49
  4P LOSS WILD-TYPE   21  289
                        clus
vv                       4P LOSS MUTATED 4P LOSS WILD-TYPE
  HISPANIC OR LATINO                   5                21
  NOT HISPANIC OR LATINO              49               289
[1] 2 2
[1] FALSE

Clustering(48) Variable = 4Q LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                 0   1
  4Q LOSS MUTATED    29   2
  4Q LOSS WILD-TYPE 318  22
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               31               340 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                2                22 
$`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-EU-5907 
         127 

$`4Q LOSS WILD-TYPE`
TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3317 
         267         1120         1436           16          735         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-A3-3374 
         319          873         2270         2274          735         1314 
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-3433 TCGA-AK-3434 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 
        1853         2192         2087         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-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-B0-4718 TCGA-B0-4813 TCGA-B0-4819 TCGA-B0-5097 
         110           26          616           18          183          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-B4-5832 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-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5159 TCGA-B8-5163 
         523          777          788          700          722          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-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G 
        1046          435          830          909          519           53 
TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 
         256          150          528          110           24         3377 
TCGA-BP-4160 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 
        2881         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-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-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-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-5184 TCGA-BP-5185 TCGA-BP-5186 
        2263         1495         1165         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-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 
         749         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-4901 TCGA-CJ-4902 TCGA-CJ-4904 TCGA-CJ-4905 
         841         1528         1450         1520         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-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-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-5463 
          25         1712         1732         1683         1430          662 
TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 
        1740          685           59          386         2439         2067 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
        1997          373          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         2016         1729 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-GK-A6C7 
         551          119          206          305         1727           61 
TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC 
         591          607          337          330 

  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 
             1291              1273 
[1] "36.0 - 2746.0 (1291.0)" "3.0 - 3668.0 (1273.0)" 
[1] "hr=" "1.1"
D48V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  4Q LOSS MUTATED        15        6        24       20
  4Q LOSS WILD-TYPE     238       51       102       60
D48V3, multiclass
           clus
vv          4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  STAGE I                15               238
  STAGE II                6                51
  STAGE III              24               102
  STAGE IV               20                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
  4Q LOSS MUTATED    16   8  36   5
  4Q LOSS WILD-TYPE 242  61 142   6
D48V4, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  T1              16               242
  T2               8                61
  T3              36               142
  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 204  15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     27    3
  4Q LOSS WILD-TYPE  204   15
   clus
vv  4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  0              27               204
  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  19
D48V6, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  M0              46               371
  M1              19                59
  MX               0                19
[1] 3 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 167 284
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     19   46
  4Q LOSS WILD-TYPE  167  284
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE              19               167
  MALE                46               284
[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                11 
       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-A54E        TCGA-B8-A54F        TCGA-B8-A54G        TCGA-B8-A8YJ 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-G6-A5PC        TCGA-G6-A8L7        TCGA-MM-A563 
"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                        43   396
D48V10, multiclass
                           clus
vv                          4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  ASIAN                                   1                 7
  BLACK OR AFRICAN AMERICAN               1                43
  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  22 295
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      4   43
  4Q LOSS WILD-TYPE   22  295
                        clus
vv                       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   4                22
  NOT HISPANIC OR LATINO              43               295
[1] 2 2
[1] FALSE

Clustering(49) Variable = 5P LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                 0   1
  5P LOSS MUTATED     2   0
  5P LOSS WILD-TYPE 345  24
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                2               369 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                0                24 
$`5P LOSS MUTATED`
TCGA-AK-3433 TCGA-CJ-4901 
        2192         1450 

$`5P LOSS WILD-TYPE`
TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 
         267         1120         1436           16          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-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 
        1610         1385          910         2688         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-A3-3378 TCGA-A3-3380 TCGA-A3-3382 
        1621         1314         1070          630          567          574 
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-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 
        2223         2017          480         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-B4-5838 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-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H 
         435          830          909          519           53          256 
TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4160 
         150          528          110           24         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-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-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-4902 TCGA-CJ-4903 TCGA-CJ-4904 
         841         1808         1528         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-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
          59          386         2439         2067         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-5905 
         355         1130         2016         1729          551          119 
TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-GK-A6C7 TCGA-MM-A563 
         206          127          305         1727           61          591 
TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC 
         607          337          330 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             1450                 3 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             2192              3668 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             1821              1266 
[1] "1450.0 - 2192.0 (1821.0)" "3.0 - 3668.0 (1266.0)"   
[1] "Remove cluster labels:" "5P LOSS MUTATED"       
D49V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  5P LOSS MUTATED         0        2         1        4
  5P LOSS WILD-TYPE     253       55       125       76
D49V3, multiclass
           clus
vv          5P LOSS MUTATED 5P LOSS WILD-TYPE
  STAGE I                 0               253
  STAGE II                2                55
  STAGE III               1               125
  STAGE IV                4                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
  5P LOSS MUTATED     0   3   2   2
  5P LOSS WILD-TYPE 258  66 176   9
D49V4, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  T1               0               258
  T2               3                66
  T3               2               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"
D49V5, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     6   0
  5P LOSS WILD-TYPE 225  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      6    0
  5P LOSS WILD-TYPE  225   18
   clus
vv  5P LOSS MUTATED 5P LOSS WILD-TYPE
  0               6               225
  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  19
D49V6, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  M0               4               413
  M1               3                75
  MX               0                19
[1] 3 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 182 327
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      4    3
  5P LOSS WILD-TYPE  182  327
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE               4               182
  MALE                 3               327
[1] 2 2
[1] FALSE
D49V8, continuous
[1] "Remove cluster labels:" "5P LOSS MUTATED"       
clus
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                1                40 
       TCGA-A3-A6NJ        TCGA-A3-A6NL        TCGA-A3-A8CQ        TCGA-AK-3426 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AK-3430        TCGA-B0-4838        TCGA-B2-5639        TCGA-B4-5377 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-B4-5378        TCGA-B4-5832        TCGA-B4-5834        TCGA-B4-5835 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-B4-5836        TCGA-B4-5838        TCGA-B4-5843        TCGA-B4-5844 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CZ-4854        TCGA-CZ-4856        TCGA-CZ-4858        TCGA-CZ-4860 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CZ-4861        TCGA-CZ-4862        TCGA-CZ-5456        TCGA-CZ-5457 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-CZ-5465        TCGA-CZ-5982        TCGA-DV-5565        TCGA-DV-5566 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DV-5567        TCGA-DV-5568        TCGA-DV-5569        TCGA-DV-5573 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DV-5574        TCGA-DV-5575        TCGA-DV-5576        TCGA-EU-5904 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EU-5905        TCGA-EU-5907        TCGA-G6-A8L6        TCGA-G6-A8L7 
"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                        44   450
D49V10, multiclass
                           clus
vv                          5P LOSS MUTATED 5P LOSS WILD-TYPE
  ASIAN                                   0                 8
  BLACK OR AFRICAN AMERICAN               0                44
  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  26 332
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      0    6
  5P LOSS WILD-TYPE   26  332
                        clus
vv                       5P LOSS MUTATED 5P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                26
  NOT HISPANIC OR LATINO               6               332
[1] 2 2
[1] FALSE

Clustering(50) Variable = 5Q LOSS MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                 0   1
  5Q LOSS MUTATED     2   0
  5Q LOSS WILD-TYPE 345  24
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                2               369 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                0                24 
$`5Q LOSS MUTATED`
TCGA-AK-3433 TCGA-CJ-4901 
        2192         1450 

$`5Q LOSS WILD-TYPE`
TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 
         267         1120         1436           16          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-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 
        1610         1385          910         2688         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-A3-3378 TCGA-A3-3380 TCGA-A3-3382 
        1621         1314         1070          630          567          574 
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-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 
        2223         2017          480         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-B4-5838 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-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H 
         435          830          909          519           53          256 
TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4160 
         150          528          110           24         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-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-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-4902 TCGA-CJ-4903 TCGA-CJ-4904 
         841         1808         1528         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-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
          59          386         2439         2067         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-5905 
         355         1130         2016         1729          551          119 
TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-GK-A6C7 TCGA-MM-A563 
         206          127          305         1727           61          591 
TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC 
         607          337          330 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             1450                 3 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             2192              3668 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             1821              1266 
[1] "1450.0 - 2192.0 (1821.0)" "3.0 - 3668.0 (1266.0)"   
[1] "Remove cluster labels:" "5Q LOSS MUTATED"       
D50V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  5Q LOSS MUTATED         0        2         1        3
  5Q LOSS WILD-TYPE     253       55       125       77
D50V3, multiclass
           clus
vv          5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  STAGE I                 0               253
  STAGE II                2                55
  STAGE III               1               125
  STAGE IV                3                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
  5Q LOSS MUTATED     0   2   2   2
  5Q LOSS WILD-TYPE 258  67 176   9
D50V4, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  T1               0               258
  T2               2                67
  T3               2               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"
D50V5, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED     5   0
  5Q LOSS WILD-TYPE 226  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      5    0
  5Q LOSS WILD-TYPE  226   18
   clus
vv  5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  0               5               226
  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  19
D50V6, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  M0               4               413
  M1               2                76
  MX               0                19
[1] 3 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 183 327
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      3    3
  5Q LOSS WILD-TYPE  183  327
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE               3               183
  MALE                 3               327
[1] 2 2
[1] FALSE
D50V8, continuous
[1] "Remove cluster labels:" "5Q LOSS MUTATED"       
clus
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                1                40 
       TCGA-A3-A6NJ        TCGA-A3-A6NL        TCGA-A3-A8CQ        TCGA-AK-3426 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AK-3430        TCGA-B0-4838        TCGA-B2-5639        TCGA-B4-5377 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-B4-5378        TCGA-B4-5832        TCGA-B4-5834        TCGA-B4-5835 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-B4-5836        TCGA-B4-5838        TCGA-B4-5843        TCGA-B4-5844 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CZ-4854        TCGA-CZ-4856        TCGA-CZ-4858        TCGA-CZ-4860 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CZ-4861        TCGA-CZ-4862        TCGA-CZ-5456        TCGA-CZ-5457 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-CZ-5465        TCGA-CZ-5982        TCGA-DV-5565        TCGA-DV-5566 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DV-5567        TCGA-DV-5568        TCGA-DV-5569        TCGA-DV-5573 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DV-5574        TCGA-DV-5575        TCGA-DV-5576        TCGA-EU-5904 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EU-5905        TCGA-EU-5907        TCGA-G6-A8L6        TCGA-G6-A8L7 
"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                        44   451
D50V10, multiclass
                           clus
vv                          5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  ASIAN                                   0                 8
  BLACK OR AFRICAN AMERICAN               0                44
  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  26 333
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      0    5
  5Q LOSS WILD-TYPE   26  333
                        clus
vv                       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                26
  NOT HISPANIC OR LATINO               5               333
[1] 2 2
[1] FALSE

Clustering(51) Variable = 6P LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                 0   1
  6P LOSS MUTATED    66   7
  6P LOSS WILD-TYPE 281  17
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               73               298 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                7                17 
$`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-DV-5568 TCGA-EU-5907 TCGA-G6-A8L7 
        1446           59         2067          370          127         1727 
TCGA-MM-A563 
         591 

$`6P LOSS WILD-TYPE`
TCGA-6D-AA2E TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3320 
         267         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-A3-3343 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 
         945         1385          910         2688         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-A3-3376 TCGA-A3-3378 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 
        1621         1070          630          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-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-3460 TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4706 
         874         1143          951          853           43           26 
TCGA-B0-4710 TCGA-B0-4718 TCGA-B0-4819 TCGA-B0-5097 TCGA-B0-5110 TCGA-B0-5113 
          96          616          183          665         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-B0-5703 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-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
        2722         1865         2963         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-B4-5378 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5843 
         507          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-B8-4622 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 
         523          788          700          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-A54E TCGA-B8-A54F 
          15         1046          435          830          909          519 
TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ 
          53          256          150          528          110           24 
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-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-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-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-4961 
         620         1124          204         1459          211         1935 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4969 TCGA-BP-4970 
        1834         1862         1871          205         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-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4993 TCGA-BP-4995 
        1014         1124          118         1413          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-5170 TCGA-BP-5174 TCGA-BP-5177 TCGA-BP-5181 
        1140         1071         2412         2257          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-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-5202 TCGA-CJ-4634 TCGA-CJ-4636 TCGA-CJ-4639 
        1355         1063           29         1820         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-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-4893 TCGA-CJ-4894 TCGA-CJ-4899 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 
         750          841         1528         1520         1560         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-6031 TCGA-CJ-6032 
        1883         1889         2231         2038         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-4854 TCGA-CZ-4856 TCGA-CZ-4859 
        3222         2552         3146         1404           18         1787 
TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-5451 TCGA-CZ-5453 TCGA-CZ-5457 
        1843         1928         2830         1929           25         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-5470 TCGA-CZ-5982 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5988 
         685          386         2439         1997          373          693 
TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5569 TCGA-DV-5573 
        1905         1329         1398         1470          355         1130 
TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-G6-A8L6 
        2016         1729          551          119          206          305 
TCGA-GK-A6C7 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC 
          61          607          337          330 

  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 
           1238.0            1285.5 
[1] "7.0 - 2718.0 (1238.0)" "3.0 - 3668.0 (1285.5)"
[1] "hr=" "1.8"
D51V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  6P LOSS MUTATED        38       13        28       21
  6P LOSS WILD-TYPE     215       44        98       59
D51V3, multiclass
           clus
vv          6P LOSS MUTATED 6P LOSS WILD-TYPE
  STAGE I                38               215
  STAGE II               13                44
  STAGE III              28                98
  STAGE IV               21                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
  6P LOSS MUTATED    38  15  43   4
  6P LOSS WILD-TYPE 220  54 135   7
D51V4, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  T1              38               220
  T2              15                54
  T3              43               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    36   8
  6P LOSS WILD-TYPE 195  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     36    8
  6P LOSS WILD-TYPE  195   10
   clus
vv  6P LOSS MUTATED 6P LOSS WILD-TYPE
  0              36               195
  1               8                10
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  6P LOSS MUTATED    79  19   2
  6P LOSS WILD-TYPE 338  59  17
D51V6, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  M0              79               338
  M1              19                59
  MX               2                17
[1] 3 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    22  78
  6P LOSS WILD-TYPE 164 252
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     22   78
  6P LOSS WILD-TYPE  164  252
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE              22               164
  MALE                78               252
[1] 2 2
[1] FALSE
D51V8, continuous
D51V9, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6P LOSS MUTATED       1                         4    93
  6P LOSS WILD-TYPE     7                        40   364
D51V10, multiclass
                           clus
vv                          6P LOSS MUTATED 6P LOSS WILD-TYPE
  ASIAN                                   1                 7
  BLACK OR AFRICAN AMERICAN               4                40
  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  65
  6P LOSS WILD-TYPE  21 273
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      5   65
  6P LOSS WILD-TYPE   21  273
                        clus
vv                       6P LOSS MUTATED 6P LOSS WILD-TYPE
  HISPANIC OR LATINO                   5                21
  NOT HISPANIC OR LATINO              65               273
[1] 2 2
[1] FALSE

