[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"        "-oTPRAD-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/PRAD-TP/11541653/PRAD-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/PRAD-TP/11546322/transformed.cor.cli.txt"

nPatients in clinical file=368, in cluster file=492, common to both=363
[1] "Reduce the number of clustering variables from 80 to 75."
[1]  75 363
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               11               352 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               11               352 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               17               346 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               17               346 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                7               356 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                7               356 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                5               358 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                5               358 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               26               337 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               26               337 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               35               328 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               35               328 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                6               357 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                6               357 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                5               358 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                5               358 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               15               348 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               15               348 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                8               355 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                8               355 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                5               358 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                5               358 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                4               359 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                4               359 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               68               295 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               68               295 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               62               301 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               62               301 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               48               315 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               48               315 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               78               285 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               78               285 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               19               344 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               19               344 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               32               331 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               32               331 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 9                354 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 9                354 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                10                353 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                10                353 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                13                350 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                13                350 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                15                348 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                15                348 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 8                355 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 8                355 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 8                355 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 8                355 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 5                358 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 5                358 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 8                355 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 8                355 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 5                358 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 5                358 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                20                343 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                20                343 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 7                356 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 7                356 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 5                358 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 5                358 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 6                357 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 6                357 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                12                351 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                12                351 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 5                358 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 5                358 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 6                357 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 6                357 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 6                357 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 6                357 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                13                350 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                13                350 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                16                347 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                16                347 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                13                350 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                13                350 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                4               359 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                4               359 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               13               350 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               13               350 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                9               354 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                9               354 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               10               353 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               10               353 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                6               357 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                6               357 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                4               359 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                4               359 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               14               349 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               14               349 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               10               353 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               10               353 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                7               356 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                7               356 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               12               351 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               12               351 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               15               348 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               15               348 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               29               334 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               29               334 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              121               242 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              121               242 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               19               344 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               19               344 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               15               348 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               15               348 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                6               357 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                6               357 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                30                333 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                30                333 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                32                331 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                32                331 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 3                360 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 3                360 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                31                332 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                31                332 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                13                350 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                13                350 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                53                310 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                53                310 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                18                345 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                18                345 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                22                341 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                22                341 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                21                342 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                21                342 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                69                294 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                69                294 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                53                310 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                53                310 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                12                351 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                12                351 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                48                315 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                48                315 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                71                292 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                71                292 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                13                350 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                13                350 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                13                350 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                13                350 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                13                350 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                13                350 
[1] "20Q LOSS MUTATION ANALYSIS"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 7                356 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 7                356 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                14                349 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                14                349 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                32                331 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                32                331 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               29               334 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               29               334 
[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] "RADIATIONTHERAPY"                      
[14] "HISTOLOGICALTYPE"                      
[15] "RADIATIONS.RADIATION.REGIMENINDICATION"
[16] "COMPLETENESS.OF.RESECTION"             
[17] "NUMBER.OF.LYMPH.NODES"                 
[18] "GLEASON_SCORE_COMBINED"                
[19] "GLEASON_SCORE_PRIMARY"                 
[20] "GLEASON_SCORE_SECONDARY"               
[21] "HIGHEST_GLEASON_SCORE"                 
[22] "GLEASON_SCORE"                         
[23] "PSA_RESULT_PREOP"                      
[24] "DAYS_TO_PREOP_PSA"                     
[25] "PSA_VALUE"                             
[26] "DAYS_TO_PSA"                           
[27] "RACE"                                  
[28] "ETHNICITY"                             
[29] "BATCHNUMBER"                           

Input Data has 29 rows and 363 columns.

[1] "Batch" "29"   
[1] "Last Follow UP"
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
         621         1332          671         1033          112          771 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
          91          212          671           31          395          425 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
          60          731           31          396         1065          943 
TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 
          31           62           28         1339          365           31 
TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 
         700           31          458          731           62          396 
TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 
         486          821          304          974         1004           91 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
         882          826         1007          595          405          906 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
        1415         1365          800         1391          880          922 
TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 
         827          727         1184         1464         1116         1476 
TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 
        1172         1102         1832         1416         1454         1590 
TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 
        1962         1578         2079         1310         1115         1179 
TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 
        1209         1832         1273         1456          884          822 
TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 
        1491         1860         2542          663          295          289 
TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 
         285          510          233          533          175          842 
TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 
         191            9          727         1167          787          781 
TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 
         625          442          430          552          596          526 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 
         114          701          606         1961         1946          821 
TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F 
          NA          314          162          129          532          299 
TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E 
          93          229          668          536          393          417 
TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-FC-7708 TCGA-FC-7961 
         560          278           91          230          864          469 
TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 
         409          273          524          494           54         1266 
TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 
        2657         2465         2068         2028         2110         1696 
TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 
         554         2089         1515         1404         1542         1501 
TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 
        1434         1415         1443         1378         1198         1363 
TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 
         101         1222         1215         1156         1226          811 
TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 
         958         1155         1393          765          830         1771 
TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 
        1726         1608         1543         1164         1185          849 
TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 
         942         1075          857          994           NA          643 
TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7077 TCGA-HC-7078 
         185          941          112          601           NA          162 
TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 
          89           61           72          440          868           24 
TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 
         870           60           51           72           89           52 
TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 
          22           64           81           53           45           51 
TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 
          63          748          792           60           34           98 
TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 
         928           45          543          747           56          589 
TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 
         682           95          726           66           69           59 
TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F 
         546          679           48          483           35          680 
TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO 
          23           54           61           67           49          167 
TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HI-7168 
          71          106           44           38          134         2391 
TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K 
        2684         2522           NA          614          374          662 
TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R 
         518          488          503          491          624          454 
TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I 
         523          183          405          528          279          279 
TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B 
         310          206          316          437          617          422 
TCGA-J9-A52C TCGA-J9-A52E TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z 
         178          323         2859         1712         1359         1879 
TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 
        3524          913         1659         4604         2056         2753 
TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AZ TCGA-KK-A7B1 
        1498         3447         2040         1770          840         1063 
TCGA-KK-A7B2 TCGA-KK-A8IB TCGA-KK-A8IF TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z 
         692           83          804           NA          158          209 
TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 
         302          400          822          763          483          573 
TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-TP-A8TT 
          97         1247         3487         1436         2620          362 
TCGA-TP-A8TV TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N 
         249          269          776          394          183          472 
TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 
         481          917         1001          459          132         3253 
TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C 
         805         2576         2879           NA         2309         1690 
TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N 
        1853         2037          663         1486          655          542 
TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DI 
         176         1131          846          119         1157         1461 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW 
         275           91          790          972          958          972 
TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU 
         868          930          889          824         1126         1206 
TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO 
         775         1611         1491         1173         1124         2183 
TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF 
        1890         1842          512         1384         1261         1373 
TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO 
          NA         1441         1395         1155          798         3247 
TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ 
        2170         1910          213          427         1259           NA 
TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX 
        1897          740         1518          862           50          150 
TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9ND 
          34          239          183 
Variable 1:'AGE':	nDistinctValues=35,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=6,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=318,	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=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=13,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 14:'HISTOLOGICAL.TYPE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 16:'COMPLETENESS.OF.RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=10,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'GLEASON_SCORE_COMBINED':	nDistinctValues=6,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'GLEASON_SCORE_PRIMARY':	nDistinctValues=5,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'GLEASON_SCORE_SECONDARY':	nDistinctValues=4,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 21:'HIGHEST_GLEASON_SCORE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 22:'GLEASON_SCORE':	nDistinctValues=5,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 23:'PSA_RESULT_PREOP':	nDistinctValues=177,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 24:'DAYS_TO_PREOP_PSA':	nDistinctValues=182,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 25:'PSA_VALUE':	nDistinctValues=81,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 26:'DAYS_TO_PSA':	nDistinctValues=287,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 27:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 28:'ETHNICITY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 29:'BATCH.NUMBER':	nDistinctValues=22,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                       "PATHOLOGY.T.STAGE"        
 [3] "PATHOLOGY.N.STAGE"         "HISTOLOGICAL.TYPE"        
 [5] "COMPLETENESS.OF.RESECTION" "NUMBER.OF.LYMPH.NODES"    
 [7] "GLEASON_SCORE_COMBINED"    "GLEASON_SCORE_PRIMARY"    
 [9] "GLEASON_SCORE_SECONDARY"   "GLEASON_SCORE"            
[11] "PSA_RESULT_PREOP"          "PSA_VALUE"                
[13] "RACE"                     
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "2"          
[1] "PATHOLOGY.N" "3"          
Output Data has 363 columns, 1 survival variables, and 13 non-survival variables.
AGE, nv=35, binary=FALSE, numeric=TRUE
PATHOLOGY.T.STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T2  T3  T4 
150 206   5 
[1] "table(vv)"
vv
 T2  T3  T4 
150 206   5 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
 T2  T3  T4 
150 206   5 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


 T2  T3  T4 
150 206   5 
PATHOLOGY.N.STAGE, nv=2, binary=FALSE, numeric=TRUE
HISTOLOGICAL.TYPE, nv=2, binary=FALSE, numeric=FALSE
COMPLETENESS.OF.RESECTION, nv=4, binary=FALSE, numeric=FALSE
NUMBER.OF.LYMPH.NODES, nv=10, binary=FALSE, numeric=TRUE
GLEASON_SCORE_COMBINED, nv=6, binary=FALSE, numeric=TRUE
GLEASON_SCORE_PRIMARY, nv=5, binary=FALSE, numeric=TRUE
GLEASON_SCORE_SECONDARY, nv=4, binary=FALSE, numeric=TRUE
GLEASON_SCORE, nv=5, binary=FALSE, numeric=TRUE
PSA_RESULT_PREOP, nv=177, binary=FALSE, numeric=TRUE
PSA_VALUE, nv=81, binary=FALSE, numeric=TRUE
RACE, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1P GAIN MUTATION ANALYSIS
D1V1, survival
                   sevent
clus2                 0   1
  1P GAIN MUTATED    11   0
  1P GAIN WILD-TYPE 344   6
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               11               350 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                0                 6 
$`1P GAIN MUTATED`
TCGA-CH-5766 TCGA-EJ-5518 TCGA-EJ-7788 TCGA-FC-7961 TCGA-FC-A4JI TCGA-G9-6499 
        1.02        52.27        14.14        15.42        13.45        50.73 
TCGA-J9-A52E TCGA-VP-A875 TCGA-XK-AAIV TCGA-YL-A8HM TCGA-YL-A8SR 
       10.62        26.47        31.50        36.95         7.00 