Clustering(52) Variable = 6Q LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                 0   1
  6Q LOSS MUTATED    92   5
  6Q LOSS WILD-TYPE 255  19
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               97               274 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                5                19 
$`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-DV-5568 TCGA-DV-5573 TCGA-DV-5575 TCGA-EU-5907 TCGA-G6-A8L7 TCGA-MM-A563 
         370         1130         1729          127         1727          591 
TCGA-MW-A4EC 
         330 

$`6Q LOSS WILD-TYPE`
TCGA-6D-AA2E TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3322 TCGA-A3-3323 
         267         1436           16          735         1478         1106 
TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3343 TCGA-A3-3349 
        1186          751         1137         1485          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-A3-3376 
         873         2270         2274          735         1621         1070 
TCGA-A3-3378 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 
         630          861         1993          617         3343         2566 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3431 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 
        2223         2017         1853         1423         1471         1280 
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-AS-3778 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4718 TCGA-B0-4813 
         853           43           26           96          616           18 
TCGA-B0-4819 TCGA-B0-5097 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 
         183          665         1092          359          797          657 
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-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 
        2741         1732         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-A4SR TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5836 TCGA-B4-5843 
         417          507          175           38          141           11 
TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 
           7          511          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-A54E TCGA-B8-A54F TCGA-B8-A54H 
        1046          435          830          909          519          256 
TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4160 
         150          528          110           24         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-4177 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 
        1893         1879         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-4765 
         970          374         2208         2372         2361         2184 
TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4781 TCGA-BP-4782 
        1462         1876         1885          411         2080          354 
TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4795 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 
        1854         1489          620         1124          204         1459 
TCGA-BP-4807 TCGA-BP-4961 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4969 
         211         1935         1862         1871          205         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-4989 TCGA-BP-4991 TCGA-BP-4993 TCGA-BP-4995 
         454         1014          118         1413          177         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-5181 TCGA-BP-5182 
        1071         2412         2257          293         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-5202 TCGA-CJ-4636 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4642 
        1063           29         1924         2308         1998         1628 
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-4894 TCGA-CJ-4899 TCGA-CJ-4902 
        1946         2085         1521          841         1528         1520 
TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-5671 
        1560         1496         1531         1657         1373         1943 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6031 
         552         1883         1889         2231         2038         1906 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6088 
        2799         2489         2226         2378         2271         3222 
TCGA-CW-6090 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4863 
        2552         3146         1404           18         1843         1928 
TCGA-CZ-4864 TCGA-CZ-5451 TCGA-CZ-5453 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 
        2830         1929           25         1683         1732         1683 
TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5470 
         330          662         1740          685           59          386 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
        1997          373          693         1905         1329         1398 
TCGA-DV-5567 TCGA-DV-5569 TCGA-DV-5574 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
        1470          355         2016          551          119          206 
TCGA-G6-A8L6 TCGA-GK-A6C7 TCGA-MM-A564 TCGA-MM-A84U 
         305           61          607          337 

  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 
           1314.0            1234.5 
[1] "3.0 - 2964.0 (1314.0)" "7.0 - 3668.0 (1234.5)"
[1] "hr=" "1.3"
D52V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  6Q LOSS MUTATED        57       17        30       24
  6Q LOSS WILD-TYPE     196       40        96       56
D52V3, multiclass
           clus
vv          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  STAGE I                57               196
  STAGE II               17                40
  STAGE III              30                96
  STAGE IV               24                56
[1] 4 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    57  19  47   5
  6Q LOSS WILD-TYPE 201  50 131   6
D52V4, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T1              57               201
  T2              19                50
  T3              47               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    45  10
  6Q LOSS WILD-TYPE 186   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     45   10
  6Q LOSS WILD-TYPE  186    8
   clus
vv  6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  0              45               186
  1              10                 8
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  6Q LOSS MUTATED   102  21   5
  6Q LOSS WILD-TYPE 315  57  14
D52V6, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  M0             102               315
  M1              21                57
  MX               5                14
[1] 3 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    37  91
  6Q LOSS WILD-TYPE 149 239
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     37   91
  6Q LOSS WILD-TYPE  149  239
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE              37               149
  MALE                91               239
[1] 2 2
[1] FALSE
D52V8, continuous
D52V9, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6Q LOSS MUTATED       2                         7   116
  6Q LOSS WILD-TYPE     6                        37   341
D52V10, multiclass
                           clus
vv                          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  ASIAN                                   2                 6
  BLACK OR AFRICAN AMERICAN               7                37
  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     8  83
  6Q LOSS WILD-TYPE  18 255
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      8   83
  6Q LOSS WILD-TYPE   18  255
                        clus
vv                       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   8                18
  NOT HISPANIC OR LATINO              83               255
[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 345  24
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                2               369 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                0                24 
$`7Q LOSS MUTATED`
TCGA-BP-4761 TCGA-CJ-4912 
         182         1657 

$`7Q LOSS WILD-TYPE`
TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 
         267         1120         1436           16          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-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 
        1610         1385          910         2688         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-A3-3378 TCGA-A3-3380 TCGA-A3-3382 
        1621         1314         1070          630          567          574 
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-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 
        2223         2017          480         1853         2192         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-B0-4710 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-A54E TCGA-B8-A54F TCGA-B8-A54G 
        1046          435          830          909          519           53 
TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 
         256          150          528          110           24         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-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-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-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-4916 TCGA-CJ-5671 
        1792         1496         1499         1531         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-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
          59          386         2439         2067         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-5905 
         355         1130         2016         1729          551          119 
TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-GK-A6C7 TCGA-MM-A563 
         206          127          305         1727           61          591 
TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC 
         607          337          330 

  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            1280.0 
[1] "182.0 - 1657.0 (919.5)" "3.0 - 3668.0 (1280.0)" 
[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     253       56       125       79
D53V3, multiclass
           clus
vv          7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  STAGE I                 0               253
  STAGE II                1                56
  STAGE III               1               125
  STAGE IV                1                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
  7Q LOSS MUTATED     0   1   1   1
  7Q LOSS WILD-TYPE 258  68 177  10
D53V4, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  T1               0               258
  T2               1                68
  T3               1               177
  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 231  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      0    1
  7Q LOSS WILD-TYPE  231   17
   clus
vv  7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  0               0               231
  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  19
D53V6, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  M0               3               414
  M1               0                78
  MX               0                19
[1] 3 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 186 327
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      0    3
  7Q LOSS WILD-TYPE  186  327
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  FEMALE               0               186
  MALE                 3               327
[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                        44   454
D53V10, multiclass
                           clus
vv                          7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  ASIAN                                   0                 8
  BLACK OR AFRICAN AMERICAN               0                44
  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  25 337
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      1    1
  7Q LOSS WILD-TYPE   25  337
                        clus
vv                       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                25
  NOT HISPANIC OR LATINO               1               337
[1] 2 2
[1] FALSE

Clustering(54) Variable = 8P LOSS MUTATION ANALYSIS
D54V1, survival
                   sevent
clus2                 0   1
  8P LOSS MUTATED    87   8
  8P LOSS WILD-TYPE 260  16
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               95               276 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                8                16 
$`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 TCGA-MM-A563 
         693         1329         2016         1729          591 

$`8P LOSS WILD-TYPE`
TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 
         267         1120         1436           16          735         1493 
TCGA-A3-3317 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3326 
        1491         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-A3-3367 
        2688         1307         2504         1559          319         2270 
TCGA-A3-3370 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3383 
        2274         1314         1070          630          567          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-3433 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 
         480         1853         2192         1423         1471         1280 
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-3778 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-5097 
         853          369           43           26           96          665 
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-B0-5697 TCGA-B0-5698 TCGA-B0-5699 
        3431         1487         3076         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-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
        1459         2931         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-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
         656          175            7           38           16          141 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 
          11            7          511          762          750          523 
TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5165 
         777          788          700          722           36          737 
TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E 
         505          434         1046          435          830          909 
TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ 
         519           53          256          528          110           24 
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-4177 TCGA-BP-4325 
          13         2718          701         1893         1670         2964 
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-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-4784 TCGA-BP-4789 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4801 
        1731         1854         1489          620         1107         1124 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 
         204         1459         1935         1785         1834         1862 
TCGA-BP-4969 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 
        1794         1487         1502         1433         1632          454 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
        1014         1413         1124          118         1413          501 
TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5006 
         177         1371         1266          563         1177          840 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5180 
        1140         1071          193         2412         2257         2263 
TCGA-BP-5181 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 
        1495         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-5202 TCGA-CJ-4634 TCGA-CJ-4635 
        1018          603         1355           29         1820         1416 
TCGA-CJ-4636 TCGA-CJ-4639 TCGA-CJ-4869 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 
        1924         2308         2554         2423         1435         2259 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4882 TCGA-CJ-4886 TCGA-CJ-4890 TCGA-CJ-4892 
        2283         2353         1883         1952         2085         1521 
TCGA-CJ-4893 TCGA-CJ-4899 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4905 TCGA-CJ-4908 
         750         1528         1450         1520         1496         1531 
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-6093 TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4863 
        3146          774           18         1943         1787         1928 
TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5456 TCGA-CZ-5458 
        2830         1868         1929         1789         1712         1732 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5464 TCGA-CZ-5470 TCGA-CZ-5982 
        1683         1430          330         1740          386         2439 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5989 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 
        2067         1997         1905         1398         1470          370 
TCGA-DV-5569 TCGA-DV-5573 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
         355         1130          551          119          206          127 
TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-GK-A6C7 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC 
         305         1727           61          607          337          330 

  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 
           1238.0            1285.5 
[1] "15.0 - 3343.0 (1238.0)" "3.0 - 3668.0 (1285.5)" 
[1] "hr=" "1.5"
D54V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  8P LOSS MUTATED        58       14        39       24
  8P LOSS WILD-TYPE     195       43        87       56
D54V3, multiclass
           clus
vv          8P LOSS MUTATED 8P LOSS WILD-TYPE
  STAGE I                58               195
  STAGE II               14                43
  STAGE III              39                87
  STAGE IV               24                56
[1] 4 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  57   3
  8P LOSS WILD-TYPE 199  53 121   8
D54V4, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  T1              59               199
  T2              16                53
  T3              57               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 176  13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     55    5
  8P LOSS WILD-TYPE  176   13
   clus
vv  8P LOSS MUTATED 8P LOSS WILD-TYPE
  0              55               176
  1               5                13
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  8P LOSS MUTATED   108  25   2
  8P LOSS WILD-TYPE 309  53  17
D54V6, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  M0             108               309
  M1              25                53
  MX               2                17
[1] 3 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  97
  8P LOSS WILD-TYPE 148 233
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     38   97
  8P LOSS WILD-TYPE  148  233
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE              38               148
  MALE                97               233
[1] 2 2
[1] FALSE
D54V8, continuous
D54V9, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8P LOSS MUTATED       3                         7   123
  8P LOSS WILD-TYPE     5                        37   334
D54V10, multiclass
                           clus
vv                          8P LOSS MUTATED 8P LOSS WILD-TYPE
  ASIAN                                   3                 5
  BLACK OR AFRICAN AMERICAN               7                37
  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  80
  8P LOSS WILD-TYPE  15 258
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     11   80
  8P LOSS WILD-TYPE   15  258
                        clus
vv                       8P LOSS MUTATED 8P LOSS WILD-TYPE
  HISPANIC OR LATINO                  11                15
  NOT HISPANIC OR LATINO              80               258
[1] 2 2
[1] FALSE

Clustering(55) Variable = 8Q LOSS MUTATION ANALYSIS
D55V1, survival
                   sevent
clus2                 0   1
  8Q LOSS MUTATED    45   3
  8Q LOSS WILD-TYPE 302  21
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               48               323 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                3                21 
$`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 TCGA-MM-A563 
         662         1446          373          693         1729          591 

$`8Q LOSS WILD-TYPE`
TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 
         267         1120         1436           16          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-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 
        1610         1385          910         2688         1307         2504 
TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3374 TCGA-A3-3376 
        1559          319         2270         2274         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-3443 TCGA-AK-3444 
        1853         2192         2087         2044         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-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3778 TCGA-B0-4706 
        1143          951          853          369           43           26 
TCGA-B0-4710 TCGA-B0-4819 TCGA-B0-5097 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 
          96          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-B0-5697 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-B4-5832 
         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-B8-5165 TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
         737          505          434           15         1046          435 
TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I 
         830          909          519           53          256          150 
TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 
         528          110           24         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-4349 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 
        1666          372          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-4782 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4795 
         411         1731          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-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4969 
        1935         1785         1834         1862         1871         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-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5169 TCGA-BP-5170 
        1177          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-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4639 
        1355           29         1820         1416         1924         2308 
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-4878 TCGA-CJ-4881 TCGA-CJ-4882 
        2259         2283         2353         2186         2014         1883 
TCGA-CJ-4884 TCGA-CJ-4886 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4899 
        1759         1952         2085         1521          750         1528 
TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4916 
        1450         1520         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-5588 TCGA-CW-5589 TCGA-CW-5591 
        2489         2609         2226         2017         2378         2271 
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-4863 TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5456 
        1928         2830         1868         1929         1789         1712 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5464 TCGA-CZ-5466 
        1732         1683         1430          330         1740          685 
TCGA-CZ-5468 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5989 
          59          386         2439         2067         1997         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-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A8L6 
        2016          551          119          206          127          305 
TCGA-G6-A8L7 TCGA-GK-A6C7 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC 
        1727           61          607          337          330 