$`1P GAIN WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 
        1.02         2.04         0.92        44.02        12.00         1.02 
TCGA-CH-5765 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 
       23.01        15.06        24.03         2.04        13.02        15.98 
TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 
       26.99         9.99        32.02        33.01         2.99        29.00 
TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
       27.16        33.11        19.56        13.32        29.79        46.52 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       44.88        26.30        45.73        28.93        30.31        27.19 
TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       23.90        38.93        48.13        36.69        48.53        38.53 
TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5519 TCGA-EJ-5521 
       36.23        60.23        46.55        47.80        64.50        51.88 
TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 
       68.35        43.07        36.66        38.76        39.75        60.23 
TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 
       41.85        47.87        29.06        27.02        49.02        61.15 
TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 
       83.57        21.80         9.70         9.50         9.37        16.77 
TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 
        7.66        17.52         5.75        27.68         6.28         0.30 
TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 
       23.90        38.37        25.87        25.68        20.55        14.53 
TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 
       18.15        19.59        17.29         3.75        23.05        19.92 
TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D 
       64.47        63.98        26.99        10.32         5.33         4.24 
TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B 
       17.49         9.83         3.06         7.53        21.96        17.62 
TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M 
       12.92        13.71        18.41         9.14         2.99         7.56 
TCGA-FC-7708 TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 
       28.41         8.98        17.23        16.24         1.78        41.62 
TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 
       87.35        81.04        67.99        66.67        69.37        55.76 
TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 
       18.21        68.68        49.81        46.16        50.70        49.35 
TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 
       47.15        46.52        47.44        45.30        39.39        44.81 
TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 
        3.32        40.18        39.95        38.01        40.31        26.66 
TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 
       31.50        37.97        45.80        25.15        27.29        58.22 
TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 
       56.75        52.87        38.27        38.96        27.91        30.97 
TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 
       35.34        28.18        32.68        26.01        21.14         6.08 
TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 
       30.94         3.68        19.76         5.33         2.93         2.01 
TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 
        2.37        14.47        28.54         0.79        28.60         1.97 
TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 
        1.68         2.37         2.93         1.71         0.72         2.10 
TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 
        2.66         1.74         1.48         1.68         2.07        24.59 
TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 
       26.04         1.97         1.12         3.22        30.51         1.48 
TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 
       17.85        24.56         1.84        19.36        22.42         3.12 
TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 
       23.87         2.17         2.27         1.94        17.95        22.32 
TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 
        1.58        15.88         1.15        22.36         0.76         1.78 
TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ 
        2.01         2.20         1.61         5.49         2.33         3.48 
TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 
        1.45         1.25         4.41        78.61        88.24        82.92 
TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M 
       43.69        20.19        12.30        21.76        17.03        16.04 
TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T 
       16.54        16.14        20.52        14.93        17.19         6.02 
TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K 
       13.32        17.36         9.17         9.17        10.19         6.77 
TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52C TCGA-KK-A59V 
       10.39        14.37        20.28        13.87         5.85        93.99 
TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 
       56.28        44.68        61.78       115.86        30.02        54.54 
TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 
      151.36        67.59        90.51        49.25       113.33        67.07 
TCGA-KK-A6E8 TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IB TCGA-KK-A8IF 
       58.19        27.62        34.95        22.75         2.73        26.43 
TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 
       20.65         5.19         6.87         9.93        13.15        27.02 
TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN 
       25.08        15.88        18.84         3.19        41.00       114.64 
TCGA-QU-A6IO TCGA-QU-A6IP TCGA-TP-A8TT TCGA-TP-A8TV TCGA-VN-A88I TCGA-VN-A88K 
       47.21        86.14        11.90         8.19         8.84        25.51 
TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q 
       12.95         6.02        15.52        15.81        30.15        32.91 
TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 
       15.09         4.34       106.95        84.69        94.65        23.93 
TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J 
       75.91        55.56        60.92        66.97        21.80        48.85 
TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR 
       21.53        17.82         5.79        37.18        27.81         3.91 
TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR 
       38.04        48.03         9.04         2.99        25.97        31.96 
TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT 
       31.96        28.54        30.58        29.23        27.09        37.02 
TCGA-XK-AAJU TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HO 
       39.65        25.48        52.96        49.02        38.56        71.77 
TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF 
       62.14        60.56        16.83        45.50        41.46        45.14 
TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO 
       28.77        47.38        45.86        37.97        26.24       106.75 
TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK 
       71.34        62.79        14.04        41.39        60.99        62.37 
TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY 
       24.33        49.91        28.34         1.64         4.93         1.12 
TCGA-ZG-A8QZ TCGA-ZG-A9ND 
        7.86         6.02 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             1.02              0.30 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            52.27            151.36 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            15.42             23.98 
[1] "1.0 - 52.3 (15.4)"  "0.3 - 151.4 (24.0)"
[1] "hr="     "9300000"
D1V2, continuous
                   vv
clus                 T2  T3  T4
  1P GAIN MUTATED     0  10   1
  1P GAIN WILD-TYPE 150 196   4
D1V3, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  T2               0               150
  T3              10               196
  T4               1                 4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V4, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     8   2
  1P GAIN WILD-TYPE 255  42
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      8    2
  1P GAIN WILD-TYPE  255   42
   clus
vv  1P GAIN MUTATED 1P GAIN WILD-TYPE
  0               8               255
  1               2                42
[1] 2 2
[1] FALSE
D1V5, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     0  11
  1P GAIN WILD-TYPE  13 339
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      0   11
  1P GAIN WILD-TYPE   13  339
                                        clus
vv                                       1P GAIN MUTATED 1P GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE               0                13
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 11               339
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  1P GAIN MUTATED     6   4   0   0
  1P GAIN WILD-TYPE 237  86   5  11
D1V6, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  R0               6               237
  R1               4                86
  R2               0                 5
  RX               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"
D1V7, continuous
D1V8, continuous
D1V9, continuous
D1V10, continuous
D1V11, continuous
D1V12, continuous
D1V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1P GAIN MUTATED       0                         0     5
  1P GAIN WILD-TYPE     2                         7   141
D1V14, multiclass
                           clus
vv                          1P GAIN MUTATED 1P GAIN WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 7
  WHITE                                   5               141
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                 0   1
  1Q GAIN MUTATED    17   0
  1Q GAIN WILD-TYPE 338   6
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               17               344 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                0                 6 
$`1Q GAIN MUTATED`
TCGA-CH-5766 TCGA-EJ-5518 TCGA-EJ-7784 TCGA-EJ-7788 TCGA-FC-7961 TCGA-FC-A4JI 
        1.02        52.27        25.68        14.14        15.42        13.45 
TCGA-G9-6362 TCGA-G9-6499 TCGA-HI-7168 TCGA-J9-A52E TCGA-M7-A725 TCGA-VN-A88K 
       47.44        50.73        78.61        10.62        18.84        25.51 
TCGA-VN-A88Q TCGA-VP-A875 TCGA-XK-AAIV TCGA-YL-A8HM TCGA-YL-A8SR 
       32.91        26.47        31.50        36.95         7.00 

$`1Q GAIN WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 
        1.02         2.04         0.92        44.02        12.00         1.02 
TCGA-CH-5765 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 
       23.01        15.06        24.03         2.04        13.02        15.98 
TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 
       26.99         9.99        32.02        33.01         2.99        29.00 
TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
       27.16        33.11        19.56        13.32        29.79        46.52 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       44.88        26.30        45.73        28.93        30.31        27.19 
TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       23.90        38.93        48.13        36.69        48.53        38.53 
TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5519 TCGA-EJ-5521 
       36.23        60.23        46.55        47.80        64.50        51.88 
TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 
       68.35        43.07        36.66        38.76        39.75        60.23 
TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 
       41.85        47.87        29.06        27.02        49.02        61.15 
TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 
       83.57        21.80         9.70         9.50         9.37        16.77 
TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 
        7.66        17.52         5.75        27.68         6.28         0.30 
TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7789 
       23.90        38.37        25.87        20.55        14.53        18.15 
TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 
       19.59        17.29         3.75        23.05        19.92        64.47 
TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E 
       63.98        26.99        10.32         5.33         4.24        17.49 
TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D 
        9.83         3.06         7.53        21.96        17.62        12.92 
TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-FC-7708 
       13.71        18.41         9.14         2.99         7.56        28.41 
TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 
        8.98        17.23        16.24         1.78        41.62        87.35 
TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 
       81.04        67.99        66.67        69.37        55.76        18.21 
TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 
       68.68        49.81        46.16        50.70        49.35        47.15 
TCGA-G9-6361 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 
       46.52        45.30        39.39        44.81         3.32        40.18 
TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 
       39.95        38.01        40.31        26.66        31.50        37.97 
TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 
       45.80        25.15        27.29        58.22        56.75        52.87 
TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 
       38.27        38.96        27.91        30.97        35.34        28.18 
TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY 
       32.68        26.01        21.14         6.08        30.94         3.68 
TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 
       19.76         5.33         2.93         2.01         2.37        14.47 
TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 
       28.54         0.79        28.60         1.97         1.68         2.37 
TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 
        2.93         1.71         0.72         2.10         2.66         1.74 
TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 
        1.48         1.68         2.07        24.59        26.04         1.97 
TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 
        1.12         3.22        30.51         1.48        17.85        24.56 
TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 
        1.84        19.36        22.42         3.12        23.87         2.17 
TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 
        2.27         1.94        17.95        22.32         1.58        15.88 
TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL 
        1.15        22.36         0.76         1.78         2.01         2.20 
TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX 
        1.61         5.49         2.33         3.48         1.45         1.25 
TCGA-HC-A6HY TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 
        4.41        88.24        82.92        43.69        20.19        12.30 
TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q 
       21.76        17.03        16.04        16.54        16.14        20.52 
TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 
       14.93        17.19         6.02        13.32        17.36         9.17 
TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N 
        9.17        10.19         6.77        10.39        14.37        20.28 
TCGA-J9-A52B TCGA-J9-A52C TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z 
       13.87         5.85        93.99        56.28        44.68        61.78 
TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 
      115.86        30.02        54.54       151.36        67.59        90.51 
TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AZ TCGA-KK-A7B1 
       49.25       113.33        67.07        58.19        27.62        34.95 
TCGA-KK-A7B2 TCGA-KK-A8IB TCGA-KK-A8IF TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z 
       22.75         2.73        26.43        20.65         5.19         6.87 
TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-QU-A6IL 
        9.93        13.15        27.02        25.08        15.88         3.19 
TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-TP-A8TT TCGA-TP-A8TV 
       41.00       114.64        47.21        86.14        11.90         8.19 
TCGA-VN-A88I TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P 
        8.84        12.95         6.02        15.52        15.81        30.15 
TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 
       15.09         4.34       106.95        84.69        94.65        23.93 
TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J 
       75.91        55.56        60.92        66.97        21.80        48.85 
TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR 
       21.53        17.82         5.79        37.18        27.81         3.91 
TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR 
       38.04        48.03         9.04         2.99        25.97        31.96 
TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT 
       31.96        28.54        30.58        29.23        27.09        37.02 
TCGA-XK-AAJU TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HO 
       39.65        25.48        52.96        49.02        38.56        71.77 
TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF 
       62.14        60.56        16.83        45.50        41.46        45.14 
TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO 
       28.77        47.38        45.86        37.97        26.24       106.75 
TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK 
       71.34        62.79        14.04        41.39        60.99        62.37 
TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY 
       24.33        49.91        28.34         1.64         4.93         1.12 
TCGA-ZG-A8QZ TCGA-ZG-A9ND 
        7.86         6.02 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             1.02              0.30 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            78.61            151.36 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            25.68             23.90 
[1] "1.0 - 78.6 (25.7)"  "0.3 - 151.4 (23.9)"
[1] "hr="     "2.6e+07"
D2V2, continuous
                   vv
clus                 T2  T3  T4
  1Q GAIN MUTATED     2  14   1
  1Q GAIN WILD-TYPE 148 192   4
D2V3, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T2               2               148
  T3              14               192
  T4               1                 4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V4, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    13   3
  1Q GAIN WILD-TYPE 250  41
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     13    3
  1Q GAIN WILD-TYPE  250   41
   clus
vv  1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  0              13               250
  1               3                41
[1] 2 2
[1] FALSE
D2V5, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED     1  16
  1Q GAIN WILD-TYPE  12 334
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      1   16
  1Q GAIN WILD-TYPE   12  334
                                        clus
vv                                       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE               1                12
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 16               334
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  1Q GAIN MUTATED    10   6   0   0
  1Q GAIN WILD-TYPE 233  84   5  11
D2V6, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  R0              10               233
  R1               6                84
  R2               0                 5
  RX               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"
D2V7, continuous
D2V8, continuous
D2V9, continuous
D2V10, continuous
D2V11, continuous
D2V12, continuous
D2V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1Q GAIN MUTATED       0                         0     8
  1Q GAIN WILD-TYPE     2                         7   138
D2V14, multiclass
                           clus
vv                          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 7
  WHITE                                   8               138
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                 0   1
  2P GAIN MUTATED     7   0
  2P GAIN WILD-TYPE 348   6
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                7               354 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                0                 6 
$`2P GAIN MUTATED`
TCGA-EJ-A65M TCGA-FC-A4JI TCGA-HC-8256 TCGA-HC-A631 TCGA-KK-A8IF TCGA-YL-A8S8 
        7.56        13.45         3.12         1.78        26.43        62.14 
TCGA-YL-A8SQ 
       62.79 

$`2P GAIN WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 
        1.02         2.04         0.92        44.02        12.00         1.02 
TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 
       23.01         1.02        15.06        24.03         2.04        13.02 
TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 
       15.98        26.99         9.99        32.02        33.01         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        27.16        33.11        19.56        13.32        29.79 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        26.30        45.73        28.93        30.31 
TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 
       27.19        23.90        38.93        48.13        36.69        48.53 
TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 
       38.53        36.23        60.23        46.55        47.80        52.27 
TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 
       64.50        51.88        68.35        43.07        36.66        38.76 
TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 
       39.75        60.23        41.85        47.87        29.06        27.02 
TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 
       49.02        61.15        83.57        21.80         9.70         9.50 
TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 
        9.37        16.77         7.66        17.52         5.75        27.68 
TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 
        6.28         0.30        23.90        38.37        25.87        25.68 
TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 
       20.55        14.53        14.14        18.15        19.59        17.29 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 
        3.75        23.05        19.92        64.47        63.98        26.99 
TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G 
       10.32         5.33         4.24        17.49         9.83         3.06 
TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F 
        7.53        21.96        17.62        12.92        13.71        18.41 
TCGA-EJ-A65G TCGA-EJ-A65J TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A5OB TCGA-FC-A66V 
        9.14         2.99        28.41        15.42         8.98        17.23 
TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 
       16.24         1.78        41.62        87.35        81.04        67.99 
TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 
       66.67        69.37        55.76        18.21        68.68        49.81 
TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 
       46.16        50.70        49.35        47.15        46.52        47.44 
TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 
       45.30        39.39        44.81         3.32        40.18        39.95 
TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 
       38.01        40.31        26.66        31.50        37.97        45.80 
TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 
       25.15        27.29        58.22        56.75        52.87        50.73 
TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 
       38.27        38.96        27.91        30.97        35.34        28.18 
TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY 
       32.68        26.01        21.14         6.08        30.94         3.68 
TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 
       19.76         5.33         2.93         2.01         2.37        14.47 
TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 
       28.54         0.79        28.60         1.97         1.68         2.37 
TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 
        2.93         1.71         0.72         2.10         2.66         1.74 
TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 
        1.48         1.68         2.07        24.59        26.04         1.97 
TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 
        1.12         3.22        30.51         1.48        17.85        24.56 
TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 
        1.84        19.36        22.42        23.87         2.17         2.27 
TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 
        1.94        17.95        22.32         1.58        15.88         1.15 
TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO 
       22.36         0.76         2.01         2.20         1.61         5.49 
TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HI-7168 
        2.33         3.48         1.45         1.25         4.41        78.61 
TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K 
       88.24        82.92        43.69        20.19        12.30        21.76 
TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R 
       17.03        16.04        16.54        16.14        20.52        14.93 
TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I 
       17.19         6.02        13.32        17.36         9.17         9.17 
TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B 
       10.19         6.77        10.39        14.37        20.28        13.87 
TCGA-J9-A52C TCGA-J9-A52E TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z 
        5.85        10.62        93.99        56.28        44.68        61.78 
TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 
      115.86        30.02        54.54       151.36        67.59        90.51 
TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AZ TCGA-KK-A7B1 
       49.25       113.33        67.07        58.19        27.62        34.95 
TCGA-KK-A7B2 TCGA-KK-A8IB TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 
       22.75         2.73        20.65         5.19         6.87         9.93 
TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL 
       13.15        27.02        25.08        15.88        18.84         3.19 
TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-TP-A8TT TCGA-TP-A8TV 
       41.00       114.64        47.21        86.14        11.90         8.19 
TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O 
        8.84        25.51        12.95         6.02        15.52        15.81 
TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 
       30.15        32.91        15.09         4.34       106.95        26.47 
TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D 
       84.69        94.65        23.93        75.91        55.56        60.92 
TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI 
       66.97        21.80        48.85        21.53        17.82         5.79 
TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK 
       37.18        27.81         3.91        38.04        48.03         9.04 
TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 
        2.99        25.97        31.96        31.50        31.96        28.54 
TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-Y6-A8TL 
       30.58        29.23        27.09        37.02        39.65        25.48 
TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S9 
       52.96        49.02        38.56        36.95        71.77        60.56 
TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI 
       16.83        45.50        41.46        45.14        28.77        47.38 
TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SR 
       45.86        37.97        26.24       106.75        71.34         7.00 
TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX 
       14.04        41.39        60.99        62.37        24.33        49.91 
TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9ND 
       28.34         1.64         4.93         1.12         7.86         6.02 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             1.78              0.30 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            62.79            151.36 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            13.45             23.98 
[1] "1.8 - 62.8 (13.4)"  "0.3 - 151.4 (24.0)"
[1] "hr="     "9400000"
D3V2, continuous
                   vv
clus                 T2  T3  T4
  2P GAIN MUTATED     3   4   0
  2P GAIN WILD-TYPE 147 202   5
D3V3, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  T2               3               147
  T3               4               202
  T4               0                 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"
D3V4, binary
                   cls
clus                  0   1
  2P GAIN MUTATED     5   0
  2P GAIN WILD-TYPE 258  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      5    0
  2P GAIN WILD-TYPE  258   44
   clus
vv  2P GAIN MUTATED 2P GAIN WILD-TYPE
  0               5               258
  1               0                44
[1] 2 2
[1] FALSE
D3V5, binary
                   cls
clus                  0   1
  2P GAIN MUTATED     0   7
  2P GAIN WILD-TYPE  13 343
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      0    7
  2P GAIN WILD-TYPE   13  343
                                        clus
vv                                       2P GAIN MUTATED 2P GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE               0                13
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  7               343
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  2P GAIN MUTATED     3   3   0   0
  2P GAIN WILD-TYPE 240  87   5  11
D3V6, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  R0               3               240
  R1               3                87
  R2               0                 5
  RX               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"
D3V7, continuous
D3V8, continuous
D3V9, continuous
D3V10, continuous
D3V11, continuous
D3V12, continuous
D3V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2P GAIN MUTATED       0                         0     0
  2P GAIN WILD-TYPE     2                         7   146
D3V14, multiclass

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                 0   1
  2Q GAIN MUTATED     5   0
  2Q GAIN WILD-TYPE 350   6
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                5               356 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                0                 6 
$`2Q GAIN MUTATED`
TCGA-EJ-A65M TCGA-FC-A4JI TCGA-HC-A631 TCGA-KK-A8IF TCGA-YL-A8SQ 
        7.56        13.45         1.78        26.43        62.79 

$`2Q GAIN WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 
        1.02         2.04         0.92        44.02        12.00         1.02 
TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 
       23.01         1.02        15.06        24.03         2.04        13.02 
TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 
       15.98        26.99         9.99        32.02        33.01         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        27.16        33.11        19.56        13.32        29.79 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        26.30        45.73        28.93        30.31 
TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 
       27.19        23.90        38.93        48.13        36.69        48.53 
TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 
       38.53        36.23        60.23        46.55        47.80        52.27 
TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 
       64.50        51.88        68.35        43.07        36.66        38.76 
TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 
       39.75        60.23        41.85        47.87        29.06        27.02 
TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 
       49.02        61.15        83.57        21.80         9.70         9.50 
TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 
        9.37        16.77         7.66        17.52         5.75        27.68 
TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 
        6.28         0.30        23.90        38.37        25.87        25.68 
TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 
       20.55        14.53        14.14        18.15        19.59        17.29 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 
        3.75        23.05        19.92        64.47        63.98        26.99 
TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G 
       10.32         5.33         4.24        17.49         9.83         3.06 
TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F 
        7.53        21.96        17.62        12.92        13.71        18.41 
TCGA-EJ-A65G TCGA-EJ-A65J TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A5OB TCGA-FC-A66V 
        9.14         2.99        28.41        15.42         8.98        17.23 
TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 
       16.24         1.78        41.62        87.35        81.04        67.99 
TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 
       66.67        69.37        55.76        18.21        68.68        49.81 
TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 
       46.16        50.70        49.35        47.15        46.52        47.44 
TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 
       45.30        39.39        44.81         3.32        40.18        39.95 
TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 
       38.01        40.31        26.66        31.50        37.97        45.80 
TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 
       25.15        27.29        58.22        56.75        52.87        50.73 
TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 
       38.27        38.96        27.91        30.97        35.34        28.18 
TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY 
       32.68        26.01        21.14         6.08        30.94         3.68 
TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 
       19.76         5.33         2.93         2.01         2.37        14.47 
TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 
       28.54         0.79        28.60         1.97         1.68         2.37 
TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 
        2.93         1.71         0.72         2.10         2.66         1.74 
TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 
        1.48         1.68         2.07        24.59        26.04         1.97 
TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 
        1.12         3.22        30.51         1.48        17.85        24.56 
TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 
        1.84        19.36        22.42         3.12        23.87         2.17 
TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 
        2.27         1.94        17.95        22.32         1.58        15.88 
TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN 
        1.15        22.36         0.76         2.01         2.20         1.61 
TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY 
        5.49         2.33         3.48         1.45         1.25         4.41 
TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 
       78.61        88.24        82.92        43.69        20.19        12.30 
TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q 
       21.76        17.03        16.04        16.54        16.14        20.52 
TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 
       14.93        17.19         6.02        13.32        17.36         9.17 
TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N 
        9.17        10.19         6.77        10.39        14.37        20.28 
TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y 
       13.87         5.85        10.62        93.99        56.28        44.68 
TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 
       61.78       115.86        30.02        54.54       151.36        67.59 
TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AZ 
       90.51        49.25       113.33        67.07        58.19        27.62 
TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IB TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z 
       34.95        22.75         2.73        20.65         5.19         6.87 
TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 
        9.93        13.15        27.02        25.08        15.88        18.84 
TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-TP-A8TT 
        3.19        41.00       114.64        47.21        86.14        11.90 
TCGA-TP-A8TV TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N 
        8.19         8.84        25.51        12.95         6.02        15.52 
TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 
       15.81        30.15        32.91        15.09         4.34       106.95 
TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C 
       26.47        84.69        94.65        23.93        75.91        55.56 
TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N 
       60.92        66.97        21.80        48.85        21.53        17.82 
TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DI 
        5.79        37.18        27.81         3.91        38.04        48.03 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW 
        9.04         2.99        25.97        31.96        31.50        31.96 
TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU 
       28.54        30.58        29.23        27.09        37.02        39.65 
TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO 
       25.48        52.96        49.02        38.56        36.95        71.77 
TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF 
       62.14        60.56        16.83        45.50        41.46        45.14 
TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO 
       28.77        47.38        45.86        37.97        26.24       106.75 
TCGA-YL-A8SP TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK 
       71.34         7.00        14.04        41.39        60.99        62.37 
TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY 
       24.33        49.91        28.34         1.64         4.93         1.12 
TCGA-ZG-A8QZ TCGA-ZG-A9ND 
        7.86         6.02 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             1.78              0.30 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            62.79            151.36 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            13.45             23.98 
[1] "1.8 - 62.8 (13.4)"  "0.3 - 151.4 (24.0)"
[1] "hr="     "9100000"
D4V2, continuous
                   vv
clus                 T2  T3  T4
  2Q GAIN MUTATED     2   3   0
  2Q GAIN WILD-TYPE 148 203   5
D4V3, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  T2               2               148
  T3               3               203
  T4               0                 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"
D4V4, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED     4   0
  2Q GAIN WILD-TYPE 259  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      4    0
  2Q GAIN WILD-TYPE  259   44
   clus
vv  2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  0               4               259
  1               0                44
[1] 2 2
[1] FALSE
D4V5, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED     0   5
  2Q GAIN WILD-TYPE  13 345
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      0    5
  2Q GAIN WILD-TYPE   13  345
                                        clus
vv                                       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE               0                13
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  5               345
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  2Q GAIN MUTATED     2   2   0   0
  2Q GAIN WILD-TYPE 241  88   5  11
D4V6, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  R0               2               241
  R1               2                88
  R2               0                 5
  RX               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"
D4V7, continuous
D4V8, continuous
D4V9, continuous
D4V10, continuous
D4V11, continuous
D4V12, continuous
D4V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2Q GAIN MUTATED       0                         0     0
  2Q GAIN WILD-TYPE     2                         7   146
D4V14, multiclass