  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 
           1337.5            1266.0 
[1] "18.0 - 3222.0 (1337.5)" "3.0 - 3668.0 (1266.0)" 
[1] "hr=" "1"  
D55V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  8Q LOSS MUTATED        27        7        20        9
  8Q LOSS WILD-TYPE     226       50       106       71
D55V3, multiclass
           clus
vv          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  STAGE I                27               226
  STAGE II                7                50
  STAGE III              20               106
  STAGE IV                9                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
  8Q LOSS MUTATED    26   7  28   2
  8Q LOSS WILD-TYPE 232  62 150   9
D55V4, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  T1              26               232
  T2               7                62
  T3              28               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 206  15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     25    3
  8Q LOSS WILD-TYPE  206   15
   clus
vv  8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  0              25               206
  1               3                15
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  8Q LOSS MUTATED    53   9   1
  8Q LOSS WILD-TYPE 364  69  18
D55V6, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  M0              53               364
  M1               9                69
  MX               1                18
[1] 3 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  49
  8Q LOSS WILD-TYPE 172 281
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     14   49
  8Q LOSS WILD-TYPE  172  281
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE              14               172
  MALE                49               281
[1] 2 2
[1] FALSE
D55V8, continuous
D55V9, continuous
[1] "Remove cluster labels:" "8Q LOSS MUTATED"       
clus
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                2                10 
       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-A54E        TCGA-B8-A54F        TCGA-B8-A54G        TCGA-B8-A8YJ 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G6-A5PC        TCGA-G6-A8L7 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8Q LOSS MUTATED       1                         2    59
  8Q LOSS WILD-TYPE     7                        42   398
D55V10, multiclass
                           clus
vv                          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  ASIAN                                   1                 7
  BLACK OR AFRICAN AMERICAN               2                42
  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  34
  8Q LOSS WILD-TYPE  20 304
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      6   34
  8Q LOSS WILD-TYPE   20  304
                        clus
vv                       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   6                20
  NOT HISPANIC OR LATINO              34               304
[1] 2 2
[1] FALSE

Clustering(56) Variable = 9P LOSS MUTATION ANALYSIS
D56V1, survival
                   sevent
clus2                 0   1
  9P LOSS MUTATED    78   7
  9P LOSS WILD-TYPE 269  17
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               85               286 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                7                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-5984 TCGA-CZ-5985 TCGA-G6-A8L7 TCGA-MM-A563 
         685           59         2067         1997         1727          591 
TCGA-MM-A84U 
         337 

$`9P LOSS WILD-TYPE`
TCGA-6D-AA2E TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3320 TCGA-A3-3322 
         267         1436           16          735         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-A3-3349 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 
         945         1385          910         2688         1307         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-A3-3374 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-3434 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 
        1853         2192         2087         1745         1423         1471 
TCGA-AK-3447 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3456 TCGA-AK-3458 
        1217         1481         1397          874         1143         1168 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3778 TCGA-B0-4699 TCGA-B0-4706 
         951          853          369           43          110           26 
TCGA-B0-4718 TCGA-B0-4813 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5115 TCGA-B0-5117 
         616           18          911         1092          797          535 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5690 TCGA-B0-5691 
          59          493          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-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 
        2741         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-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5835 
         417          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-B8-4621 TCGA-B8-5159 TCGA-B8-5162 
         762          750          523          788          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-A54E TCGA-B8-A54F TCGA-B8-A54G 
        1046          435          830          909          519           53 
TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 
         256          150          528          110           24         3377 
TCGA-BP-4160 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4169 
        2881         3074         2839         3037           13          701 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 
        1893         1879         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-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 
        1367          372          374         2208         2372         2361 
TCGA-BP-4761 TCGA-BP-4765 TCGA-BP-4769 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 
         182         2184         1876         1885         1843          411 
TCGA-BP-4777 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4795 TCGA-BP-4801 TCGA-BP-4804 
        1731         1854         1489          620         1124         1459 
TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4961 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 
         211         2660         1935         1871          205         1746 
TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4975 TCGA-BP-4976 
        1794          433         1487         1502         1433         1632 
TCGA-BP-4977 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 
         454         1014         1413         1124          118         1413 
TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5001 TCGA-BP-5004 
         501          177          932         1266         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-5181 TCGA-BP-5182 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 
        1495         1165         1133         1132          693          406 
TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5199 TCGA-BP-5200 
        1011          714          408          749         1355         1063 
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-4873 
        1793          646         2554         1498         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-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-4856 TCGA-CZ-4859 
        2271         3222         3146          774           18         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-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5463 
          25         1683         1732         1683         1430          662 
TCGA-CZ-5464 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5986 TCGA-CZ-5988 TCGA-CZ-5989 
        1740          386         2439          373          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 
        2016         1729          551          119          206          127 
TCGA-G6-A8L6 TCGA-GK-A6C7 TCGA-MM-A564 TCGA-MW-A4EC 
         305           61          607          330 

  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 
           1291.0            1241.5 
[1] "7.0 - 3343.0 (1291.0)" "3.0 - 3668.0 (1241.5)"
[1] "hr=" "1.4"
D56V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  9P LOSS MUTATED        51       11        50       35
  9P LOSS WILD-TYPE     202       46        76       45
D56V3, multiclass
           clus
vv          9P LOSS MUTATED 9P LOSS WILD-TYPE
  STAGE I                51               202
  STAGE II               11                46
  STAGE III              50                76
  STAGE IV               35                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
  9P LOSS MUTATED    54  15  73   5
  9P LOSS WILD-TYPE 204  54 105   6
D56V4, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  T1              54               204
  T2              15                54
  T3              73               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    60   8
  9P LOSS WILD-TYPE 171  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     60    8
  9P LOSS WILD-TYPE  171   10
   clus
vv  9P LOSS MUTATED 9P LOSS WILD-TYPE
  0              60               171
  1               8                10
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  9P LOSS MUTATED   109  35   3
  9P LOSS WILD-TYPE 308  43  16
D56V6, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  M0             109               308
  M1              35                43
  MX               3                16
[1] 3 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    36 111
  9P LOSS WILD-TYPE 150 219
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     36  111
  9P LOSS WILD-TYPE  150  219
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE              36               150
  MALE               111               219
[1] 2 2
[1] FALSE
D56V8, continuous
D56V9, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9P LOSS MUTATED       1                         8   134
  9P LOSS WILD-TYPE     7                        36   323
D56V10, multiclass
                           clus
vv                          9P LOSS MUTATED 9P LOSS WILD-TYPE
  ASIAN                                   1                 7
  BLACK OR AFRICAN AMERICAN               8                36
  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  98
  9P LOSS WILD-TYPE  20 240
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      6   98
  9P LOSS WILD-TYPE   20  240
                        clus
vv                       9P LOSS MUTATED 9P LOSS WILD-TYPE
  HISPANIC OR LATINO                   6                20
  NOT HISPANIC OR LATINO              98               240
[1] 2 2
[1] FALSE

Clustering(57) Variable = 9Q LOSS MUTATION ANALYSIS
D57V1, survival
                   sevent
clus2                 0   1
  9Q LOSS MUTATED    81   6
  9Q LOSS WILD-TYPE 266  18
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               87               284 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                6                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-5984 TCGA-CZ-5985 
        1712          330         1446          685         2067         1997 
TCGA-G6-A8L7 TCGA-MM-A563 TCGA-MM-A84U 
        1727          591          337 

$`9Q LOSS WILD-TYPE`
TCGA-6D-AA2E TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3320 TCGA-A3-3322 
         267         1436           16          735         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-A3-3349 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 
         945         1385          910         2688         1307         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-A3-3374 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-3434 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 
        1853         2192         2087         1745         1423         1471 
TCGA-AK-3447 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3458 TCGA-AK-3460 
        1217         1481         1397          874         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-B0-5121 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-B0-5697 TCGA-B0-5698 TCGA-B0-5699 
        1487         3076         1420         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-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H 
         435          830          909          519           53          256 
TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4160 
         150          528          110           24         3377         2881 
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-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-4784 TCGA-BP-4789 TCGA-BP-4795 TCGA-BP-4801 TCGA-BP-4804 
        1731         1854         1489          620         1124         1459 
TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4961 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 
         211         2660         1935         1871          205         1746 
TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4975 TCGA-BP-4976 
        1794          433         1487         1502         1433         1632 
TCGA-BP-4977 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 
         454         1014         1413         1124          118         1413 
TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5001 TCGA-BP-5004 
         501          177          932         1266         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-5181 TCGA-BP-5182 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 
        1495         1165         1133         1132          693          406 
TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5199 TCGA-BP-5200 
        1011          714          408          749         1355         1063 
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-4869 TCGA-CJ-4870 TCGA-CJ-4872 TCGA-CJ-4874 TCGA-CJ-4875 
        1793         2554         1498         1435         2283         2353 
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-4854 TCGA-CZ-4856 TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4863 
         774         1404           18         1787         1843         1928 
TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5453 TCGA-CZ-5457 TCGA-CZ-5458 
        2830         1868         1929           25         1683         1732 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5468 TCGA-CZ-5470 
        1683         1430          662         1740           59          386 
TCGA-CZ-5982 TCGA-CZ-5986 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
        2439          373          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         2016         1729 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A8L6 TCGA-GK-A6C7 
         551          119          206          127          305           61 
TCGA-MM-A564 TCGA-MW-A4EC 
         607          330 

  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 
             1308              1210 
[1] "7.0 - 3343.0 (1308.0)" "3.0 - 3668.0 (1210.0)"
[1] "hr=" "1.1"
D57V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  9Q LOSS MUTATED        48       14        52       34
  9Q LOSS WILD-TYPE     205       43        74       46
D57V3, multiclass
           clus
vv          9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  STAGE I                48               205
  STAGE II               14                43
  STAGE III              52                74
  STAGE IV               34                46
[1] 4 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    50  18  76   4
  9Q LOSS WILD-TYPE 208  51 102   7
D57V4, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T1              50               208
  T2              18                51
  T3              76               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    63   8
  9Q LOSS WILD-TYPE 168  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     63    8
  9Q LOSS WILD-TYPE  168   10
   clus
vv  9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  0              63               168
  1               8                10
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  9Q LOSS MUTATED   111  34   3
  9Q LOSS WILD-TYPE 306  44  16
D57V6, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  M0             111               306
  M1              34                44
  MX               3                16
[1] 3 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    36 112
  9Q LOSS WILD-TYPE 150 218
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     36  112
  9Q LOSS WILD-TYPE  150  218
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE              36               150
  MALE               112               218
[1] 2 2
[1] FALSE
D57V8, continuous
D57V9, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9Q LOSS MUTATED       1                         8   135
  9Q LOSS WILD-TYPE     7                        36   322
D57V10, multiclass
                           clus
vv                          9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  ASIAN                                   1                 7
  BLACK OR AFRICAN AMERICAN               8                36
  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  97
  9Q LOSS WILD-TYPE  18 241
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      8   97
  9Q LOSS WILD-TYPE   18  241
                        clus
vv                       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   8                18
  NOT HISPANIC OR LATINO              97               241
[1] 2 2
[1] FALSE

Clustering(58) Variable = 10P LOSS MUTATION ANALYSIS
D58V1, survival
                    sevent
clus2                  0   1
  10P LOSS MUTATED    43   3
  10P LOSS WILD-TYPE 304  21
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                46                325 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 3                 21 
$`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-5470 TCGA-CZ-5982 TCGA-DV-5566 TCGA-EU-5907 
         386         2439         1398          127 

$`10P LOSS WILD-TYPE`
TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 
         267         1120         1436           16          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-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 
        1610         1385          910         2688         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-A3-3376 TCGA-A3-3378 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 
        1621         1070          630          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-3444 TCGA-AK-3445 
         480         1853         2087         2044         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-AS-3777 TCGA-AS-3778 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4718 
         951         1238           43           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-B0-5119 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-B0-5702 
        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-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
        2722         1865         2963         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-B4-5832 TCGA-B4-5834 TCGA-B4-5836 TCGA-B4-5838 
         291          175            7           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-B8-4620 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-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E 
         505           15         1046          435          830          909 
TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 
         519           53          256          150          528          110 
TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 
          24         3377         2881         3074         2839         3037 
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-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-4768 
        2372         2361          182         2184         1462          400 
TCGA-BP-4769 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 
        1876         1885          411         1731         2080          354 
TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4795 TCGA-BP-4801 TCGA-BP-4804 TCGA-BP-4807 
        1854         1489          620         1124         1459          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-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
         205         1746         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-5004 TCGA-BP-5006 
         932         1266          563         1177         1126          840 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5177 
        1140         1071         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-5199 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 
         408          749         1355         1063           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-4875 
        2554         1498         2423         1435         2259         2353 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
        1955         2186         2014         1759         2125         1952 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4894 TCGA-CJ-4899 TCGA-CJ-4902 
        1946         2085         1521          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-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-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-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 
         693         1905         1329         1470          370          355 
TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
        1130         2016         1729          551          119          206 
TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U 
         305         1727           61          591          607          337 
TCGA-MW-A4EC 
         330 

  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 
            1137.5             1291.0 
[1] "13.0 - 2746.0 (1137.5)" "3.0 - 3668.0 (1291.0)" 
[1] "hr=" "1.2"
D58V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  10P LOSS MUTATED        23        6        23       13
  10P LOSS WILD-TYPE     230       51       103       67
D58V3, multiclass
           clus
vv          10P LOSS MUTATED 10P LOSS WILD-TYPE
  STAGE I                 23                230
  STAGE II                 6                 51
  STAGE III               23                103
  STAGE IV                13                 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
  10P LOSS MUTATED    23   7  31   4
  10P LOSS WILD-TYPE 235  62 147   7
D58V4, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  T1               23                235
  T2                7                 62
  T3               31                147
  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 201  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     30    0
  10P LOSS WILD-TYPE  201   18
   clus
vv  10P LOSS MUTATED 10P LOSS WILD-TYPE
  0               30                201
  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  19
D58V6, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  M0               53                364
  M1               12                 66
  MX                0                 19
[1] 3 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 167 284
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     19   46
  10P LOSS WILD-TYPE  167  284
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE               19                167
  MALE                 46                284
[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                        41   398
D58V10, multiclass
                           clus
vv                          10P LOSS MUTATED 10P LOSS WILD-TYPE
  ASIAN                                    0                  8
  BLACK OR AFRICAN AMERICAN                3                 41
  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  21 301
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      5   37
  10P LOSS WILD-TYPE   21  301
                        clus
vv                       10P LOSS MUTATED 10P LOSS WILD-TYPE
  HISPANIC OR LATINO                    5                 21
  NOT HISPANIC OR LATINO               37                301
[1] 2 2
[1] FALSE

Clustering(59) Variable = 10Q LOSS MUTATION ANALYSIS
D59V1, survival
                    sevent
clus2                  0   1
  10Q LOSS MUTATED    58   4
  10Q LOSS WILD-TYPE 289  20
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                62                309 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 4                 20 
$`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-5470 TCGA-CZ-5982 TCGA-DV-5565 
        1683         1430         1446          386         2439         1329 
TCGA-DV-5566 TCGA-EU-5907 
        1398          127 