Clustering(5) Variable = 3P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                 0   1
  3P GAIN MUTATED    25   1
  3P GAIN WILD-TYPE 330   5
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               26               335 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                1                 5 
$`3P GAIN MUTATED`
TCGA-CH-5751 TCGA-CH-5761 TCGA-CH-5771 TCGA-CH-5791 TCGA-EJ-5514 TCGA-EJ-5518 
       35.01         0.92        13.02        33.01        36.23        52.27 
TCGA-EJ-5531 TCGA-EJ-7782 TCGA-EJ-7792 TCGA-FC-7961 TCGA-FC-A4JI TCGA-G9-6499 
       41.85        38.37        17.29        15.42        13.45        50.73 
TCGA-G9-A9S0 TCGA-HC-8216 TCGA-HC-A631 TCGA-HC-A6AS TCGA-HI-7168 TCGA-KK-A8IB 
       26.01        22.42         1.78         1.45        78.61         2.73 
TCGA-KK-A8IF TCGA-VP-A872 TCGA-VP-A87H TCGA-XJ-A83G TCGA-XK-AAIV TCGA-YL-A8S8 
       26.43       106.95        21.80        38.04        31.50        62.14 
TCGA-YL-A9WH TCGA-YL-A9WI 
       14.04        41.39 

$`3P GAIN WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5753 
        1.97        24.03         1.02        13.02        31.00         1.02 
TCGA-CH-5754 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 
        2.04        44.02        12.00         1.02        23.01         1.02 
TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 
       15.06        24.03         2.04        15.98        26.99         9.99 
TCGA-CH-5790 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 
       32.02         2.99        29.00        27.16        33.11        19.56 
TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 
       13.32        29.79        46.52        44.88        26.30        45.73 
TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 
       28.93        30.31        27.19        23.90        38.93        48.13 
TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 
       36.69        48.53        38.53        60.23        46.55        47.80 
TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 
       64.50        51.88        68.35        43.07        36.66        38.76 
TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 
       39.75        60.23        47.87        29.06        27.02        49.02 
TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 
       61.15        83.57        21.80         9.70         9.50         9.37 
TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 
       16.77         7.66        17.52         5.75        27.68         6.28 
TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 
        0.30        23.90        25.87        25.68        20.55        14.53 
TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 
       14.14        18.15        19.59         3.75        23.05        19.92 
TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D 
       64.47        63.98        26.99        10.32         5.33         4.24 
TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B 
       17.49         9.83         3.06         7.53        21.96        17.62 
TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M 
       12.92        13.71        18.41         9.14         2.99         7.56 
TCGA-FC-7708 TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 
       28.41         8.98        17.23        16.24         1.78        41.62 
TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 
       87.35        81.04        67.99        66.67        69.37        55.76 
TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 
       18.21        68.68        49.81        46.16        50.70        49.35 
TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 
       47.15        46.52        47.44        45.30        39.39        44.81 
TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 
        3.32        40.18        39.95        38.01        40.31        26.66 
TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 
       31.50        37.97        45.80        25.15        27.29        58.22 
TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 
       56.75        52.87        38.27        38.96        27.91        30.97 
TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX 
       35.34        28.18        32.68        21.14         6.08        30.94 
TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 
        3.68        19.76         5.33         2.93         2.01         2.37 
TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 
       14.47        28.54         0.79        28.60         1.97         1.68 
TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 
        2.37         2.93         1.71         0.72         2.10         2.66 
TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 
        1.74         1.48         1.68         2.07        24.59        26.04 
TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 
        1.97         1.12         3.22        30.51         1.48        17.85 
TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 
       24.56         1.84        19.36         3.12        23.87         2.17 
TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 
        2.27         1.94        17.95        22.32         1.58        15.88 
TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN 
        1.15        22.36         0.76         2.01         2.20         1.61 
TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HI-7169 
        5.49         2.33         3.48         1.25         4.41        88.24 
TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L 
       82.92        43.69        20.19        12.30        21.76        17.03 
TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S 
       16.04        16.54        16.14        20.52        14.93        17.19 
TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J 
        6.02        13.32        17.36         9.17         9.17        10.19 
TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52C 
        6.77        10.39        14.37        20.28        13.87         5.85 
TCGA-J9-A52E TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY 
       10.62        93.99        56.28        44.68        61.78       115.86 
TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 
       30.02        54.54       151.36        67.59        90.51        49.25 
TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 
      113.33        67.07        58.19        27.62        34.95        22.75 
TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 
       20.65         5.19         6.87         9.93        13.15        27.02 
TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN 
       25.08        15.88        18.84         3.19        41.00       114.64 
TCGA-QU-A6IO TCGA-QU-A6IP TCGA-TP-A8TT TCGA-TP-A8TV TCGA-VN-A88I TCGA-VN-A88K 
       47.21        86.14        11.90         8.19         8.84        25.51 
TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q 
       12.95         6.02        15.52        15.81        30.15        32.91 
TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 
       15.09         4.34        26.47        84.69        94.65        23.93 
TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87J TCGA-VP-A87K 
       75.91        55.56        60.92        66.97        48.85        21.53 
TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A9DI 
       17.82         5.79        37.18        27.81         3.91        48.03 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIW TCGA-XK-AAJ3 
        9.04         2.99        25.97        31.96        31.96        28.54 
TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-Y6-A8TL 
       30.58        29.23        27.09        37.02        39.65        25.48 
TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S9 
       52.96        49.02        38.56        36.95        71.77        60.56 
TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI 
       16.83        45.50        41.46        45.14        28.77        47.38 
TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ 
       45.86        37.97        26.24       106.75        71.34        62.79 
TCGA-YL-A8SR TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY 
        7.00        60.99        62.37        24.33        49.91        28.34 
TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9ND 
        1.64         4.93         1.12         7.86         6.02 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             0.92              0.30 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           106.95            151.36 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           28.965            23.900 
[1] "0.9 - 107.0 (29.0)" "0.3 - 151.4 (23.9)"
[1] "hr=" "2.3"
D5V2, continuous
                   vv
clus                 T2  T3  T4
  3P GAIN MUTATED     6  18   2
  3P GAIN WILD-TYPE 144 188   3
D5V3, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  T2               6               144
  T3              18               188
  T4               2                 3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V4, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    20   5
  3P GAIN WILD-TYPE 243  39
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     20    5
  3P GAIN WILD-TYPE  243   39
   clus
vv  3P GAIN MUTATED 3P GAIN WILD-TYPE
  0              20               243
  1               5                39
[1] 2 2
[1] FALSE
D5V5, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     1  25
  3P GAIN WILD-TYPE  12 325
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      1   25
  3P GAIN WILD-TYPE   12  325
                                        clus
vv                                       3P GAIN MUTATED 3P GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE               1                12
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 25               325
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  3P GAIN MUTATED    15   8   1   0
  3P GAIN WILD-TYPE 228  82   4  11
D5V6, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  R0              15               228
  R1               8                82
  R2               1                 4
  RX               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"
D5V7, continuous
D5V8, continuous
D5V9, continuous
D5V10, continuous
D5V11, continuous
D5V12, continuous
D5V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3P GAIN MUTATED       0                         1    11
  3P GAIN WILD-TYPE     2                         6   135
D5V14, multiclass
                           clus
vv                          3P GAIN MUTATED 3P GAIN WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               1                 6
  WHITE                                  11               135
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = 3Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                 0   1
  3Q GAIN MUTATED    33   2
  3Q GAIN WILD-TYPE 322   4
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               35               326 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                2                 4 
$`3Q GAIN MUTATED`
TCGA-CH-5751 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5791 TCGA-EJ-5514 TCGA-EJ-5518 
       35.01        13.02        26.99        33.01        36.23        52.27 
TCGA-EJ-5521 TCGA-EJ-5527 TCGA-EJ-5531 TCGA-EJ-7782 TCGA-EJ-7792 TCGA-EJ-A65J 
       51.88        39.75        41.85        38.37        17.29         2.99 
TCGA-FC-7961 TCGA-FC-A4JI TCGA-G9-6338 TCGA-G9-6363 TCGA-G9-6499 TCGA-G9-A9S0 
       15.42        13.45        66.67        45.30        50.73        26.01 
TCGA-HC-8216 TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A6AS TCGA-HI-7168 TCGA-KK-A8IB 
       22.42         0.76         1.78         1.45        78.61         2.73 
TCGA-KK-A8IF TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A87H TCGA-XJ-A83G TCGA-XK-AAIV 
       26.43        15.09       106.95        21.80        38.04        31.50 
TCGA-YL-A8S8 TCGA-YL-A8SP TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ 
       62.14        71.34        14.04        41.39        60.99 

$`3Q GAIN WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5753 
        1.97        24.03         1.02        13.02        31.00         1.02 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 
        2.04         0.92        44.02        12.00         1.02        23.01 
TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5772 TCGA-CH-5789 
        1.02        15.06        24.03         2.04        15.98         9.99 
TCGA-CH-5790 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 
       32.02         2.99        29.00        27.16        33.11        19.56 
TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 
       13.32        29.79        46.52        44.88        26.30        45.73 
TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 
       28.93        30.31        27.19        23.90        38.93        48.13 
TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 
       36.69        48.53        38.53        60.23        46.55        47.80 
TCGA-EJ-5519 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5530 
       64.50        68.35        43.07        36.66        38.76        60.23 
TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 
       47.87        29.06        27.02        49.02        61.15        83.57 
TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 
       21.80         9.70         9.50         9.37        16.77         7.66 
TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 
       17.52         5.75        27.68         6.28         0.30        23.90 
TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 
       25.87        25.68        20.55        14.53        14.14        18.15 
TCGA-EJ-7791 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 
       19.59         3.75        23.05        19.92        64.47        63.98 
TCGA-EJ-8470 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F 
       26.99        10.32         5.33         4.24        17.49         9.83 
TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E 
        3.06         7.53        21.96        17.62        12.92        13.71 
TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65M TCGA-FC-7708 TCGA-FC-A5OB TCGA-FC-A66V 
       18.41         9.14         7.56        28.41         8.98        17.23 
TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 
       16.24         1.78        41.62        87.35        81.04        67.99 
TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 
       69.37        55.76        18.21        68.68        49.81        46.16 
TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6364 
       50.70        49.35        47.15        46.52        47.44        39.39 
TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 
       44.81         3.32        40.18        39.95        38.01        40.31 
TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 
       26.66        31.50        37.97        45.80        25.15        27.29 
TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 
       58.22        56.75        52.87        38.27        38.96        27.91 
TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S7 TCGA-H9-7775 
       30.97        35.34        28.18        32.68        21.14         6.08 
TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 
       30.94         3.68        19.76         5.33         2.93         2.01 
TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 
        2.37        14.47        28.54         0.79        28.60         1.97 
TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 
        1.68         2.37         2.93         1.71         0.72         2.10 
TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 
        2.66         1.74         1.48         1.68         2.07        24.59 
TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 
       26.04         1.97         1.12         3.22        30.51         1.48 
TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8256 TCGA-HC-8257 
       17.85        24.56         1.84        19.36         3.12        23.87 
TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 
        2.17         2.27         1.94        17.95        22.32         1.58 
TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN 
       15.88         1.15        22.36         2.01         2.20         1.61 
TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HI-7169 
        5.49         2.33         3.48         1.25         4.41        88.24 
TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L 
       82.92        43.69        20.19        12.30        21.76        17.03 
TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S 
       16.04        16.54        16.14        20.52        14.93        17.19 
TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J 
        6.02        13.32        17.36         9.17         9.17        10.19 
TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52C 
        6.77        10.39        14.37        20.28        13.87         5.85 
TCGA-J9-A52E TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY 
       10.62        93.99        56.28        44.68        61.78       115.86 
TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 
       30.02        54.54       151.36        67.59        90.51        49.25 
TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 
      113.33        67.07        58.19        27.62        34.95        22.75 
TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 
       20.65         5.19         6.87         9.93        13.15        27.02 
TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN 
       25.08        15.88        18.84         3.19        41.00       114.64 
TCGA-QU-A6IO TCGA-QU-A6IP TCGA-TP-A8TT TCGA-TP-A8TV TCGA-VN-A88I TCGA-VN-A88K 
       47.21        86.14        11.90         8.19         8.84        25.51 
TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q 
       12.95         6.02        15.52        15.81        30.15        32.91 
TCGA-VN-A943 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B 
        4.34        26.47        84.69        94.65        23.93        75.91 
TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N 
       55.56        60.92        66.97        48.85        21.53        17.82 
TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A9DI TCGA-XJ-A9DK 
        5.79        37.18        27.81         3.91        48.03         9.04 
TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA 
        2.99        25.97        31.96        31.96        28.54        30.58 
TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-Y6-A8TL TCGA-YL-A8HJ 
       29.23        27.09        37.02        39.65        25.48        52.96 
TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S9 TCGA-YL-A8SA 
       49.02        38.56        36.95        71.77        60.56        16.83 
TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ 
       45.50        41.46        45.14        28.77        47.38        45.86 
TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WK 
       37.97        26.24       106.75        62.79         7.00        62.37 
TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY 
       24.33        49.91        28.34         1.64         4.93         1.12 
TCGA-ZG-A8QZ TCGA-ZG-A9ND 
        7.86         6.02 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             0.76              0.30 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           106.95            151.36 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            33.01             23.03 
[1] "0.8 - 107.0 (33.0)" "0.3 - 151.4 (23.0)"
[1] "hr=" "3.3"
D6V2, continuous
                   vv
clus                 T2  T3  T4
  3Q GAIN MUTATED     7  25   3
  3Q GAIN WILD-TYPE 143 181   2
D6V3, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  T2               7               143
  T3              25               181
  T4               3                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V4, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    26   7
  3Q GAIN WILD-TYPE 237  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     26    7
  3Q GAIN WILD-TYPE  237   37
   clus
vv  3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  0              26               237
  1               7                37
[1] 2 2
[1] FALSE
D6V5, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED     1  34
  3Q GAIN WILD-TYPE  12 316
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      1   34
  3Q GAIN WILD-TYPE   12  316
                                        clus
vv                                       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE               1                12
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 34               316
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  3Q GAIN MUTATED    20  12   1   0
  3Q GAIN WILD-TYPE 223  78   4  11
D6V6, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  R0              20               223
  R1              12                78
  R2               1                 4
  RX               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"
D6V7, continuous
D6V8, continuous
D6V9, continuous
D6V10, continuous
D6V11, continuous
D6V12, continuous
D6V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3Q GAIN MUTATED       0                         1    15
  3Q GAIN WILD-TYPE     2                         6   131
D6V14, multiclass
                           clus
vv                          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               1                 6
  WHITE                                  15               131
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = 4P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                 0   1
  4P GAIN MUTATED     6   0
  4P GAIN WILD-TYPE 349   6
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                6               355 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                0                 6 
$`4P GAIN MUTATED`
TCGA-EJ-5542 TCGA-G9-6499 TCGA-HC-7080 TCGA-VP-A875 TCGA-YL-A8HO TCGA-YL-A8SR 
       29.06        50.73         2.01        26.47        71.77         7.00 

$`4P GAIN WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 
        1.02         2.04         0.92        44.02        12.00         1.02 
TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 
       23.01         1.02        15.06        24.03         2.04        13.02 
TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 
       15.98        26.99         9.99        32.02        33.01         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        27.16        33.11        19.56        13.32        29.79 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        26.30        45.73        28.93        30.31 
TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 
       27.19        23.90        38.93        48.13        36.69        48.53 
TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 
       38.53        36.23        60.23        46.55        47.80        52.27 
TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 
       64.50        51.88        68.35        43.07        36.66        38.76 
TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7123 
       39.75        60.23        41.85        47.87        27.02        49.02 
TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 
       61.15        83.57        21.80         9.70         9.50         9.37 
TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 
       16.77         7.66        17.52         5.75        27.68         6.28 
TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 
        0.30        23.90        38.37        25.87        25.68        20.55 
TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 
       14.53        14.14        18.15        19.59        17.29         3.75 
TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8474 
       23.05        19.92        64.47        63.98        26.99        10.32 
TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H 
        5.33         4.24        17.49         9.83         3.06         7.53 
TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G 
       21.96        17.62        12.92        13.71        18.41         9.14 
TCGA-EJ-A65J TCGA-EJ-A65M TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB 
        2.99         7.56        28.41        15.42        13.45         8.98 
TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 
       17.23        16.24         1.78        41.62        87.35        81.04 
TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 
       67.99        66.67        69.37        55.76        18.21        68.68 
TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 
       49.81        46.16        50.70        49.35        47.15        46.52 
TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 
       47.44        45.30        39.39        44.81         3.32        40.18 
TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 
       39.95        38.01        40.31        26.66        31.50        37.97 
TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 
       45.80        25.15        27.29        58.22        56.75        52.87 
TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 
       38.27        38.96        27.91        30.97        35.34        28.18 
TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY 
       32.68        26.01        21.14         6.08        30.94         3.68 
TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 
       19.76         5.33         2.93         2.37        14.47        28.54 
TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 
        0.79        28.60         1.97         1.68         2.37         2.93 
TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 
        1.71         0.72         2.10         2.66         1.74         1.48 
TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 
        1.68         2.07        24.59        26.04         1.97         1.12 
TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 
        3.22        30.51         1.48        17.85        24.56         1.84 
TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 
       19.36        22.42         3.12        23.87         2.17         2.27 
TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 
        1.94        17.95        22.32         1.58        15.88         1.15 
TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN 
       22.36         0.76         1.78         2.01         2.20         1.61 
TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY 
        5.49         2.33         3.48         1.45         1.25         4.41 
TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 
       78.61        88.24        82.92        43.69        20.19        12.30 
TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q 
       21.76        17.03        16.04        16.54        16.14        20.52 
TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 
       14.93        17.19         6.02        13.32        17.36         9.17 
TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N 
        9.17        10.19         6.77        10.39        14.37        20.28 
TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y 
       13.87         5.85        10.62        93.99        56.28        44.68 
TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 
       61.78       115.86        30.02        54.54       151.36        67.59 
TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AZ 
       90.51        49.25       113.33        67.07        58.19        27.62 
TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IB TCGA-KK-A8IF TCGA-KK-A8IL TCGA-M7-A71Y 
       34.95        22.75         2.73        26.43        20.65         5.19 
TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 
        6.87         9.93        13.15        27.02        25.08        15.88 
TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP 
       18.84         3.19        41.00       114.64        47.21        86.14 
TCGA-TP-A8TT TCGA-TP-A8TV TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M 
       11.90         8.19         8.84        25.51        12.95         6.02 
TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 
       15.52        15.81        30.15        32.91        15.09         4.34 
TCGA-VP-A872 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C 
      106.95        84.69        94.65        23.93        75.91        55.56 
TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N 
       60.92        66.97        21.80        48.85        21.53        17.82 
TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DI 
        5.79        37.18        27.81         3.91        38.04        48.03 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW 
        9.04         2.99        25.97        31.96        31.50        31.96 
TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU 
       28.54        30.58        29.23        27.09        37.02        39.65 
TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8S8 
       25.48        52.96        49.02        38.56        36.95        62.14 
TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH 
       60.56        16.83        45.50        41.46        45.14        28.77 
TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP 
       47.38        45.86        37.97        26.24       106.75        71.34 
TCGA-YL-A8SQ TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL 
       62.79        14.04        41.39        60.99        62.37        24.33 
TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       49.91        28.34         1.64         4.93         1.12         7.86 
TCGA-ZG-A9ND 
        6.02 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             2.01              0.30 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            71.77            151.36 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
           27.765            23.900 
[1] "2.0 - 71.8 (27.8)"  "0.3 - 151.4 (23.9)"
[1] "hr="     "9200000"
D7V2, continuous
                   vv
clus                 T2  T3  T4
  4P GAIN MUTATED     1   5   0
  4P GAIN WILD-TYPE 149 201   5
D7V3, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  T2               1               149
  T3               5               201
  T4               0                 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"
D7V4, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     6   0
  4P GAIN WILD-TYPE 257  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      6    0
  4P GAIN WILD-TYPE  257   44
   clus
vv  4P GAIN MUTATED 4P GAIN WILD-TYPE
  0               6               257
  1               0                44
[1] 2 2
[1] FALSE
D7V5, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     0   6
  4P GAIN WILD-TYPE  13 344
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      0    6
  4P GAIN WILD-TYPE   13  344
                                        clus
vv                                       4P GAIN MUTATED 4P GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE               0                13
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  6               344
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  4P GAIN MUTATED     4   2   0   0
  4P GAIN WILD-TYPE 239  88   5  11
D7V6, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  R0               4               239
  R1               2                88
  R2               0                 5
  RX               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"
D7V7, continuous
D7V8, continuous
D7V9, continuous
D7V10, continuous
D7V11, continuous
D7V12, continuous
D7V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4P GAIN MUTATED       0                         0     3
  4P GAIN WILD-TYPE     2                         7   143
D7V14, multiclass
                           clus
vv                          4P GAIN MUTATED 4P GAIN WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 7
  WHITE                                   3               143
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = 4Q GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                 0   1
  4Q GAIN MUTATED     5   0
  4Q GAIN WILD-TYPE 350   6
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                5               356 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                0                 6 
$`4Q GAIN MUTATED`
TCGA-EJ-5542 TCGA-HC-7080 TCGA-VP-A875 TCGA-XK-AAJT TCGA-YL-A8HO 
       29.06         2.01        26.47        37.02        71.77 