$`10Q LOSS WILD-TYPE`
TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3317 
         267         1120         1436           16          735         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-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3347 TCGA-A3-3349 
        1137          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-A3-3382 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-3434 TCGA-AK-3436 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 
        2087         2044         1471         1280         1217         1779 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3456 TCGA-AK-3460 TCGA-AS-3777 
        1481         1397          874         1143          951         1238 
TCGA-AS-3778 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4813 TCGA-B0-5097 TCGA-B0-5108 
          43           26           96           18          665          911 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 
        1092          359          797          657           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-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 
        3076         1420         1727         1835         2583         2741 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5705 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
        1732         1605         3668         3117         1459         2931 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
        2722         1865         2963         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-B4-5832 TCGA-B4-5834 TCGA-B4-5836 TCGA-B4-5843 
         291          175            7           38          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-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F 
          15         1046          435          830          909          519 
TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A8YJ TCGA-BP-4158 
          53          256          150          528           24         3377 
TCGA-BP-4160 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4167 TCGA-BP-4169 
        2881         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-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-4768 TCGA-BP-4769 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 
        2184          400         1876         1885          411         1731 
TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4795 TCGA-BP-4801 
        2080          354         1854         1489          620         1124 
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-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 
        1862         1871          205         1746         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-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5170 TCGA-BP-5174 
        1126          840         1140         1071         2412         2257 
TCGA-BP-5175 TCGA-BP-5177 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
         932          293         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-5199 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 
         408          749         1355         1063           29         1820 
TCGA-CJ-4636 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 
        1924         2308         1998         1793          646         2554 
TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4873 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
        1498         2423         2259         2353         1955         2186 
TCGA-CJ-4881 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4889 TCGA-CJ-4890 
        2014         1759         2125         1952         1946         2085 
TCGA-CJ-4892 TCGA-CJ-4894 TCGA-CJ-4899 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 
        1521          841         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-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-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 
        1906         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-5988 TCGA-CZ-5989 TCGA-DV-5567 
        2067         1997          373          693         1905         1470 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5904 
         370          355         1130         2016         1729          551 
TCGA-EU-5905 TCGA-EU-5906 TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-GK-A6C7 TCGA-MM-A563 
         119          206          305         1727           61          591 
TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC 
         607          337          330 

  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 
            1255.5             1280.0 
[1] "13.0 - 2746.0 (1255.5)" "3.0 - 3668.0 (1280.0)" 
[1] "hr=" "1.1"
D59V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  10Q LOSS MUTATED        32       11        27       17
  10Q LOSS WILD-TYPE     221       46        99       63
D59V3, multiclass
           clus
vv          10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  STAGE I                 32                221
  STAGE II                11                 46
  STAGE III               27                 99
  STAGE IV                17                 63
[1] 4 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 226  57 141   5
D59V4, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T1               32                226
  T2               12                 57
  T3               37                141
  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 193  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     38    1
  10Q LOSS WILD-TYPE  193   17
   clus
vv  10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  0               38                193
  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  19
D59V6, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  M0               71                346
  M1               15                 63
  MX                0                 19
[1] 3 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 162 267
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     24   63
  10Q LOSS WILD-TYPE  162  267
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE               24                162
  MALE                 63                267
[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                        40   377
D59V10, multiclass
                           clus
vv                          10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  ASIAN                                    0                  8
  BLACK OR AFRICAN AMERICAN                4                 40
  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  20 286
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      6   52
  10Q LOSS WILD-TYPE   20  286
                        clus
vv                       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    6                 20
  NOT HISPANIC OR LATINO               52                286
[1] 2 2
[1] FALSE

Clustering(60) Variable = 11P LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                  0   1
  11P LOSS MUTATED     9   1
  11P LOSS WILD-TYPE 338  23
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                10                361 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 1                 23 
$`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 
         400          951         2017         1446 

$`11P LOSS WILD-TYPE`
TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3317 
         267         1120         1436           16          735         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-AS-3777 TCGA-AS-3778 TCGA-B0-4699 TCGA-B0-4706 TCGA-B0-4710 
         853         1238           43          110           26           96 
TCGA-B0-4718 TCGA-B0-4813 TCGA-B0-5097 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 
         616           18          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-B0-5703 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-B2-3923 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-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 
         417          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-B8-5164 
         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-A54E TCGA-B8-A54F TCGA-B8-A54G 
        1046          435          830          909          519           53 
TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 
         256          150          528          110           24         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-4769 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 
        1462         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-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-5468 TCGA-CZ-5470 
         330          662         1740          685           59          386 
TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5988 TCGA-CZ-5989 
        2439         2067         1997          373          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 
        2016         1729          551          119          206          127 
TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U 
         305         1727           61          591          607          337 
TCGA-MW-A4EC 
         330 

  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 
             803.5             1291.0 
[1] "166.0 - 2017.0 (803.5)" "3.0 - 3668.0 (1291.0)" 
[1] "hr=" "2.1"
D60V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  11P LOSS MUTATED         6        3         5        4
  11P LOSS WILD-TYPE     247       54       121       76
D60V3, multiclass
           clus
vv          11P LOSS MUTATED 11P LOSS WILD-TYPE
  STAGE I                  6                247
  STAGE II                 3                 54
  STAGE III                5                121
  STAGE IV                 4                 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
  11P LOSS MUTATED     6   3   9   0
  11P LOSS WILD-TYPE 252  66 169  11
D60V4, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  T1                6                252
  T2                3                 66
  T3                9                169
  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 223  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      8    2
  11P LOSS WILD-TYPE  223   16
   clus
vv  11P LOSS MUTATED 11P LOSS WILD-TYPE
  0                8                223
  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  19
D60V6, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  M0               14                403
  M1                4                 74
  MX                0                 19
[1] 3 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 180 318
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      6   12
  11P LOSS WILD-TYPE  180  318
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE                6                180
  MALE                 12                318
[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                        43   441
D60V10, multiclass
                           clus
vv                          11P LOSS MUTATED 11P LOSS WILD-TYPE
  ASIAN                                    0                  8
  BLACK OR AFRICAN AMERICAN                1                 43
  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  26 325
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      0   13
  11P LOSS WILD-TYPE   26  325
                        clus
vv                       11P LOSS MUTATED 11P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 26
  NOT HISPANIC OR LATINO               13                325
[1] 2 2
[1] FALSE

Clustering(61) Variable = 11Q LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                  0   1
  11Q LOSS MUTATED    12   2
  11Q LOSS WILD-TYPE 335  22
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                14                357 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 2                 22 
$`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 
        1446           59 

$`11Q LOSS WILD-TYPE`
TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3317 
         267         1120         1436           16          735         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-3427 TCGA-AK-3428 TCGA-AK-3429 
        1993          617            3         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-B4-5834 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-B8-4620 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-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I 
         830          909          519           53          256          150 
TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 
         528          110           24         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-4769 
        2372         2361          182         2184         1462         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-4987 TCGA-BP-4989 TCGA-BP-4991 
         454         1014         1413         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-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
         685          386         2439         2067         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-5905 
         355         1130         2016         1729          551          119 
TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-GK-A6C7 TCGA-MM-A563 
         206          127          305         1727           61          591 
TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC 
         607          337          330 

  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 
             720.5             1307.0 
[1] "7.0 - 3343.0 (720.5)"  "3.0 - 3668.0 (1307.0)"
[1] "hr=" "3"  
D61V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  11Q LOSS MUTATED         9        3         6        5
  11Q LOSS WILD-TYPE     244       54       120       75
D61V3, multiclass
           clus
vv          11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  STAGE I                  9                244
  STAGE II                 3                 54
  STAGE III                6                120
  STAGE IV                 5                 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
  11Q LOSS MUTATED     9   3  11   0
  11Q LOSS WILD-TYPE 249  66 167  11
D61V4, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T1                9                249
  T2                3                 66
  T3               11                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"
D61V5, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    11   2
  11Q LOSS WILD-TYPE 220  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     11    2
  11Q LOSS WILD-TYPE  220   16
   clus
vv  11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  0               11                220
  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  19
D61V6, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  M0               18                399
  M1                5                 73
  MX                0                 19
[1] 3 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 180 313
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      6   17
  11Q LOSS WILD-TYPE  180  313
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE                6                180
  MALE                 17                313
[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                        43   436
D61V10, multiclass
                           clus
vv                          11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  ASIAN                                    0                  8
  BLACK OR AFRICAN AMERICAN                1                 43
  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  25 322
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      1   16
  11Q LOSS WILD-TYPE   25  322
                        clus
vv                       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 25
  NOT HISPANIC OR LATINO               16                322
[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 344  24
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 3                368 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 0                 24 
$`12P LOSS MUTATED`
TCGA-BP-4166 TCGA-BP-4775 TCGA-CZ-5457 
          13         1843         1683 

$`12P LOSS WILD-TYPE`
TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 
         267         1120         1436           16          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-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 
        1610         1385          910         2688         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-A3-3378 TCGA-A3-3380 TCGA-A3-3382 
        1621         1314         1070          630          567          574 
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-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 
        2223         2017          480         1853         2192         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-B0-4710 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-A54E TCGA-B8-A54F TCGA-B8-A54G 
        1046          435          830          909          519           53 
TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 
         256          150          528          110           24         3377 
TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4167 
        2881         2746         3074         2839         3037         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-4776 TCGA-BP-4777 TCGA-BP-4781 
         400         1876         1885          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-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-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-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5988 
         386         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         2016         1729          551          119          206 
TCGA-EU-5907 TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 
         127          305         1727           61          591          607 
TCGA-MM-A84U TCGA-MW-A4EC 
         337          330 

  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               1273 
[1] "13.0 - 1843.0 (1683.0)" "3.0 - 3668.0 (1273.0)" 
[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     252       57       124       80
D62V3, multiclass
           clus
vv          12P LOSS MUTATED 12P LOSS WILD-TYPE
  STAGE I                  1                252
  STAGE II                 0                 57
  STAGE III                2                124
  STAGE IV                 0                 80
[1] 4 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 257  69 176  11
D62V4, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  T1                1                257
  T2                0                 69
  T3                2                176
  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 230  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      1    0
  12P LOSS WILD-TYPE  230   18
   clus
vv  12P LOSS MUTATED 12P LOSS WILD-TYPE
  0                1                230
  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  19
D62V6, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  M0                3                414
  M1                0                 78
  MX                0                 19
[1] 3 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 185 328
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      1    2
  12P LOSS WILD-TYPE  185  328
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE                1                185
  MALE                  2                328
[1] 2 2
[1] FALSE
D62V8, continuous
[1] "Remove cluster labels:" "12P LOSS MUTATED"      
clus
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 1                 40 
        TCGA-A3-A6NJ         TCGA-A3-A6NL         TCGA-A3-A8CQ 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AK-3426         TCGA-AK-3430         TCGA-B0-4838 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-B2-5639         TCGA-B4-5377         TCGA-B4-5378 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-B4-5832         TCGA-B4-5834         TCGA-B4-5835 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-B4-5836         TCGA-B4-5838         TCGA-B4-5843 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-B4-5844         TCGA-CZ-4854         TCGA-CZ-4856 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CZ-4858         TCGA-CZ-4860         TCGA-CZ-4861 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CZ-4862         TCGA-CZ-5456         TCGA-CZ-5465 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CZ-5469         TCGA-CZ-5982         TCGA-DV-5565 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DV-5566         TCGA-DV-5567         TCGA-DV-5568 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DV-5569         TCGA-DV-5573         TCGA-DV-5574 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DV-5575         TCGA-DV-5576         TCGA-EU-5904 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EU-5905         TCGA-EU-5907         TCGA-G6-A8L6 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G6-A8L7 
"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                        44   454
D62V10, multiclass
                           clus
vv                          12P LOSS MUTATED 12P LOSS WILD-TYPE
  ASIAN                                    0                  8
  BLACK OR AFRICAN AMERICAN                0                 44
  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  26 337
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      0    1
  12P LOSS WILD-TYPE   26  337
                        clus
vv                       12P LOSS MUTATED 12P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 26
  NOT HISPANIC OR LATINO                1                337
[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 344  24
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 3                368 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 0                 24 
$`12Q LOSS MUTATED`
TCGA-BP-4166 TCGA-BP-4775 TCGA-CZ-5457 
          13         1843         1683 

$`12Q LOSS WILD-TYPE`
TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 
         267         1120         1436           16          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-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 
        1610         1385          910         2688         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-A3-3378 TCGA-A3-3380 TCGA-A3-3382 
        1621         1314         1070          630          567          574 
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-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 
        2223         2017          480         1853         2192         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-B0-4710 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-A54E TCGA-B8-A54F TCGA-B8-A54G 
        1046          435          830          909          519           53 
TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 
         256          150          528          110           24         3377 
TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4167 
        2881         2746         3074         2839         3037         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-4776 TCGA-BP-4777 TCGA-BP-4781 
         400         1876         1885          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-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-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-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5988 
         386         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         2016         1729          551          119          206 
TCGA-EU-5907 TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 
         127          305         1727           61          591          607 
TCGA-MM-A84U TCGA-MW-A4EC 
         337          330 

  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               1273 
[1] "13.0 - 1843.0 (1683.0)" "3.0 - 3668.0 (1273.0)" 
[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     252       57       123       80
D63V3, multiclass
           clus
vv          12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  STAGE I                  1                252
  STAGE II                 0                 57
  STAGE III                3                123
  STAGE IV                 0                 80
[1] 4 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 257  69 175  11
D63V4, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  T1                1                257
  T2                0                 69
  T3                3                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"
D63V5, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     2   0
  12Q LOSS WILD-TYPE 229  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      2    0
  12Q LOSS WILD-TYPE  229   18
   clus
vv  12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  0                2                229
  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  19
D63V6, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  M0                4                413
  M1                0                 78
  MX                0                 19
[1] 3 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 185 327
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      1    3
  12Q LOSS WILD-TYPE  185  327
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE                1                185
  MALE                  3                327
[1] 2 2
[1] FALSE
D63V8, continuous
[1] "Remove cluster labels:" "12Q LOSS MUTATED"      
clus
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 1                 40 
        TCGA-A3-A6NJ         TCGA-A3-A6NL         TCGA-A3-A8CQ 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AK-3426         TCGA-AK-3430         TCGA-B0-4838 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B2-5639         TCGA-B4-5377         TCGA-B4-5378 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B4-5832         TCGA-B4-5834         TCGA-B4-5835 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B4-5836         TCGA-B4-5838         TCGA-B4-5843 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B4-5844         TCGA-CZ-4854         TCGA-CZ-4856 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CZ-4858         TCGA-CZ-4860         TCGA-CZ-4861 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CZ-4862         TCGA-CZ-5456         TCGA-CZ-5465 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CZ-5469         TCGA-CZ-5982         TCGA-DV-5565 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DV-5566         TCGA-DV-5567         TCGA-DV-5568 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DV-5569         TCGA-DV-5573         TCGA-DV-5574 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DV-5575         TCGA-DV-5576         TCGA-EU-5904 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EU-5905         TCGA-EU-5907         TCGA-G6-A8L6 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-G6-A8L7 
"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                        44   453
D63V10, multiclass
                           clus
vv                          12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  ASIAN                                    0                  8
  BLACK OR AFRICAN AMERICAN                0                 44
  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  26 336
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      0    2
  12Q LOSS WILD-TYPE   26  336
                        clus
vv                       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 26
  NOT HISPANIC OR LATINO                2                336
[1] 2 2
[1] FALSE