$`4Q GAIN WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 
        1.02         2.04         0.92        44.02        12.00         1.02 
TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 
       23.01         1.02        15.06        24.03         2.04        13.02 
TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 
       15.98        26.99         9.99        32.02        33.01         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        27.16        33.11        19.56        13.32        29.79 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        26.30        45.73        28.93        30.31 
TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 
       27.19        23.90        38.93        48.13        36.69        48.53 
TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 
       38.53        36.23        60.23        46.55        47.80        52.27 
TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 
       64.50        51.88        68.35        43.07        36.66        38.76 
TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7123 
       39.75        60.23        41.85        47.87        27.02        49.02 
TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 
       61.15        83.57        21.80         9.70         9.50         9.37 
TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 
       16.77         7.66        17.52         5.75        27.68         6.28 
TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 
        0.30        23.90        38.37        25.87        25.68        20.55 
TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 
       14.53        14.14        18.15        19.59        17.29         3.75 
TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8474 
       23.05        19.92        64.47        63.98        26.99        10.32 
TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H 
        5.33         4.24        17.49         9.83         3.06         7.53 
TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G 
       21.96        17.62        12.92        13.71        18.41         9.14 
TCGA-EJ-A65J TCGA-EJ-A65M TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB 
        2.99         7.56        28.41        15.42        13.45         8.98 
TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 
       17.23        16.24         1.78        41.62        87.35        81.04 
TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 
       67.99        66.67        69.37        55.76        18.21        68.68 
TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 
       49.81        46.16        50.70        49.35        47.15        46.52 
TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 
       47.44        45.30        39.39        44.81         3.32        40.18 
TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 
       39.95        38.01        40.31        26.66        31.50        37.97 
TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 
       45.80        25.15        27.29        58.22        56.75        52.87 
TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 
       50.73        38.27        38.96        27.91        30.97        35.34 
TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX 
       28.18        32.68        26.01        21.14         6.08        30.94 
TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7081 TCGA-HC-7209 
        3.68        19.76         5.33         2.93         2.37        14.47 
TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 
       28.54         0.79        28.60         1.97         1.68         2.37 
TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 
        2.93         1.71         0.72         2.10         2.66         1.74 
TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 
        1.48         1.68         2.07        24.59        26.04         1.97 
TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 
        1.12         3.22        30.51         1.48        17.85        24.56 
TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 
        1.84        19.36        22.42         3.12        23.87         2.17 
TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 
        2.27         1.94        17.95        22.32         1.58        15.88 
TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL 
        1.15        22.36         0.76         1.78         2.01         2.20 
TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX 
        1.61         5.49         2.33         3.48         1.45         1.25 
TCGA-HC-A6HY TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 
        4.41        78.61        88.24        82.92        43.69        20.19 
TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O 
       12.30        21.76        17.03        16.04        16.54        16.14 
TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 
       20.52        14.93        17.19         6.02        13.32        17.36 
TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M 
        9.17         9.17        10.19         6.77        10.39        14.37 
TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-KK-A59V TCGA-KK-A59X 
       20.28        13.87         5.85        10.62        93.99        56.28 
TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 
       44.68        61.78       115.86        30.02        54.54       151.36 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 
       67.59        90.51        49.25       113.33        67.07        58.19 
TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IB TCGA-KK-A8IF TCGA-KK-A8IL 
       27.62        34.95        22.75         2.73        26.43        20.65 
TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 
        5.19         6.87         9.93        13.15        27.02        25.08 
TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO 
       15.88        18.84         3.19        41.00       114.64        47.21 
TCGA-QU-A6IP TCGA-TP-A8TT TCGA-TP-A8TV TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L 
       86.14        11.90         8.19         8.84        25.51        12.95 
TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R 
        6.02        15.52        15.81        30.15        32.91        15.09 
TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B 
        4.34       106.95        84.69        94.65        23.93        75.91 
TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K 
       55.56        60.92        66.97        21.80        48.85        21.53 
TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83G 
       17.82         5.79        37.18        27.81         3.91        38.04 
TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV 
       48.03         9.04         2.99        25.97        31.96        31.50 
TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJU 
       31.96        28.54        30.58        29.23        27.09        39.65 
TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8S8 
       25.48        52.96        49.02        38.56        36.95        62.14 
TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH 
       60.56        16.83        45.50        41.46        45.14        28.77 
TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP 
       47.38        45.86        37.97        26.24       106.75        71.34 
TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK 
       62.79         7.00        14.04        41.39        60.99        62.37 
TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY 
       24.33        49.91        28.34         1.64         4.93         1.12 
TCGA-ZG-A8QZ TCGA-ZG-A9ND 
        7.86         6.02 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
             2.01              0.30 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            71.77            151.36 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            29.06             23.90 
[1] "2.0 - 71.8 (29.1)"  "0.3 - 151.4 (23.9)"
[1] "hr="     "9200000"
D8V2, continuous
                   vv
clus                 T2  T3  T4
  4Q GAIN MUTATED     1   4   0
  4Q GAIN WILD-TYPE 149 202   5
D8V3, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  T2               1               149
  T3               4               202
  T4               0                 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"
D8V4, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     5   0
  4Q GAIN WILD-TYPE 258  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      5    0
  4Q GAIN WILD-TYPE  258   44
   clus
vv  4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  0               5               258
  1               0                44
[1] 2 2
[1] FALSE
D8V5, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     0   5
  4Q GAIN WILD-TYPE  13 345
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      0    5
  4Q GAIN WILD-TYPE   13  345
                                        clus
vv                                       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE               0                13
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  5               345
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  4Q GAIN MUTATED     3   2   0   0
  4Q GAIN WILD-TYPE 240  88   5  11
D8V6, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  R0               3               240
  R1               2                88
  R2               0                 5
  RX               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"
D8V7, continuous
D8V8, continuous
D8V9, continuous
D8V10, continuous
D8V11, continuous
D8V12, continuous
D8V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4Q GAIN MUTATED       0                         0     2
  4Q GAIN WILD-TYPE     2                         7   144
D8V14, multiclass
[1] "Remove cluster labels:" "4Q GAIN MUTATED"       
clus
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                2               153 
       TCGA-CH-5737        TCGA-CH-5738        TCGA-CH-5739        TCGA-CH-5740 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CH-5741        TCGA-CH-5743        TCGA-CH-5744        TCGA-CH-5746 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CH-5748        TCGA-CH-5750        TCGA-CH-5751        TCGA-CH-5752 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CH-5753        TCGA-CH-5754        TCGA-CH-5761        TCGA-CH-5762 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CH-5763        TCGA-CH-5764        TCGA-CH-5765        TCGA-CH-5766 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CH-5767        TCGA-CH-5768        TCGA-CH-5769        TCGA-CH-5771 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CH-5772        TCGA-CH-5788        TCGA-CH-5789        TCGA-CH-5790 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CH-5791        TCGA-CH-5792        TCGA-CH-5794        TCGA-EJ-5494 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EJ-5495        TCGA-EJ-5496        TCGA-EJ-5497        TCGA-EJ-5498 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EJ-5499        TCGA-EJ-5501        TCGA-EJ-5503        TCGA-EJ-5504 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EJ-5505        TCGA-EJ-5506        TCGA-EJ-5507        TCGA-EJ-5508 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EJ-5509        TCGA-EJ-5510        TCGA-EJ-5511        TCGA-EJ-5512 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EJ-5514        TCGA-EJ-5515        TCGA-EJ-5516        TCGA-EJ-5517 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EJ-5518        TCGA-EJ-5519        TCGA-EJ-5521        TCGA-EJ-5522 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EJ-5524        TCGA-EJ-5525        TCGA-EJ-5526        TCGA-EJ-5527 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EJ-5530        TCGA-EJ-5531        TCGA-EJ-5532        TCGA-EJ-7115 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EJ-7123        TCGA-EJ-7125        TCGA-EJ-7314        TCGA-EJ-7315 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EJ-7317        TCGA-EJ-7321        TCGA-EJ-7327        TCGA-EJ-7328 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EJ-7330        TCGA-EJ-7331        TCGA-EJ-7781        TCGA-EJ-7782 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EJ-7783        TCGA-EJ-7784        TCGA-EJ-7785        TCGA-EJ-7786 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EJ-7788        TCGA-EJ-7789        TCGA-EJ-7791        TCGA-EJ-7792 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EJ-7793        TCGA-EJ-7794        TCGA-EJ-7797        TCGA-FC-7708 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-FC-7961        TCGA-G9-6329        TCGA-G9-6332        TCGA-G9-6333 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G9-6336        TCGA-G9-6338        TCGA-G9-6342        TCGA-G9-6343 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G9-6348        TCGA-G9-6351        TCGA-G9-6353        TCGA-G9-6356 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G9-6361        TCGA-G9-6362        TCGA-G9-6363        TCGA-G9-6364 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G9-6365        TCGA-G9-6366        TCGA-G9-6367        TCGA-G9-6369 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G9-6370        TCGA-G9-6371        TCGA-G9-6373        TCGA-G9-6377 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G9-6378        TCGA-G9-6384        TCGA-G9-6385        TCGA-G9-6494 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G9-6496        TCGA-G9-6499        TCGA-H9-7775        TCGA-HC-7075 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-HC-7077        TCGA-HC-7078        TCGA-HC-7079        TCGA-HC-7081 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-HC-7209        TCGA-HC-7210        TCGA-HC-7211        TCGA-HC-7212 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-HC-7213        TCGA-HC-7230        TCGA-HC-7231        TCGA-HC-7232 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-HC-7233        TCGA-HC-7736        TCGA-HC-7737        TCGA-HC-7738 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-HC-7740        TCGA-HC-7742        TCGA-HC-7744        TCGA-HC-7745 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-HC-7747        TCGA-HC-7748        TCGA-HC-7749        TCGA-HC-7750 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-HC-7752        TCGA-HC-7818        TCGA-HC-7819        TCGA-HC-7820 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-HC-7821        TCGA-HI-7168        TCGA-HI-7169        TCGA-HI-7170 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-HI-7171 
"4Q GAIN WILD-TYPE" 

Clustering(9) Variable = 5P GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                 0   1
  5P GAIN MUTATED    15   0
  5P GAIN WILD-TYPE 340   6
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               15               346 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                0                 6 
$`5P GAIN MUTATED`
TCGA-CH-5761 TCGA-EJ-5495 TCGA-FC-A4JI TCGA-HC-A4ZV TCGA-J9-A52E TCGA-KK-A8IB 
        0.92        33.11        13.45         0.76        10.62         2.73 
TCGA-KK-A8IF TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A87H TCGA-XK-AAIV TCGA-YL-A8HO 
       26.43       106.95        26.47        21.80        31.50        71.77 
TCGA-YL-A8SL TCGA-YL-A9WH TCGA-ZG-A8QZ 
       26.24        14.04         7.86 