Clustering(64) Variable = 13Q LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                  0   1
  13Q LOSS MUTATED    37   7
  13Q LOSS WILD-TYPE 310  17
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                44                327 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 7                 17 
$`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-5984 
        1928         1868         1683         1446           59         2067 
TCGA-DV-5568 TCGA-G6-A8L7 
         370         1727 

$`13Q LOSS WILD-TYPE`
TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 
         267         1120         1436           16          735         1493 
TCGA-A3-3317 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 
        1491         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-A3-3372 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 
         873         2270          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-3436 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3447 TCGA-AK-3450 
        2087         2044         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-AS-3778 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4718 TCGA-B0-4813 
         853           43           26           96          616           18 
TCGA-B0-5097 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 
         665          911         1092          797          657           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-B0-5697 TCGA-B0-5698 
        3431         1487         3076         1420         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-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 
         175           38          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-B8-5164 
         788          700          636          722           36           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-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H 
         435          830          909          519           53          256 
TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4160 
         150          528          110           24         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-4335 TCGA-BP-4344 TCGA-BP-4347 
         845         1888         1133          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-4761 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4774 TCGA-BP-4775 
         182         2184         1462         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-4965 
        2660         2172         1935         1785         1834         1871 
TCGA-BP-4967 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4975 
         205         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-5006 TCGA-BP-5007 TCGA-BP-5008 
        1266          563         1177          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-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-4635 TCGA-CJ-4636 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4642 TCGA-CJ-4643 
        1416         1924         2308         1998         1628         1793 
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-4882 TCGA-CJ-4884 TCGA-CJ-4885 
        2353         1955         2186         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-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 
        1808         1528         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-5589 TCGA-CW-5591 TCGA-CW-6088 TCGA-CW-6093 TCGA-CZ-4853 
        2226         2378         2271         3222         3146          774 
TCGA-CZ-4856 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4864 TCGA-CZ-5451 
          18         1943         1787         1843         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-5461 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5470 TCGA-CZ-5982 
         330          662         1740          685          386         2439 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
        1997          373          693         1905         1329         1398 
TCGA-DV-5567 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5904 
        1470          355         1130         2016         1729          551 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A8L6 TCGA-GK-A6C7 TCGA-MM-A563 
         119          206          127          305           61          591 
TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC 
         607          337          330 

  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 
              1311               1217 
[1] "7.0 - 2859.0 (1311.0)" "3.0 - 3668.0 (1217.0)"
[1] "hr=" "3.2"
D64V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  13Q LOSS MUTATED        24        2        25       19
  13Q LOSS WILD-TYPE     229       55       101       61
D64V3, multiclass
           clus
vv          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  STAGE I                 24                229
  STAGE II                 2                 55
  STAGE III               25                101
  STAGE IV                19                 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
  13Q LOSS MUTATED    26   3  34   7
  13Q LOSS WILD-TYPE 232  66 144   4
D64V4, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T1               26                232
  T2                3                 66
  T3               34                144
  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    34   4
  13Q LOSS WILD-TYPE 197  14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     34    4
  13Q LOSS WILD-TYPE  197   14
   clus
vv  13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  0               34                197
  1                4                 14
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  13Q LOSS MUTATED    52  17   1
  13Q LOSS WILD-TYPE 365  61  18
D64V6, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  M0               52                365
  M1               17                 61
  MX                1                 18
[1] 3 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    21  49
  13Q LOSS WILD-TYPE 165 281
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     21   49
  13Q LOSS WILD-TYPE  165  281
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE               21                165
  MALE                 49                281
[1] 2 2
[1] FALSE
D64V8, continuous
D64V9, continuous
[1] "Remove cluster labels:" "13Q LOSS MUTATED"      
clus
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 1                 11 
        TCGA-A3-A8CQ         TCGA-B2-A4SR         TCGA-B8-4621 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-B8-5158         TCGA-B8-5164         TCGA-B8-A54E 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-B8-A54F         TCGA-B8-A54G         TCGA-B8-A8YJ 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G6-A5PC         TCGA-MM-A563 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  13Q LOSS MUTATED       0                         3    66
  13Q LOSS WILD-TYPE     8                        41   391
D64V10, multiclass
                           clus
vv                          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  ASIAN                                    0                  8
  BLACK OR AFRICAN AMERICAN                3                 41
  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  48
  13Q LOSS WILD-TYPE  25 290
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      1   48
  13Q LOSS WILD-TYPE   25  290
                        clus
vv                       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 25
  NOT HISPANIC OR LATINO               48                290
[1] 2 2
[1] FALSE

Clustering(65) Variable = 14Q LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                  0   1
  14Q LOSS MUTATED   125  13
  14Q LOSS WILD-TYPE 222  11
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               138                233 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                13                 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-5470 
        1712          330          662         1446           59          386 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5989 TCGA-DV-5573 TCGA-MM-A563 TCGA-MM-A84U 
        2067         1997         1905         1130          591          337 

$`14Q LOSS WILD-TYPE`
TCGA-6D-AA2E TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3322 TCGA-A3-3323 
         267         1436           16          735         1478         1106 
TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3343 TCGA-A3-3349 TCGA-A3-3358 
         751         1137         1485          945         1385         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-A3-3372 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3380 TCGA-A3-3383 
         735         1621         1314         1070          567          861 
TCGA-A3-3385 TCGA-A3-A8CQ TCGA-AK-3425 TCGA-AK-3428 TCGA-AK-3431 TCGA-AK-3433 
        1993            3         3343         2223         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-3453 TCGA-AK-3456 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 
        1397         1143          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-B0-5108 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-B0-5402 TCGA-B0-5690 TCGA-B0-5691 
         493          554          652          449         2408         3431 
TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5699 TCGA-B0-5702 TCGA-B0-5703 
        3076         1420         1727         2741         1605         1203 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 
        3668         2414         3117         1865         2963          992 
TCGA-B2-3924 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 
        1092          374          648          507          291          175 
TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
          38           16            7          511          826          838 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5159 
         762          750          777          788          700          722 
TCGA-B8-5163 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5552 
         822          737          522          505          194         1046 
TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54H TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ 
         909          519          256          528          110           24 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4165 TCGA-BP-4166 
        3377         2881         2746         3074         3037           13 
TCGA-BP-4169 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 
         701         1670         2964         1625          845         1888 
TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4338 TCGA-BP-4344 TCGA-BP-4349 
        1133          645          461         2859         1666          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-4775 TCGA-BP-4776 TCGA-BP-4782 
        1462         1876         1885         1843          411          354 
TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4795 TCGA-BP-4801 TCGA-BP-4804 TCGA-BP-4807 
        1854         1489          620         1124         1459          211 
TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 
        2172         1935         1834         1862          205         1746 
TCGA-BP-4969 TCGA-BP-4972 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4982 TCGA-BP-4987 
        1794         1502         1433         1632         1014         1124 
TCGA-BP-4991 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 
        1413          177         1308         1371          932         1266 
TCGA-BP-5001 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5177 TCGA-BP-5181 
        1177          840         1140         1071          293         1495 
TCGA-BP-5182 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5192 TCGA-BP-5194 
        1165         1133          693          406          714          408 
TCGA-BP-5195 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 
         749         1355         1063           29         1820         1416 
TCGA-CJ-4639 TCGA-CJ-4643 TCGA-CJ-4870 TCGA-CJ-4872 TCGA-CJ-4878 TCGA-CJ-4882 
        2308         1793         1498         1435         2186         1883 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4899 
        2125         1952         1946         2085         1521         1528 
TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-5681 TCGA-CJ-5683 
        1450         1520         1792         1496          552         1889 
TCGA-CJ-5684 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 
        2231         1906         2548         2799         2489         2609 
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-5451 TCGA-CZ-5453 TCGA-CZ-5457 TCGA-CZ-5458 
        1787         1843         1929           25         1683         1732 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5982 TCGA-CZ-5986 
        1683         1430         1740          685         2439          373 
TCGA-CZ-5988 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 
         693         1329         1398         1470          370          355 
TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
        2016         1729          551          119          206          127 
TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-GK-A6C7 TCGA-MM-A564 TCGA-MW-A4EC 
         305         1727           61          607          330 

  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             1217.0 
[1] "7.0 - 2931.0 (1378.5)" "3.0 - 3668.0 (1217.0)"
[1] "hr=" "2"  
D65V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  14Q LOSS MUTATED        78       26        64       45
  14Q LOSS WILD-TYPE     175       31        62       35
D65V3, multiclass
           clus
vv          14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  STAGE I                 78                175
  STAGE II                26                 31
  STAGE III               64                 62
  STAGE IV                45                 35
[1] 4 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    83  34  93   3
  14Q LOSS WILD-TYPE 175  35  85   8
D65V4, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  T1               83                175
  T2               34                 35
  T3               93                 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 139   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     92   14
  14Q LOSS WILD-TYPE  139    4
   clus
vv  14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  0               92                139
  1               14                  4
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  14Q LOSS MUTATED   162  46   5
  14Q LOSS WILD-TYPE 255  32  14
D65V6, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  M0              162                255
  M1               46                 32
  MX                5                 14
[1] 3 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    64 149
  14Q LOSS WILD-TYPE 122 181
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     64  149
  14Q LOSS WILD-TYPE  122  181
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE               64                122
  MALE                149                181
[1] 2 2
[1] FALSE
D65V8, continuous
D65V9, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  14Q LOSS MUTATED       2                        11   196
  14Q LOSS WILD-TYPE     6                        33   261
D65V10, multiclass
                           clus
vv                          14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  ASIAN                                    2                  6
  BLACK OR AFRICAN AMERICAN               11                 33
  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    12 144
  14Q LOSS WILD-TYPE  14 194
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     12  144
  14Q LOSS WILD-TYPE   14  194
                        clus
vv                       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   12                 14
  NOT HISPANIC OR LATINO              144                194
[1] 2 2
[1] FALSE

Clustering(66) Variable = 15Q LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                  0   1
  15Q LOSS MUTATED    17   1
  15Q LOSS WILD-TYPE 330  23
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                18                353 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 1                 23 
$`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-5984 
        1063         1450         1499         1683          330         2067 

$`15Q LOSS WILD-TYPE`
TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 
         267         1120         1436           16          735         1493 
TCGA-A3-3317 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 
        1491         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-A3-3383 TCGA-A3-3385 
        1314         1070          630          567          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-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
         359          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-B4-5834 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-B8-4621 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-B8-5550 TCGA-B8-5551 
          26          737          522          505          434           15 
TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G 
        1046          435          830          909          519           53 
TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 
         256          150          528          110           24         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-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-4769 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 
        1876         1885          411         1731         2080          354 
TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4795 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 
        1854         1489          620         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-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-5198 TCGA-BP-5199 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 
         603         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-4902 TCGA-CJ-4903 TCGA-CJ-4904 
         841         1808         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-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-5460 TCGA-CZ-5463 
          25         1712         1732         1683         1430          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-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
        1997          373          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         2016         1729 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A8L6 TCGA-G6-A8L7 
         551          119          206          127          305         1727 
TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC 
          61          591          607          337          330 

  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 
             997.5             1308.0 
[1] "7.0 - 2718.0 (997.5)"  "3.0 - 3668.0 (1308.0)"
[1] "hr=" "1"  
D66V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  15Q LOSS MUTATED         8        2        13       12
  15Q LOSS WILD-TYPE     245       55       113       68
D66V3, multiclass
           clus
vv          15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  STAGE I                  8                245
  STAGE II                 2                 55
  STAGE III               13                113
  STAGE IV                12                 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
  15Q LOSS MUTATED     9   2  21   3
  15Q LOSS WILD-TYPE 249  67 157   8
D66V4, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T1                9                249
  T2                2                 67
  T3               21                157
  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 214  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     17    1
  15Q LOSS WILD-TYPE  214   17
   clus
vv  15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  0               17                214
  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  19
D66V6, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  M0               24                393
  M1               11                 67
  MX                0                 19
[1] 3 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 179 302
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      7   28
  15Q LOSS WILD-TYPE  179  302
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE                7                179
  MALE                 28                302
[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                        44   423
D66V10, multiclass
                           clus
vv                          15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  ASIAN                                    1                  7
  BLACK OR AFRICAN AMERICAN                0                 44
  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  26 317
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      0   21
  15Q LOSS WILD-TYPE   26  317
                        clus
vv                       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 26
  NOT HISPANIC OR LATINO               21                317
[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 343  24
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 4                367 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 0                 24 
$`16P LOSS MUTATED`
TCGA-A3-3316 TCGA-B8-5551 TCGA-BP-4797 TCGA-CZ-5982 
        1493           15         1107         2439 

$`16P LOSS WILD-TYPE`
TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3317 
         267         1120         1436           16          735         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-B8-5552 TCGA-B8-5553 
         522          505          194          434         1046          435 
TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I 
         830          909          519           53          256          150 
TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 
         528          110           24         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-5470 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5988 TCGA-CZ-5989 
         386         2067         1997          373          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 
        2016         1729          551          119          206          127 
TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U 
         305         1727           61          591          607          337 
TCGA-MW-A4EC 
         330 