$`5P GAIN WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 
        1.02         2.04        44.02        12.00         1.02        23.01 
TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 
        1.02        15.06        24.03         2.04        13.02        15.98 
TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 
       26.99         9.99        32.02        33.01         2.99        29.00 
TCGA-EJ-5494 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 
       27.16        19.56        13.32        29.79        46.52        44.88 
TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 
       26.30        45.73        28.93        30.31        27.19        23.90 
TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 
       38.93        48.13        36.69        48.53        38.53        36.23 
TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 
       60.23        46.55        47.80        52.27        64.50        51.88 
TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 
       68.35        43.07        36.66        38.76        39.75        60.23 
TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 
       41.85        47.87        29.06        27.02        49.02        61.15 
TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 
       83.57        21.80         9.70         9.50         9.37        16.77 
TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 
        7.66        17.52         5.75        27.68         6.28         0.30 
TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 
       23.90        38.37        25.87        25.68        20.55        14.53 
TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 
       14.14        18.15        19.59        17.29         3.75        23.05 
TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8474 TCGA-EJ-A46B 
       19.92        64.47        63.98        26.99        10.32         5.33 
TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I 
        4.24        17.49         9.83         3.06         7.53        21.96 
TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J 
       17.62        12.92        13.71        18.41         9.14         2.99 
TCGA-EJ-A65M TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD 
        7.56        28.41        15.42         8.98        17.23        16.24 
TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 
        1.78        41.62        87.35        81.04        67.99        66.67 
TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 
       69.37        55.76        18.21        68.68        49.81        46.16 
TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 
       50.70        49.35        47.15        46.52        47.44        45.30 
TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 
       39.39        44.81         3.32        40.18        39.95        38.01 
TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 
       40.31        26.66        31.50        37.97        45.80        25.15 
TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 
       27.29        58.22        56.75        52.87        50.73        38.27 
TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 
       38.96        27.91        30.97        35.34        28.18        32.68 
TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 
       26.01        21.14         6.08        30.94         3.68        19.76 
TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 
        5.33         2.93         2.01         2.37        14.47        28.54 
TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 
        0.79        28.60         1.97         1.68         2.37         2.93 
TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 
        1.71         0.72         2.10         2.66         1.74         1.48 
TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 
        1.68         2.07        24.59        26.04         1.97         1.12 
TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 
        3.22        30.51         1.48        17.85        24.56         1.84 
TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 
       19.36        22.42         3.12        23.87         2.17         2.27 
TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 
        1.94        17.95        22.32         1.58        15.88         1.15 
TCGA-HC-A48F TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO 
       22.36         1.78         2.01         2.20         1.61         5.49 
TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HI-7168 
        2.33         3.48         1.45         1.25         4.41        78.61 
TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K 
       88.24        82.92        43.69        20.19        12.30        21.76 
TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R 
       17.03        16.04        16.54        16.14        20.52        14.93 
TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I 
       17.19         6.02        13.32        17.36         9.17         9.17 
TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B 
       10.19         6.77        10.39        14.37        20.28        13.87 
TCGA-J9-A52C TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY 
        5.85        93.99        56.28        44.68        61.78       115.86 
TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 
       30.02        54.54       151.36        67.59        90.51        49.25 
TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 
      113.33        67.07        58.19        27.62        34.95        22.75 
TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 
       20.65         5.19         6.87         9.93        13.15        27.02 
TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN 
       25.08        15.88        18.84         3.19        41.00       114.64 
TCGA-QU-A6IO TCGA-QU-A6IP TCGA-TP-A8TT TCGA-TP-A8TV TCGA-VN-A88I TCGA-VN-A88K 
       47.21        86.14        11.90         8.19         8.84        25.51 
TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q 
       12.95         6.02        15.52        15.81        30.15        32.91 
TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B 
       15.09         4.34        84.69        94.65        23.93        75.91 
TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N 
       55.56        60.92        66.97        48.85        21.53        17.82 
TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DI 
        5.79        37.18        27.81         3.91        38.04        48.03 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIW TCGA-XK-AAJ3 
        9.04         2.99        25.97        31.96        31.96        28.54 
TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-Y6-A8TL 
       30.58        29.23        27.09        37.02        39.65        25.48 
TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8S8 TCGA-YL-A8S9 
       52.96        49.02        38.56        36.95        62.14        60.56 
TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI 
       16.83        45.50        41.46        45.14        28.77        47.38 
TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR 
       45.86        37.97       106.75        71.34        62.79         7.00 
TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY 
       41.39        60.99        62.37        24.33        49.91        28.34 
TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A9ND 
        1.64         4.93         1.12         6.02 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             0.76              0.30 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           106.95            151.36 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            21.80             23.98 
[1] "0.8 - 107.0 (21.8)" "0.3 - 151.4 (24.0)"
[1] "hr="     "2.6e+07"
D9V2, continuous
                   vv
clus                 T2  T3  T4
  5P GAIN MUTATED     0  15   0
  5P GAIN WILD-TYPE 150 191   5
D9V3, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  T2               0               150
  T3              15               191
  T4               0                 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"
D9V4, binary
                   cls
clus                  0   1
  5P GAIN MUTATED     9   5
  5P GAIN WILD-TYPE 254  39
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      9    5
  5P GAIN WILD-TYPE  254   39
   clus
vv  5P GAIN MUTATED 5P GAIN WILD-TYPE
  0               9               254
  1               5                39
[1] 2 2
[1] FALSE
D9V5, binary
                   cls
clus                  0   1
  5P GAIN MUTATED     1  14
  5P GAIN WILD-TYPE  12 336
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      1   14
  5P GAIN WILD-TYPE   12  336
                                        clus
vv                                       5P GAIN MUTATED 5P GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE               1                12
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 14               336
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  5P GAIN MUTATED     8   6   1   0
  5P GAIN WILD-TYPE 235  84   4  11
D9V6, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  R0               8               235
  R1               6                84
  R2               1                 4
  RX               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"
D9V7, continuous
D9V8, continuous
D9V9, continuous
D9V10, continuous
D9V11, continuous
D9V12, continuous
D9V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5P GAIN MUTATED       0                         0     2
  5P GAIN WILD-TYPE     2                         7   144
D9V14, multiclass
[1] "Remove cluster labels:" "5P GAIN MUTATED"       
clus
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                2               153 
       TCGA-CH-5737        TCGA-CH-5738        TCGA-CH-5739        TCGA-CH-5740 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CH-5741        TCGA-CH-5743        TCGA-CH-5744        TCGA-CH-5746 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CH-5748        TCGA-CH-5750        TCGA-CH-5751        TCGA-CH-5752 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CH-5753        TCGA-CH-5754        TCGA-CH-5762        TCGA-CH-5763 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CH-5764        TCGA-CH-5765        TCGA-CH-5766        TCGA-CH-5767 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CH-5768        TCGA-CH-5769        TCGA-CH-5771        TCGA-CH-5772 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CH-5788        TCGA-CH-5789        TCGA-CH-5790        TCGA-CH-5791 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-CH-5792        TCGA-CH-5794        TCGA-EJ-5494        TCGA-EJ-5496 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EJ-5497        TCGA-EJ-5498        TCGA-EJ-5499        TCGA-EJ-5501 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EJ-5503        TCGA-EJ-5504        TCGA-EJ-5505        TCGA-EJ-5506 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EJ-5507        TCGA-EJ-5508        TCGA-EJ-5509        TCGA-EJ-5510 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EJ-5511        TCGA-EJ-5512        TCGA-EJ-5514        TCGA-EJ-5515 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EJ-5516        TCGA-EJ-5517        TCGA-EJ-5518        TCGA-EJ-5519 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EJ-5521        TCGA-EJ-5522        TCGA-EJ-5524        TCGA-EJ-5525 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EJ-5526        TCGA-EJ-5527        TCGA-EJ-5530        TCGA-EJ-5531 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EJ-5532        TCGA-EJ-5542        TCGA-EJ-7115        TCGA-EJ-7123 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EJ-7125        TCGA-EJ-7314        TCGA-EJ-7315        TCGA-EJ-7317 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EJ-7321        TCGA-EJ-7327        TCGA-EJ-7328        TCGA-EJ-7330 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EJ-7331        TCGA-EJ-7781        TCGA-EJ-7782        TCGA-EJ-7783 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EJ-7784        TCGA-EJ-7785        TCGA-EJ-7786        TCGA-EJ-7788 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EJ-7789        TCGA-EJ-7791        TCGA-EJ-7792        TCGA-EJ-7793 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EJ-7794        TCGA-EJ-7797        TCGA-FC-7708        TCGA-FC-7961 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-G9-6329        TCGA-G9-6332        TCGA-G9-6333        TCGA-G9-6336 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-G9-6338        TCGA-G9-6342        TCGA-G9-6343        TCGA-G9-6348 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-G9-6351        TCGA-G9-6353        TCGA-G9-6356        TCGA-G9-6361 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-G9-6362        TCGA-G9-6363        TCGA-G9-6364        TCGA-G9-6365 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-G9-6366        TCGA-G9-6367        TCGA-G9-6369        TCGA-G9-6370 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-G9-6371        TCGA-G9-6373        TCGA-G9-6377        TCGA-G9-6378 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-G9-6384        TCGA-G9-6385        TCGA-G9-6494        TCGA-G9-6496 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-G9-6499        TCGA-H9-7775        TCGA-HC-7075        TCGA-HC-7077 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-HC-7078        TCGA-HC-7079        TCGA-HC-7080        TCGA-HC-7081 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-HC-7209        TCGA-HC-7210        TCGA-HC-7211        TCGA-HC-7212 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-HC-7213        TCGA-HC-7230        TCGA-HC-7231        TCGA-HC-7232 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-HC-7233        TCGA-HC-7736        TCGA-HC-7737        TCGA-HC-7738 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-HC-7740        TCGA-HC-7742        TCGA-HC-7744        TCGA-HC-7745 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-HC-7747        TCGA-HC-7748        TCGA-HC-7749        TCGA-HC-7750 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-HC-7752        TCGA-HC-7818        TCGA-HC-7819        TCGA-HC-7820 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-HC-7821        TCGA-HI-7168        TCGA-HI-7169        TCGA-HI-7170 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-HI-7171 
"5P GAIN WILD-TYPE" 

Clustering(10) Variable = 5Q GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                 0   1
  5Q GAIN MUTATED     8   0
  5Q GAIN WILD-TYPE 347   6
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                8               353 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                0                 6 
$`5Q GAIN MUTATED`
TCGA-EJ-5495 TCGA-J9-A52E TCGA-KK-A8IB TCGA-VP-A875 TCGA-VP-A87H TCGA-YL-A8HO 
       33.11        10.62         2.73        26.47        21.80        71.77 
TCGA-YL-A8SL TCGA-ZG-A8QZ 
       26.24         7.86 