  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               1280 
[1] "15.0 - 2439.0 (1300.0)" "3.0 - 3668.0 (1280.0)" 
[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     251       55       123       78
D67V3, multiclass
           clus
vv          16P LOSS MUTATED 16P LOSS WILD-TYPE
  STAGE I                  2                251
  STAGE II                 2                 55
  STAGE III                3                123
  STAGE IV                 2                 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
  16P LOSS MUTATED     2   2   3   2
  16P LOSS WILD-TYPE 256  67 175   9
D67V4, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  T1                2                256
  T2                2                 67
  T3                3                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"
D67V5, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     5   1
  16P LOSS WILD-TYPE 226  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      5    1
  16P LOSS WILD-TYPE  226   17
   clus
vv  16P LOSS MUTATED 16P LOSS WILD-TYPE
  0                5                226
  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  19
D67V6, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  M0                8                409
  M1                1                 77
  MX                0                 19
[1] 3 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 183 324
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      3    6
  16P LOSS WILD-TYPE  183  324
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE                3                183
  MALE                  6                324
[1] 2 2
[1] FALSE
D67V8, continuous
[1] "Remove cluster labels:" "16P LOSS MUTATED"      
clus
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 1                 40 
        TCGA-A3-A6NJ         TCGA-A3-A6NL         TCGA-A3-A8CQ 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AK-3426         TCGA-AK-3430         TCGA-B0-4838 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B2-5639         TCGA-B4-5377         TCGA-B4-5378 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B4-5832         TCGA-B4-5834         TCGA-B4-5835 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B4-5836         TCGA-B4-5838         TCGA-B4-5843 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B4-5844         TCGA-CZ-4854         TCGA-CZ-4856 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CZ-4858         TCGA-CZ-4860         TCGA-CZ-4861 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CZ-4862         TCGA-CZ-5456         TCGA-CZ-5457 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CZ-5465         TCGA-CZ-5469         TCGA-DV-5565 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DV-5566         TCGA-DV-5567         TCGA-DV-5568 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DV-5569         TCGA-DV-5573         TCGA-DV-5574 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DV-5575         TCGA-DV-5576         TCGA-EU-5904 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EU-5905         TCGA-EU-5907         TCGA-G6-A8L6 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G6-A8L7 
"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                        43   449
D67V10, multiclass
                           clus
vv                          16P LOSS MUTATED 16P LOSS WILD-TYPE
  ASIAN                                    0                  8
  BLACK OR AFRICAN AMERICAN                1                 43
  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  26 334
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      0    4
  16P LOSS WILD-TYPE   26  334
                        clus
vv                       16P LOSS MUTATED 16P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 26
  NOT HISPANIC OR LATINO                4                334
[1] 2 2
[1] FALSE

Clustering(68) Variable = 16Q LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                  0   1
  16Q LOSS MUTATED     8   0
  16Q LOSS WILD-TYPE 339  24
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 8                363 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 0                 24 
$`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 TCGA-MM-A564 
        2439          607 

$`16Q LOSS WILD-TYPE`
TCGA-6D-AA2E TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3319 
         267         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-B0-5108 TCGA-B0-5110 TCGA-B0-5113 
         616           18          183          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-B0-5690 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-B0-5703 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-A54E TCGA-B8-A54F 
         434         1046          435          830          909          519 
TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ 
          53          256          150          528          110           24 
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-5470 TCGA-CZ-5984 TCGA-CZ-5985 
        1446          685           59          386         2067         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         2016         1729          551 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-GK-A6C7 
         119          206          127          305         1727           61 
TCGA-MM-A563 TCGA-MM-A84U TCGA-MW-A4EC 
         591          337          330 

  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 
               886               1307 
[1] "15.0 - 2439.0 (886.0)" "3.0 - 3668.0 (1307.0)"
[1] "hr="     "9200000"
D68V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  16Q LOSS MUTATED         4        3         3        4
  16Q LOSS WILD-TYPE     249       54       123       76
D68V3, multiclass
           clus
vv          16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  STAGE I                  4                249
  STAGE II                 3                 54
  STAGE III                3                123
  STAGE IV                 4                 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
  16Q LOSS MUTATED     4   3   4   3
  16Q LOSS WILD-TYPE 254  66 174   8
D68V4, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  T1                4                254
  T2                3                 66
  T3                4                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"
D68V5, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED     7   1
  16Q LOSS WILD-TYPE 224  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      7    1
  16Q LOSS WILD-TYPE  224   17
   clus
vv  16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  0                7                224
  1                1                 17
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  16Q LOSS MUTATED    11   2   1
  16Q LOSS WILD-TYPE 406  76  18
D68V6, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  M0               11                406
  M1                2                 76
  MX                1                 18
[1] 3 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  10
  16Q LOSS WILD-TYPE 182 320
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      4   10
  16Q LOSS WILD-TYPE  182  320
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE                4                182
  MALE                 10                320
[1] 2 2
[1] FALSE
D68V8, continuous
[1] "Remove cluster labels:" "16Q LOSS MUTATED"      
clus
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 1                 40 
        TCGA-A3-A6NJ         TCGA-A3-A6NL         TCGA-A3-A8CQ 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AK-3426         TCGA-AK-3430         TCGA-B0-4838 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B2-5639         TCGA-B4-5377         TCGA-B4-5378 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B4-5832         TCGA-B4-5834         TCGA-B4-5835 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B4-5836         TCGA-B4-5838         TCGA-B4-5843 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B4-5844         TCGA-CZ-4854         TCGA-CZ-4856 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CZ-4858         TCGA-CZ-4860         TCGA-CZ-4861 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CZ-4862         TCGA-CZ-5456         TCGA-CZ-5457 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CZ-5465         TCGA-CZ-5469         TCGA-DV-5565 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DV-5566         TCGA-DV-5567         TCGA-DV-5568 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DV-5569         TCGA-DV-5573         TCGA-DV-5574 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DV-5575         TCGA-DV-5576         TCGA-EU-5904 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EU-5905         TCGA-EU-5907         TCGA-G6-A8L6 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G6-A8L7 
"16Q LOSS WILD-TYPE" 
D68V9, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16Q LOSS MUTATED       0                         2    12
  16Q LOSS WILD-TYPE     8                        42   445
D68V10, multiclass
                           clus
vv                          16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  ASIAN                                    0                  8
  BLACK OR AFRICAN AMERICAN                2                 42
  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   9
  16Q LOSS WILD-TYPE  26 329
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      0    9
  16Q LOSS WILD-TYPE   26  329
                        clus
vv                       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 26
  NOT HISPANIC OR LATINO                9                329
[1] 2 2
[1] FALSE

Clustering(69) Variable = 17P LOSS MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                  0   1
  17P LOSS MUTATED    29   5
  17P LOSS WILD-TYPE 318  19
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                34                337 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 5                 19 
$`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 TCGA-G6-A8L7 
        1446           59         1329         1727 

$`17P LOSS WILD-TYPE`
TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3317 
         267         1120         1436           16          735         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-A3-3376 
         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-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-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 
        1397          874         1168          951          853           43 
TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4718 TCGA-B0-4819 TCGA-B0-5097 TCGA-B0-5108 
          26           96          616          183          665          911 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 
        1092          359          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-B0-5696 TCGA-B0-5697 TCGA-B0-5698 
        1487         3076         1420         1727         1835         2583 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 
        2741         1732         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-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 
          38          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-A54E TCGA-B8-A54F 
          15         1046          435          830          909          519 
TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ 
          53          256          150          528          110           24 
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-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-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-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-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-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 
         749         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-4873 TCGA-CJ-4874 TCGA-CJ-4875 
         646         2554         1498         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-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 
        2430          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-4859 TCGA-CZ-4862 TCGA-CZ-4863 
         774         1404           18         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-5466 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
         685          386         2439         2067         1997          373 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 
         693         1905         1398         1470          370          355 
TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
        1130         2016         1729          551          119          206 
TCGA-EU-5907 TCGA-G6-A8L6 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U 
         127          305           61          591          607          337 
TCGA-MW-A4EC 
         330 

  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 
            1227.5             1291.0 
[1] "13.0 - 2575.0 (1227.5)" "3.0 - 3668.0 (1291.0)" 
[1] "hr=" "2.9"
D69V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  17P LOSS MUTATED        17        6        11       11
  17P LOSS WILD-TYPE     236       51       115       69
D69V3, multiclass
           clus
vv          17P LOSS MUTATED 17P LOSS WILD-TYPE
  STAGE I                 17                236
  STAGE II                 6                 51
  STAGE III               11                115
  STAGE IV                11                 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
  17P LOSS MUTATED    17   7  19   2
  17P LOSS WILD-TYPE 241  62 159   9
D69V4, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  T1               17                241
  T2                7                 62
  T3               19                159
  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    19   0
  17P LOSS WILD-TYPE 212  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     19    0
  17P LOSS WILD-TYPE  212   18
   clus
vv  17P LOSS MUTATED 17P LOSS WILD-TYPE
  0               19                212
  1                0                 18
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  17P LOSS MUTATED    32  12   1
  17P LOSS WILD-TYPE 385  66  18
D69V6, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  M0               32                385
  M1               12                 66
  MX                1                 18
[1] 3 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    12  33
  17P LOSS WILD-TYPE 174 297
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     12   33
  17P LOSS WILD-TYPE  174  297
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE               12                174
  MALE                 33                297
[1] 2 2
[1] FALSE
D69V8, continuous
D69V9, continuous
[1] "Remove cluster labels:" "17P LOSS MUTATED"      
clus
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 1                 11 
        TCGA-A3-A8CQ         TCGA-B2-A4SR         TCGA-B8-4621 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-B8-5158         TCGA-B8-5164         TCGA-B8-A54E 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-B8-A54F         TCGA-B8-A54G         TCGA-B8-A8YJ 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-G6-A5PC         TCGA-MM-A563 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17P LOSS MUTATED       0                         4    40
  17P LOSS WILD-TYPE     8                        40   417
D69V10, multiclass
                           clus
vv                          17P LOSS MUTATED 17P LOSS WILD-TYPE
  ASIAN                                    0                  8
  BLACK OR AFRICAN AMERICAN                4                 40
  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  30
  17P LOSS WILD-TYPE  25 308
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      1   30
  17P LOSS WILD-TYPE   25  308
                        clus
vv                       17P LOSS MUTATED 17P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 25
  NOT HISPANIC OR LATINO               30                308
[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 326  22
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                23                348 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 2                 22 
$`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-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3317 
         267         1120         1436           16          735         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-A3-3376 
         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-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3450 
        1853         2087         1423         1471         1280         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-B0-4710 TCGA-B0-4718 TCGA-B0-4813 
         853           43           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-B0-5119 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-B0-5702 
        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-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
        2722         1865         2963         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-A54E TCGA-B8-A54F TCGA-B8-A54G 
        1046          435          830          909          519           53 
TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 
         256          150          528          110           24         3377 
TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4167 
        2881         2746         3074         2839         3037         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-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-4801 TCGA-BP-4803 TCGA-BP-4804 
        1854         1489          620         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-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-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-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-4872 TCGA-CJ-4873 TCGA-CJ-4874 
         646         2554         1498         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-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-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-5461 
          25         1712         1683         1732         1683          330 
TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5470 TCGA-CZ-5982 
         662         1740          685           59          386         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         2016 
TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A8L6 
        1729          551          119          206          127          305 
TCGA-G6-A8L7 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC 
        1727           61          591          607          337          330 

  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 
            1238.0             1285.5 
[1] "13.0 - 2575.0 (1238.0)" "3.0 - 3668.0 (1285.5)" 
[1] "hr=" "1.4"
D70V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  17Q LOSS MUTATED        10        4         7        7
  17Q LOSS WILD-TYPE     243       53       119       73
D70V3, multiclass
           clus
vv          17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  STAGE I                 10                243
  STAGE II                 4                 53
  STAGE III                7                119
  STAGE IV                 7                 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
  17Q LOSS MUTATED    10   5  12   1
  17Q LOSS WILD-TYPE 248  64 166  10
D70V4, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  T1               10                248
  T2                5                 64
  T3               12                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"
D70V5, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    10   0
  17Q LOSS WILD-TYPE 221  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     10    0
  17Q LOSS WILD-TYPE  221   18
   clus
vv  17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  0               10                221
  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  19
D70V6, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  M0               21                396
  M1                7                 71
  MX                0                 19
[1] 3 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 179 309
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      7   21
  17Q LOSS WILD-TYPE  179  309
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE                7                179
  MALE                 21                309
[1] 2 2
[1] FALSE
D70V8, continuous
[1] "Remove cluster labels:" "17Q LOSS MUTATED"      
clus
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 1                 40 
        TCGA-A3-A6NJ         TCGA-A3-A6NL         TCGA-A3-A8CQ 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-AK-3426         TCGA-AK-3430         TCGA-B0-4838 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-B2-5639         TCGA-B4-5377         TCGA-B4-5378 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-B4-5832         TCGA-B4-5834         TCGA-B4-5835 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-B4-5836         TCGA-B4-5838         TCGA-B4-5843 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-B4-5844         TCGA-CZ-4854         TCGA-CZ-4856 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CZ-4858         TCGA-CZ-4860         TCGA-CZ-4861 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CZ-4862         TCGA-CZ-5456         TCGA-CZ-5457 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CZ-5469         TCGA-CZ-5982         TCGA-DV-5565 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DV-5566         TCGA-DV-5567         TCGA-DV-5568 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DV-5569         TCGA-DV-5573         TCGA-DV-5574 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DV-5575         TCGA-DV-5576         TCGA-EU-5904 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EU-5905         TCGA-EU-5907         TCGA-G6-A8L6 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-G6-A8L7 
"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                        42   432
D70V10, multiclass
                           clus
vv                          17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  ASIAN                                    0                  8
  BLACK OR AFRICAN AMERICAN                2                 42
  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  25 320
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      1   18
  17Q LOSS WILD-TYPE   25  320
                        clus
vv                       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 25
  NOT HISPANIC OR LATINO               18                320
[1] 2 2
[1] FALSE

Clustering(71) Variable = 18P LOSS MUTATION ANALYSIS
D71V1, survival
                    sevent
clus2                  0   1
  18P LOSS MUTATED    51   7
  18P LOSS WILD-TYPE 296  17
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                58                313 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 7                 17 
$`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 TCGA-MM-A84U 
        2067         1997          693          337 

$`18P LOSS WILD-TYPE`
TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 
         267         1120         1436           16          735         1493 
TCGA-A3-3317 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 
        1491         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-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
         910         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-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-A8CQ TCGA-AK-3427 
         567          574          861         1993            3         2566 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3443 
        2223         2017         1853         2192         2087         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-B0-4706 TCGA-B0-4710 TCGA-B0-4718 TCGA-B0-4813 TCGA-B0-5108 
          43           26           96          616           18          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-B2-4099 TCGA-B2-4101 TCGA-B2-4102 
        2963          992         1092          374          648          952 
TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 
         358          315          417          507          291          175 
TCGA-B4-5834 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 
          38          141          166           11            7          511 
TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4622 
         826          838          762          750          523          700 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
         636          722           36           26          737          522 
TCGA-B8-5546 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E 
         505           15         1046          435          830          909 
TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 
         519           53          256          150          528          110 
TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
          24         3377         2881         2746         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-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-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 
        2208         2372         2361         2184         1462          400 
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-4804 TCGA-BP-4807 
        1854         1489          620         1124         1459          211 
TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 
        2660         2172         1935         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-4982 TCGA-BP-4983 TCGA-BP-4986 
        1384         1433         1632         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-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-5182 
        1071         2412         2257          293         2263         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-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-4872 TCGA-CJ-4874 
         646         2554         1498         2423         1435         2283 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
        2353         1955         2186         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-CJ-6032 
        1883         1889         2231         2038         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-4864 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
        1787         1843         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-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5986 
        1740         1446          685          386         2439          373 
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         2016         1729          551          119          206 
TCGA-EU-5907 TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 
         127          305         1727           61          591          607 
TCGA-MW-A4EC 
         330 

  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 
               959               1355 
[1] "7.0 - 3343.0 (959.0)"  "3.0 - 3668.0 (1355.0)"
[1] "hr=" "2.5"
D71V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  18P LOSS MUTATED        30        7        33       22
  18P LOSS WILD-TYPE     223       50        93       58
D71V3, multiclass
           clus
vv          18P LOSS MUTATED 18P LOSS WILD-TYPE
  STAGE I                 30                223
  STAGE II                 7                 50
  STAGE III               33                 93
  STAGE IV                22                 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
  18P LOSS MUTATED    32   9  46   5
  18P LOSS WILD-TYPE 226  60 132   6
D71V4, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  T1               32                226
  T2                9                 60
  T3               46                132
  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 189  15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     42    3
  18P LOSS WILD-TYPE  189   15
   clus
vv  18P LOSS MUTATED 18P LOSS WILD-TYPE
  0               42                189
  1                3                 15
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  18P LOSS MUTATED    71  20   1
  18P LOSS WILD-TYPE 346  58  18
D71V6, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  M0               71                346
  M1               20                 58
  MX                1                 18
[1] 3 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    27  65
  18P LOSS WILD-TYPE 159 265
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     27   65
  18P LOSS WILD-TYPE  159  265
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE               27                159
  MALE                 65                265
[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                 11 
        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-A54E         TCGA-B8-A54F 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-B8-A54G         TCGA-B8-A8YJ         TCGA-G6-A5PC 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G6-A8L7         TCGA-MM-A563 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18P LOSS MUTATED       2                         5    85
  18P LOSS WILD-TYPE     6                        39   372
D71V10, multiclass
                           clus
vv                          18P LOSS MUTATED 18P LOSS WILD-TYPE
  ASIAN                                    2                  6
  BLACK OR AFRICAN AMERICAN                5                 39
  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  61
  18P LOSS WILD-TYPE  25 277
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      1   61
  18P LOSS WILD-TYPE   25  277
                        clus
vv                       18P LOSS MUTATED 18P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 25
  NOT HISPANIC OR LATINO               61                277
[1] 2 2
[1] FALSE

Clustering(72) Variable = 18Q LOSS MUTATION ANALYSIS
D72V1, survival
                    sevent
clus2                  0   1
  18Q LOSS MUTATED    54   9
  18Q LOSS WILD-TYPE 293  15
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                63                308 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 9                 15 
$`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 TCGA-MM-A84U 
        1997          693          337 

$`18Q LOSS WILD-TYPE`
TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3316 TCGA-A3-3317 
         267         1120         1436           16         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-B0-5399 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-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 
        1092          374          648          952          358          315 
TCGA-B2-5639 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5836 
         417          507          291          175           38          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-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
         762          750          523          700          636          722 
TCGA-B8-5162 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5551 
          36           26          737          522          505           15 
TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G 
        1046          435          830          909          519           53 
TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 
         256          150          528          110           24         3377 
TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4167 
        2881         2746         3074         2839         3037         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-4758 TCGA-BP-4759 
        1666         1367          372          970         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-4782 TCGA-BP-4784 TCGA-BP-4789 
        1843          411         1731          354         1854         1489 
TCGA-BP-4795 TCGA-BP-4801 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 
         620         1124         1459          211         2660         2172 
TCGA-BP-4961 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 
        1935         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-4982 TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4989 
        1632         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-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-5180 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
        2257          293         2263         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-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4882 
        2423         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-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-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5587 
        2038         1906         2799         2489         2609         2226 
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-4856 TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4864 TCGA-CZ-5451 TCGA-CZ-5452 
          18         1787         1843         2830         1929         1789 
TCGA-CZ-5453 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 
          25         1683         1732         1683         1430          330 
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-5986 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 
         373         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         2016         1729          551          119 
TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-GK-A6C7 TCGA-MM-A563 
         206          127          305         1727           61          591 
TCGA-MM-A564 TCGA-MW-A4EC 
         607          330 

  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 
               967               1361 
[1] "7.0 - 3343.0 (967.0)"  "3.0 - 3668.0 (1361.0)"
[1] "hr=" "3.3"
D72V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  18Q LOSS MUTATED        34        8        30       22
  18Q LOSS WILD-TYPE     219       49        96       58
D72V3, multiclass
           clus
vv          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  STAGE I                 34                219
  STAGE II                 8                 49
  STAGE III               30                 96
  STAGE IV                22                 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
  18Q LOSS MUTATED    36  10  43   5
  18Q LOSS WILD-TYPE 222  59 135   6
D72V4, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T1               36                222
  T2               10                 59
  T3               43                135
  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 186  15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     45    3
  18Q LOSS WILD-TYPE  186   15
   clus
vv  18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  0               45                186
  1                3                 15
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  18Q LOSS MUTATED    73  20   1
  18Q LOSS WILD-TYPE 344  58  18
D72V6, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  M0               73                344
  M1               20                 58
  MX                1                 18
[1] 3 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    27  67
  18Q LOSS WILD-TYPE 159 263
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     27   67
  18Q LOSS WILD-TYPE  159  263
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE               27                159
  MALE                 67                263
[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                 11 
        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-A54E         TCGA-B8-A54F 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-B8-A54G         TCGA-B8-A8YJ         TCGA-G6-A5PC 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G6-A8L7         TCGA-MM-A563 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18Q LOSS MUTATED       2                         5    87
  18Q LOSS WILD-TYPE     6                        39   370
D72V10, multiclass
                           clus
vv                          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  ASIAN                                    2                  6
  BLACK OR AFRICAN AMERICAN                5                 39
  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  62
  18Q LOSS WILD-TYPE  24 276
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      2   62
  18Q LOSS WILD-TYPE   24  276
                        clus
vv                       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                 24
  NOT HISPANIC OR LATINO               62                276
[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 345  24
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 2                369 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 0                 24 
$`19P LOSS MUTATED`
TCGA-A3-3319 TCGA-AK-3425 
        1130         3343 

$`19P LOSS WILD-TYPE`
TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 
         267         1120         1436           16          735         1493 
TCGA-A3-3317 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 
        1491         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-3427 TCGA-AK-3428 TCGA-AK-3429 
        1993          617            3         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-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I 
         830          909          519           53          256          150 
TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 
         528          110           24         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-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-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-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-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
          59          386         2439         2067         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-5905 
         355         1130         2016         1729          551          119 
TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-GK-A6C7 TCGA-MM-A563 
         206          127          305         1727           61          591 
TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC 
         607          337          330 

  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             1280.0 
[1] "1130.0 - 3343.0 (2236.5)" "3.0 - 3668.0 (1280.0)"   
[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     251       57       121       76
D73V3, multiclass
           clus
vv          19P LOSS MUTATED 19P LOSS WILD-TYPE
  STAGE I                  2                251
  STAGE II                 0                 57
  STAGE III                5                121
  STAGE IV                 4                 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
  19P LOSS MUTATED     2   1   5   3
  19P LOSS WILD-TYPE 256  68 173   8
D73V4, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  T1                2                256
  T2                1                 68
  T3                5                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"
D73V5, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     6   0
  19P LOSS WILD-TYPE 225  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      6    0
  19P LOSS WILD-TYPE  225   18
   clus
vv  19P LOSS MUTATED 19P LOSS WILD-TYPE
  0                6                225
  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  19
D73V6, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  M0                8                409
  M1                3                 75
  MX                0                 19
[1] 3 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 183 322
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      3    8
  19P LOSS WILD-TYPE  183  322
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE                3                183
  MALE                  8                322
[1] 2 2
[1] FALSE
D73V8, continuous
[1] "Remove cluster labels:" "19P LOSS MUTATED"      
clus
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 1                 40 
        TCGA-A3-A6NJ         TCGA-A3-A6NL         TCGA-A3-A8CQ 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AK-3426         TCGA-AK-3430         TCGA-B0-4838 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B2-5639         TCGA-B4-5377         TCGA-B4-5378 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B4-5832         TCGA-B4-5834         TCGA-B4-5835 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B4-5836         TCGA-B4-5838         TCGA-B4-5843 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B4-5844         TCGA-CZ-4854         TCGA-CZ-4856 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CZ-4858         TCGA-CZ-4861         TCGA-CZ-4862 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CZ-5456         TCGA-CZ-5457         TCGA-CZ-5465 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CZ-5469         TCGA-CZ-5982         TCGA-DV-5565 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DV-5566         TCGA-DV-5567         TCGA-DV-5568 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DV-5569         TCGA-DV-5573         TCGA-DV-5574 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DV-5575         TCGA-DV-5576         TCGA-EU-5904 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EU-5905         TCGA-EU-5907         TCGA-G6-A8L6 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G6-A8L7 
"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                        44   447
D73V10, multiclass
                           clus
vv                          19P LOSS MUTATED 19P LOSS WILD-TYPE
  ASIAN                                    1                  7
  BLACK OR AFRICAN AMERICAN                0                 44
  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  26 332
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      0    6
  19P LOSS WILD-TYPE   26  332
                        clus
vv                       19P LOSS MUTATED 19P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 26
  NOT HISPANIC OR LATINO                6                332
[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 346  24
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 1                370 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 0                 24 
$`19Q LOSS MUTATED`
TCGA-A3-3319 
        1130 

$`19Q LOSS WILD-TYPE`
TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 
         267         1120         1436           16          735         1493 
TCGA-A3-3317 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 
        1491         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-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H 
         435          830          909          519           53          256 
TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4160 
         150          528          110           24         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-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-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-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
         685           59          386         2439         2067         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         2016         1729          551 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-GK-A6C7 
         119          206          127          305         1727           61 
TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC 
         591          607          337          330 

  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 
            1130.0             1285.5 
[1] "1130.0 - 1130.0 (1130.0)" "3.0 - 3668.0 (1285.5)"   
[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     252       57       125       78
D74V3, multiclass
           clus
vv          19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  STAGE I                  1                252
  STAGE II                 0                 57
  STAGE III                1                125
  STAGE IV                 2                 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
  19Q LOSS MUTATED     1   0   1   2
  19Q LOSS WILD-TYPE 257  69 177   9
D74V4, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  T1                1                257
  T2                0                 69
  T3                1                177
  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 230  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      1    0
  19Q LOSS WILD-TYPE  230   18
   clus
vv  19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  0                1                230
  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  19
D74V6, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  M0                2                415
  M1                2                 76
  MX                0                 19
[1] 3 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 185 327
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      1    3
  19Q LOSS WILD-TYPE  185  327
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE                1                185
  MALE                  3                327
[1] 2 2
[1] FALSE
D74V8, continuous
[1] "Remove cluster labels:" "19Q LOSS MUTATED"      
clus
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 1                 40 
        TCGA-A3-A6NJ         TCGA-A3-A6NL         TCGA-A3-A8CQ 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AK-3426         TCGA-AK-3430         TCGA-B0-4838 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-B2-5639         TCGA-B4-5377         TCGA-B4-5378 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-B4-5832         TCGA-B4-5834         TCGA-B4-5835 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-B4-5836         TCGA-B4-5838         TCGA-B4-5843 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-B4-5844         TCGA-CZ-4854         TCGA-CZ-4856 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CZ-4858         TCGA-CZ-4861         TCGA-CZ-4862 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CZ-5456         TCGA-CZ-5457         TCGA-CZ-5465 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-CZ-5469         TCGA-CZ-5982         TCGA-DV-5565 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DV-5566         TCGA-DV-5567         TCGA-DV-5568 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DV-5569         TCGA-DV-5573         TCGA-DV-5574 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DV-5575         TCGA-DV-5576         TCGA-EU-5904 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EU-5905         TCGA-EU-5907         TCGA-G6-A8L6 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G6-A8L7 
"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                        44   453
D74V10, multiclass
                           clus
vv                          19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  ASIAN                                    0                  8
  BLACK OR AFRICAN AMERICAN                0                 44
  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  26 337
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      0    1
  19Q LOSS WILD-TYPE   26  337
                        clus
vv                       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 26
  NOT HISPANIC OR LATINO                1                337
[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 342  24
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 5                366 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 0                 24 
$`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-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 
         267         1120         1436           16          735         1493 
TCGA-A3-3317 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 
        1491         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-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H 
         435          830          909          519           53          256 
TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4160 
         150          528          110           24         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-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 
        1935         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-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 
         932         1266         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-5183 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 
        2263         1495         1291         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-5470 TCGA-CZ-5982 
        1740         1446          685           59          386         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         2016 
TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A8L6 
        1729          551          119          206          127          305 
TCGA-G6-A8L7 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC 
        1727           61          591          607          337          330 

  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               1299 
[1] "563.0 - 1785.0 (1133.0)" "3.0 - 3668.0 (1299.0)"  
[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     249       56       125       78
D75V3, multiclass
           clus
vv          20P LOSS MUTATED 20P LOSS WILD-TYPE
  STAGE I                  4                249
  STAGE II                 1                 56
  STAGE III                1                125
  STAGE IV                 2                 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
  20P LOSS MUTATED     4   2   2   0
  20P LOSS WILD-TYPE 254  67 176  11
D75V4, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  T1                4                254
  T2                2                 67
  T3                2                176
  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 228  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      3    0
  20P LOSS WILD-TYPE  228   18
   clus
vv  20P LOSS MUTATED 20P LOSS WILD-TYPE
  0                3                228
  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  19
D75V6, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  M0                6                411
  M1                2                 76
  MX                0                 19
[1] 3 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 183 325
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      3    5
  20P LOSS WILD-TYPE  183  325
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE                3                183
  MALE                  5                325
[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                        44   450
D75V10, multiclass
                           clus
vv                          20P LOSS MUTATED 20P LOSS WILD-TYPE
  ASIAN                                    1                  7
  BLACK OR AFRICAN AMERICAN                0                 44
  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  25 335
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      1    3
  20P LOSS WILD-TYPE   25  335
                        clus
vv                       20P LOSS MUTATED 20P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 25
  NOT HISPANIC OR LATINO                3                335
[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 345  24
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 2                369 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 0                 24 
$`20Q LOSS MUTATED`
TCGA-BP-4962 TCGA-BP-5000 
        1785          563 

$`20Q LOSS WILD-TYPE`
TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 
         267         1120         1436           16          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-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 
        1610         1385          910         2688         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-A3-3378 TCGA-A3-3380 TCGA-A3-3382 
        1621         1314         1070          630          567          574 
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-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 
        2223         2017          480         1853         2192         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-B0-4710 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-A54E TCGA-B8-A54F TCGA-B8-A54G 
        1046          435          830          909          519           53 
TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 
         256          150          528          110           24         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-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-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-5001 TCGA-BP-5004 TCGA-BP-5006 
        1371          932         1266         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-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-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
          59          386         2439         2067         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-5905 
         355         1130         2016         1729          551          119 
TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-GK-A6C7 TCGA-MM-A563 
         206          127          305         1727           61          591 
TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC 
         607          337          330 

  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               1280 
[1] "563.0 - 1785.0 (1174.0)" "3.0 - 3668.0 (1280.0)"  
[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     252       56       126       79
D76V3, multiclass
           clus
vv          20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  STAGE I                  1                252
  STAGE II                 1                 56
  STAGE III                0                126
  STAGE IV                 1                 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
  20Q LOSS MUTATED     1   2   0   0
  20Q LOSS WILD-TYPE 257  67 178  11
D76V4, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  T1                1                257
  T2                2                 67
  T3                0                178
  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 231  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      0    0
  20Q LOSS WILD-TYPE  231   18
                    vv
clus                  M0  M1  MX
  20Q LOSS MUTATED     2   1   0
  20Q LOSS WILD-TYPE 415  77  19
D76V6, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  M0                2                415
  M1                1                 77
  MX                0                 19
[1] 3 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 185 328
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      1    2
  20Q LOSS WILD-TYPE  185  328
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  FEMALE                1                185
  MALE                  2                328
[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                        44   454
D76V10, multiclass
                           clus
vv                          20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  ASIAN                                    0                  8
  BLACK OR AFRICAN AMERICAN                0                 44
  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  25 338
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      1    0
  20Q LOSS WILD-TYPE   25  338
                        clus
vv                       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 25
  NOT HISPANIC OR LATINO                0                338
[1] 2 2
[1] FALSE

Clustering(77) Variable = 21Q LOSS MUTATION ANALYSIS
D77V1, survival
                    sevent
clus2                  0   1
  21Q LOSS MUTATED    36   3
  21Q LOSS WILD-TYPE 311  21
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                39                332 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 3                 21 
$`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 TCGA-MM-A563 
        1446          685          591 

$`21Q LOSS WILD-TYPE`
TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 
         267         1120         1436           16          735         1493 
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-3428 TCGA-AK-3429 TCGA-AK-3431 
         617            3         3343         2223         2017         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-B0-4718 TCGA-B0-4813 
         951          853           43           26          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-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
         657           59          493          554          652         1132 
TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5696 TCGA-B0-5698 
        2408         3431         1487         3076         1727         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-B4-5843 
         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-B8-4620 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-A54D TCGA-B8-A54E TCGA-B8-A54F 
         434           15         1046          830          909          519 
TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ 
          53          256          150          528          110           24 
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-4174 TCGA-BP-4176 TCGA-BP-4177 
          13         2718          701         1879         1955         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-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-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-4804 
        1854         1489          620         1107         1124         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-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-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-5175 
         840         1140         1071         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-5199 TCGA-BP-5200 
         714          408          749         1018         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-4902 
        2085         1521          750          841         1528         1520 
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-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-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
        1928         2830         1868         1929         1789           25 
TCGA-CZ-5456 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5464 
        1712         1683         1430          330          662         1740 
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-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         2016         1729          551          119 
TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-GK-A6C7 TCGA-MM-A564 
         206          127          305         1727           61          607 
TCGA-MM-A84U TCGA-MW-A4EC 
         337          330 

  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 
              1413               1210 
[1] "96.0 - 2964.0 (1413.0)" "3.0 - 3668.0 (1210.0)" 
[1] "hr=" "1.3"
D77V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  21Q LOSS MUTATED        21        4        18       11
  21Q LOSS WILD-TYPE     232       53       108       69
D77V3, multiclass
           clus
vv          21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  STAGE I                 21                232
  STAGE II                 4                 53
  STAGE III               18                108
  STAGE IV                11                 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
  21Q LOSS MUTATED    20   5  24   5
  21Q LOSS WILD-TYPE 238  64 154   6
D77V4, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  T1               20                238
  T2                5                 64
  T3               24                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 210  14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     21    4
  21Q LOSS WILD-TYPE  210   14
   clus
vv  21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  0               21                210
  1                4                 14
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  21Q LOSS MUTATED    45   8   1
  21Q LOSS WILD-TYPE 372  70  18
D77V6, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  M0               45                372
  M1                8                 70
  MX                1                 18
[1] 3 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  37
  21Q LOSS WILD-TYPE 169 293
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     17   37
  21Q LOSS WILD-TYPE  169  293
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE               17                169
  MALE                 37                293
[1] 2 2
[1] FALSE
D77V8, continuous
D77V9, continuous
[1] "Remove cluster labels:" "21Q LOSS MUTATED"      
clus
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 1                 11 
        TCGA-A3-A8CQ         TCGA-B2-A4SR         TCGA-B8-4621 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-B8-5158         TCGA-B8-5164         TCGA-B8-A54E 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-B8-A54F         TCGA-B8-A54G         TCGA-B8-A8YJ 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-G6-A5PC         TCGA-G6-A8L7 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  21Q LOSS MUTATED       1                         3    47
  21Q LOSS WILD-TYPE     7                        41   410
D77V10, multiclass
                           clus
vv                          21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  ASIAN                                    1                  7
  BLACK OR AFRICAN AMERICAN                3                 41
  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  35
  21Q LOSS WILD-TYPE  24 303
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      2   35
  21Q LOSS WILD-TYPE   24  303
                        clus
vv                       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                 24
  NOT HISPANIC OR LATINO               35                303
[1] 2 2
[1] FALSE

Clustering(78) Variable = 22Q LOSS MUTATION ANALYSIS
D78V1, survival
                    sevent
clus2                  0   1
  22Q LOSS MUTATED    18   4
  22Q LOSS WILD-TYPE 329  20
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                22                349 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 4                 20 
$`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-B8-A54E TCGA-BP-4768 TCGA-BP-4960 TCGA-BP-4967 TCGA-BP-4986 TCGA-BP-4992 
         909          400         2172          205          785          501 
TCGA-BP-5175 TCGA-BP-5196 TCGA-CJ-4640 TCGA-CJ-4897 TCGA-CJ-4901 TCGA-CZ-4866 
         932         1018         1998         1808         1450         1868 
TCGA-CZ-5457 TCGA-CZ-5461 TCGA-CZ-5468 TCGA-DV-5566 
        1683          330           59         1398 

$`22Q LOSS WILD-TYPE`
TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 
         267         1120         1436           16          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-A3-3349 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-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 
        1481          874         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-B0-5702 
        1420         1727         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-B2-4099 
        2722         1865         2963          992         1092          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-B8-A8YJ TCGA-BP-4158 TCGA-BP-4160 
         150          528          110           24         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-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-4961 TCGA-BP-4962 
         204         1459          211         2660         1935         1785 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 
        1834         1862         1871         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-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4993 
        1014         1413         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-5177 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 
        2257          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-5198 TCGA-BP-5199 
         967          714          408          749          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-4642 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
        2308         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-4899 
        1946         2085         1521          750          841         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-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-5465 TCGA-CZ-5466 
        1683         1430          662         1740         1446          685 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5988 
         386         2439         2067         1997          373          693 
TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 
        1905         1329         1470          370          355         1130 
TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
        2016         1729          551          119          206          127 
TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U 
         305         1727           61          591          607          337 
TCGA-MW-A4EC 
         330 

  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             1291.0 
[1] "51.0 - 2172.0 (1080.5)" "3.0 - 3668.0 (1291.0)" 
[1] "hr=" "3.6"
D78V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  22Q LOSS MUTATED        11        4        14       10
  22Q LOSS WILD-TYPE     242       53       112       70
D78V3, multiclass
           clus
vv          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  STAGE I                 11                242
  STAGE II                 4                 53
  STAGE III               14                112
  STAGE IV                10                 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
  22Q LOSS MUTATED    14   6  19   0
  22Q LOSS WILD-TYPE 244  63 159  11
D78V4, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T1               14                244
  T2                6                 63
  T3               19                159
  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 215  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     16    1
  22Q LOSS WILD-TYPE  215   17
   clus
vv  22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  0               16                215
  1                1                 17
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  22Q LOSS MUTATED    28  10   1
  22Q LOSS WILD-TYPE 389  68  18
D78V6, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  M0               28                389
  M1               10                 68
  MX                1                 18
[1] 3 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    13  26
  22Q LOSS WILD-TYPE 173 304
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     13   26
  22Q LOSS WILD-TYPE  173  304
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE               13                173
  MALE                 26                304
[1] 2 2
[1] FALSE
D78V8, continuous
D78V9, continuous
[1] "Remove cluster labels:" "22Q LOSS MUTATED"      
clus
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 1                 11 
        TCGA-A3-A8CQ         TCGA-B2-A4SR         TCGA-B8-4621 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-B8-5158         TCGA-B8-5164         TCGA-B8-A54F 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-B8-A54G         TCGA-B8-A8YJ         TCGA-G6-A5PC 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G6-A8L7         TCGA-MM-A563 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  22Q LOSS MUTATED       0                         4    35
  22Q LOSS WILD-TYPE     8                        40   422
D78V10, multiclass
                           clus
vv                          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  ASIAN                                    0                  8
  BLACK OR AFRICAN AMERICAN                4                 40
  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     6  23
  22Q LOSS WILD-TYPE  20 315
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      6   23
  22Q LOSS WILD-TYPE   20  315
                        clus
vv                       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    6                 20
  NOT HISPANIC OR LATINO               23                315
[1] 2 2
[1] FALSE

Clustering(79) Variable = XQ LOSS MUTATION ANALYSIS
D79V1, survival
                   sevent
clus2                 0   1
  XQ LOSS MUTATED    29   4
  XQ LOSS WILD-TYPE 318  20
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               33               338 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                4                20 
$`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-EU-5907 TCGA-MM-A563 
        1997          127          591 

$`XQ LOSS WILD-TYPE`
TCGA-6D-AA2E TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3320 
         267         1436           16          735         1493         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-A3-3383 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-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3450 
        2192         2087         2044         1423         1471         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-B0-4710 TCGA-B0-4718 TCGA-B0-4819 
         853           43           26           96          616          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-B0-5695 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-B0-5706 
        2583         2741         1732         1605         1203         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-B2-3924 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-B8-5162 
         523          777          788          700          636           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-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G 
          15         1046          435          909          519           53 
TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 
         256          150          528          110           24         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-4758 
        2859         1666         1367          372          970         2208 
TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 
        2372         2361         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-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
        1459          211         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-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5169 
         563         1177          840         1140         1071          193 
TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5177 TCGA-BP-5181 TCGA-BP-5182 
        2412         2257          932          293         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-5198 
        1011          967          714          408          749          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-4643 TCGA-CJ-4868 TCGA-CJ-4869 
        1924         2308         1998         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-4897 
        1952         1946         2085         1521          750         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-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-6093 TCGA-CZ-4853 
        2017         2378         2271         3222         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-5466 TCGA-CZ-5468 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 
        1740          685           59          386         2439         2067 
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         2016         1729          551 
TCGA-EU-5905 TCGA-EU-5906 TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-GK-A6C7 TCGA-MM-A564 
         119          206          305         1727           61          607 
TCGA-MM-A84U TCGA-MW-A4EC 
         337          330 

  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              1361 
[1] "18.0 - 3668.0 (1018.0)" "3.0 - 3431.0 (1361.0)" 
[1] "hr=" "2.3"
D79V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  XQ LOSS MUTATED        21        6        10        9
  XQ LOSS WILD-TYPE     232       51       116       71
D79V3, multiclass
           clus
vv          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  STAGE I                21               232
  STAGE II                6                51
  STAGE III              10               116
  STAGE IV                9                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
  XQ LOSS MUTATED    20   6  17   3
  XQ LOSS WILD-TYPE 238  63 161   8
D79V4, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T1              20               238
  T2               6                63
  T3              17               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 217  16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     14    2
  XQ LOSS WILD-TYPE  217   16
   clus
vv  XQ LOSS MUTATED XQ LOSS WILD-TYPE
  0              14               217
  1               2                16
[1] 2 2
[1] FALSE
                   vv
clus                 M0  M1  MX
  XQ LOSS MUTATED    37   7   2
  XQ LOSS WILD-TYPE 380  71  17
D79V6, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  M0              37               380
  M1               7                71
  MX               2                17
[1] 3 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  35
  XQ LOSS WILD-TYPE 175 295
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     11   35
  XQ LOSS WILD-TYPE  175  295
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE              11               175
  MALE                35               295
[1] 2 2
[1] FALSE
D79V8, continuous
[1] "Remove cluster labels:" "XQ LOSS MUTATED"       
clus
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                2                39 
       TCGA-A3-A6NJ        TCGA-A3-A6NL        TCGA-A3-A8CQ        TCGA-AK-3426 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AK-3430        TCGA-B0-4838        TCGA-B2-5639        TCGA-B4-5377 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B4-5378        TCGA-B4-5832        TCGA-B4-5834        TCGA-B4-5835 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B4-5836        TCGA-B4-5838        TCGA-B4-5843        TCGA-B4-5844 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CZ-4854        TCGA-CZ-4856        TCGA-CZ-4858        TCGA-CZ-4860 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CZ-4861        TCGA-CZ-4862        TCGA-CZ-5456        TCGA-CZ-5457 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-CZ-5469        TCGA-CZ-5982        TCGA-DV-5565        TCGA-DV-5566 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DV-5567        TCGA-DV-5568        TCGA-DV-5569        TCGA-DV-5573 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DV-5574        TCGA-DV-5575        TCGA-DV-5576        TCGA-EU-5904 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EU-5905        TCGA-G6-A8L6        TCGA-G6-A8L7 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
D79V9, continuous
[1] "Remove cluster labels:" "XQ LOSS MUTATED"       
clus
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                1                11 
       TCGA-A3-A8CQ        TCGA-B2-A4SR        TCGA-B8-4621        TCGA-B8-5158 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B8-5164        TCGA-B8-A54E        TCGA-B8-A54F        TCGA-B8-A54G 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B8-A8YJ        TCGA-G6-A5PC        TCGA-G6-A8L7 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XQ LOSS MUTATED       1                         4    39
  XQ LOSS WILD-TYPE     7                        40   418
D79V10, multiclass
                           clus
vv                          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  ASIAN                                   1                 7
  BLACK OR AFRICAN AMERICAN               4                40
  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  31
  XQ LOSS WILD-TYPE  26 307
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      0   31
  XQ LOSS WILD-TYPE   26  307
                        clus
vv                       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                26
  NOT HISPANIC OR LATINO              31               307
[1] 2 2
[1] FALSE