$`5Q GAIN WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 
        1.02         2.04         0.92        44.02        12.00         1.02 
TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 
       23.01         1.02        15.06        24.03         2.04        13.02 
TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 
       15.98        26.99         9.99        32.02        33.01         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
       29.00        27.16        19.56        13.32        29.79        46.52 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       44.88        26.30        45.73        28.93        30.31        27.19 
TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       23.90        38.93        48.13        36.69        48.53        38.53 
TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 
       36.23        60.23        46.55        47.80        52.27        64.50 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 
       51.88        68.35        43.07        36.66        38.76        39.75 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 
       60.23        41.85        47.87        29.06        27.02        49.02 
TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 
       61.15        83.57        21.80         9.70         9.50         9.37 
TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 
       16.77         7.66        17.52         5.75        27.68         6.28 
TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 
        0.30        23.90        38.37        25.87        25.68        20.55 
TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 
       14.53        14.14        18.15        19.59        17.29         3.75 
TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8474 
       23.05        19.92        64.47        63.98        26.99        10.32 
TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H 
        5.33         4.24        17.49         9.83         3.06         7.53 
TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G 
       21.96        17.62        12.92        13.71        18.41         9.14 
TCGA-EJ-A65J TCGA-EJ-A65M TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB 
        2.99         7.56        28.41        15.42        13.45         8.98 
TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 
       17.23        16.24         1.78        41.62        87.35        81.04 
TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 
       67.99        66.67        69.37        55.76        18.21        68.68 
TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 
       49.81        46.16        50.70        49.35        47.15        46.52 
TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 
       47.44        45.30        39.39        44.81         3.32        40.18 
TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 
       39.95        38.01        40.31        26.66        31.50        37.97 
TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 
       45.80        25.15        27.29        58.22        56.75        52.87 
TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 
       50.73        38.27        38.96        27.91        30.97        35.34 
TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX 
       28.18        32.68        26.01        21.14         6.08        30.94 
TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 
        3.68        19.76         5.33         2.93         2.01         2.37 
TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 
       14.47        28.54         0.79        28.60         1.97         1.68 
TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 
        2.37         2.93         1.71         0.72         2.10         2.66 
TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 
        1.74         1.48         1.68         2.07        24.59        26.04 
TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 
        1.97         1.12         3.22        30.51         1.48        17.85 
TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 
       24.56         1.84        19.36        22.42         3.12        23.87 
TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 
        2.17         2.27         1.94        17.95        22.32         1.58 
TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 
       15.88         1.15        22.36         0.76         1.78         2.01 
TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS 
        2.20         1.61         5.49         2.33         3.48         1.45 
TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
        1.25         4.41        78.61        88.24        82.92        43.69 
TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N 
       20.19        12.30        21.76        17.03        16.04        16.54 
TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 
       16.14        20.52        14.93        17.19         6.02        13.32 
TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L 
       17.36         9.17         9.17        10.19         6.77        10.39 
TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52C TCGA-KK-A59V TCGA-KK-A59X 
       14.37        20.28        13.87         5.85        93.99        56.28 
TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 
       44.68        61.78       115.86        30.02        54.54       151.36 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 
       67.59        90.51        49.25       113.33        67.07        58.19 
TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IF TCGA-KK-A8IL TCGA-M7-A71Y 
       27.62        34.95        22.75        26.43        20.65         5.19 
TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 
        6.87         9.93        13.15        27.02        25.08        15.88 
TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP 
       18.84         3.19        41.00       114.64        47.21        86.14 
TCGA-TP-A8TT TCGA-TP-A8TV TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M 
       11.90         8.19         8.84        25.51        12.95         6.02 
TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 
       15.52        15.81        30.15        32.91        15.09         4.34 
TCGA-VP-A872 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C 
      106.95        84.69        94.65        23.93        75.91        55.56 
TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI 
       60.92        66.97        48.85        21.53        17.82         5.79 
TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK 
       37.18        27.81         3.91        38.04        48.03         9.04 
TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 
        2.99        25.97        31.96        31.50        31.96        28.54 
TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-Y6-A8TL 
       30.58        29.23        27.09        37.02        39.65        25.48 
TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8S8 TCGA-YL-A8S9 
       52.96        49.02        38.56        36.95        62.14        60.56 
TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI 
       16.83        45.50        41.46        45.14        28.77        47.38 
TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR 
       45.86        37.97       106.75        71.34        62.79         7.00 
TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX 
       14.04        41.39        60.99        62.37        24.33        49.91 
TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A9ND 
       28.34         1.64         4.93         1.12         6.02 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             2.73              0.30 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            71.77            151.36 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            24.02             23.93 
[1] "2.7 - 71.8 (24.0)"  "0.3 - 151.4 (23.9)"
[1] "hr="     "9200000"
D10V2, continuous
                   vv
clus                 T2  T3  T4
  5Q GAIN MUTATED     0   8   0
  5Q GAIN WILD-TYPE 150 198   5
D10V3, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T2               0               150
  T3               8               198
  T4               0                 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"
D10V4, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     5   3
  5Q GAIN WILD-TYPE 258  41
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      5    3
  5Q GAIN WILD-TYPE  258   41
   clus
vv  5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  0               5               258
  1               3                41
[1] 2 2
[1] FALSE
D10V5, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     0   8
  5Q GAIN WILD-TYPE  13 342
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      0    8
  5Q GAIN WILD-TYPE   13  342
                                        clus
vv                                       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE               0                13
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  8               342
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  5Q GAIN MUTATED     4   3   1   0
  5Q GAIN WILD-TYPE 239  87   4  11
D10V6, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  R0               4               239
  R1               3                87
  R2               1                 4
  RX               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"
D10V7, continuous
D10V8, continuous
D10V9, continuous
D10V10, continuous
D10V11, continuous
D10V12, continuous
D10V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5Q GAIN MUTATED       0                         0     1
  5Q GAIN WILD-TYPE     2                         7   145
D10V14, multiclass
[1] "Remove cluster labels:" "5Q GAIN MUTATED"       
clus
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                1               154 
       TCGA-CH-5737        TCGA-CH-5738        TCGA-CH-5739        TCGA-CH-5740 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CH-5741        TCGA-CH-5743        TCGA-CH-5744        TCGA-CH-5746 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CH-5748        TCGA-CH-5750        TCGA-CH-5751        TCGA-CH-5752 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CH-5753        TCGA-CH-5754        TCGA-CH-5761        TCGA-CH-5762 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CH-5763        TCGA-CH-5764        TCGA-CH-5765        TCGA-CH-5766 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CH-5767        TCGA-CH-5768        TCGA-CH-5769        TCGA-CH-5771 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CH-5772        TCGA-CH-5788        TCGA-CH-5789        TCGA-CH-5790 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CH-5791        TCGA-CH-5792        TCGA-CH-5794        TCGA-EJ-5494 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EJ-5496        TCGA-EJ-5497        TCGA-EJ-5498        TCGA-EJ-5499 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EJ-5501        TCGA-EJ-5503        TCGA-EJ-5504        TCGA-EJ-5505 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EJ-5506        TCGA-EJ-5507        TCGA-EJ-5508        TCGA-EJ-5509 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EJ-5510        TCGA-EJ-5511        TCGA-EJ-5512        TCGA-EJ-5514 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EJ-5515        TCGA-EJ-5516        TCGA-EJ-5517        TCGA-EJ-5518 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EJ-5519        TCGA-EJ-5521        TCGA-EJ-5522        TCGA-EJ-5524 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EJ-5525        TCGA-EJ-5526        TCGA-EJ-5527        TCGA-EJ-5530 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EJ-5531        TCGA-EJ-5532        TCGA-EJ-5542        TCGA-EJ-7115 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EJ-7123        TCGA-EJ-7125        TCGA-EJ-7314        TCGA-EJ-7315 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EJ-7317        TCGA-EJ-7321        TCGA-EJ-7327        TCGA-EJ-7328 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EJ-7330        TCGA-EJ-7331        TCGA-EJ-7781        TCGA-EJ-7782 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EJ-7783        TCGA-EJ-7784        TCGA-EJ-7785        TCGA-EJ-7786 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EJ-7788        TCGA-EJ-7789        TCGA-EJ-7791        TCGA-EJ-7792 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EJ-7793        TCGA-EJ-7794        TCGA-EJ-7797        TCGA-FC-7708 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-FC-7961        TCGA-G9-6329        TCGA-G9-6332        TCGA-G9-6333 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-G9-6336        TCGA-G9-6338        TCGA-G9-6342        TCGA-G9-6343 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-G9-6348        TCGA-G9-6351        TCGA-G9-6353        TCGA-G9-6356 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-G9-6361        TCGA-G9-6362        TCGA-G9-6363        TCGA-G9-6364 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-G9-6365        TCGA-G9-6366        TCGA-G9-6367        TCGA-G9-6369 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-G9-6370        TCGA-G9-6371        TCGA-G9-6373        TCGA-G9-6377 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-G9-6378        TCGA-G9-6384        TCGA-G9-6385        TCGA-G9-6494 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-G9-6496        TCGA-G9-6499        TCGA-H9-7775        TCGA-HC-7075 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-HC-7077        TCGA-HC-7078        TCGA-HC-7079        TCGA-HC-7080 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-HC-7081        TCGA-HC-7209        TCGA-HC-7210        TCGA-HC-7211 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-HC-7212        TCGA-HC-7213        TCGA-HC-7230        TCGA-HC-7231 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-HC-7232        TCGA-HC-7233        TCGA-HC-7736        TCGA-HC-7737 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-HC-7738        TCGA-HC-7740        TCGA-HC-7742        TCGA-HC-7744 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-HC-7745        TCGA-HC-7747        TCGA-HC-7748        TCGA-HC-7749 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-HC-7750        TCGA-HC-7752        TCGA-HC-7818        TCGA-HC-7819 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-HC-7820        TCGA-HC-7821        TCGA-HI-7168        TCGA-HI-7169 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-HI-7170        TCGA-HI-7171 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 

Clustering(11) Variable = 6P GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                 0   1
  6P GAIN MUTATED     4   1
  6P GAIN WILD-TYPE 351   5
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                5               356 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                1                 5 
$`6P GAIN MUTATED`
TCGA-HI-7168 TCGA-KK-A59Z TCGA-XJ-A9DX TCGA-XK-AAJT TCGA-YL-A9WJ 
       78.61        61.78        25.97        37.02        60.99 

$`6P GAIN WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 
        1.02         2.04         0.92        44.02        12.00         1.02 
TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 
       23.01         1.02        15.06        24.03         2.04        13.02 
TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 
       15.98        26.99         9.99        32.02        33.01         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        27.16        33.11        19.56        13.32        29.79 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        26.30        45.73        28.93        30.31 
TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 
       27.19        23.90        38.93        48.13        36.69        48.53 
TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 
       38.53        36.23        60.23        46.55        47.80        52.27 
TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 
       64.50        51.88        68.35        43.07        36.66        38.76 
TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 
       39.75        60.23        41.85        47.87        29.06        27.02 
TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 
       49.02        61.15        83.57        21.80         9.70         9.50 
TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 
        9.37        16.77         7.66        17.52         5.75        27.68 
TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 
        6.28         0.30        23.90        38.37        25.87        25.68 
TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 
       20.55        14.53        14.14        18.15        19.59        17.29 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 
        3.75        23.05        19.92        64.47        63.98        26.99 
TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G 
       10.32         5.33         4.24        17.49         9.83         3.06 
TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F 
        7.53        21.96        17.62        12.92        13.71        18.41 
TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI 
        9.14         2.99         7.56        28.41        15.42        13.45 
TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 
        8.98        17.23        16.24         1.78        41.62        87.35 
TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 
       81.04        67.99        66.67        69.37        55.76        18.21 
TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 
       68.68        49.81        46.16        50.70        49.35        47.15 
TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 
       46.52        47.44        45.30        39.39        44.81         3.32 
TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 
       40.18        39.95        38.01        40.31        26.66        31.50 
TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 
       37.97        45.80        25.15        27.29        58.22        56.75 
TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 
       52.87        50.73        38.27        38.96        27.91        30.97 
TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 
       35.34        28.18        32.68        26.01        21.14         6.08 
TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 
       30.94         3.68        19.76         5.33         2.93         2.01 
TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 
        2.37        14.47        28.54         0.79        28.60         1.97 
TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 
        1.68         2.37         2.93         1.71         0.72         2.10 
TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 
        2.66         1.74         1.48         1.68         2.07        24.59 
TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 
       26.04         1.97         1.12         3.22        30.51         1.48 
TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 
       17.85        24.56         1.84        19.36        22.42         3.12 
TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 
       23.87         2.17         2.27         1.94        17.95        22.32 
TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 
        1.58        15.88         1.15        22.36         0.76         1.78 
TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ 
        2.01         2.20         1.61         5.49         2.33         3.48 
TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
        1.45         1.25         4.41        88.24        82.92        43.69 
TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N 
       20.19        12.30        21.76        17.03        16.04        16.54 
TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 
       16.14        20.52        14.93        17.19         6.02        13.32 
TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L 
       17.36         9.17         9.17        10.19         6.77        10.39 
TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-KK-A59V 
       14.37        20.28        13.87         5.85        10.62        93.99 
TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 
       56.28        44.68       115.86        30.02        54.54       151.36 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 
       67.59        90.51        49.25       113.33        67.07        58.19 
TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IB TCGA-KK-A8IF TCGA-KK-A8IL 
       27.62        34.95        22.75         2.73        26.43        20.65 
TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 
        5.19         6.87         9.93        13.15        27.02        25.08 
TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO 
       15.88        18.84         3.19        41.00       114.64        47.21 
TCGA-QU-A6IP TCGA-TP-A8TT TCGA-TP-A8TV TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L 
       86.14        11.90         8.19         8.84        25.51        12.95 
TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R 
        6.02        15.52        15.81        30.15        32.91        15.09 
TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 
        4.34       106.95        26.47        84.69        94.65        23.93 
TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J 
       75.91        55.56        60.92        66.97        21.80        48.85 
TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR 
       21.53        17.82         5.79        37.18        27.81         3.91 
TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XK-AAIR TCGA-XK-AAIV 
       38.04        48.03         9.04         2.99        31.96        31.50 
TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJU 
       31.96        28.54        30.58        29.23        27.09        39.65 
TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO 
       25.48        52.96        49.02        38.56        36.95        71.77 
TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF 
       62.14        60.56        16.83        45.50        41.46        45.14 
TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO 
       28.77        47.38        45.86        37.97        26.24       106.75 
TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WK 
       71.34        62.79         7.00        14.04        41.39        62.37 
TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY 
       24.33        49.91        28.34         1.64         4.93         1.12 
TCGA-ZG-A8QZ TCGA-ZG-A9ND 
        7.86         6.02 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            25.97              0.30 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            78.61            151.36 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           60.990            23.885 
[1] "26.0 - 78.6 (61.0)" "0.3 - 151.4 (23.9)"
[1] "hr=" "5.4"
D11V2, continuous
                   vv
clus                 T2  T3  T4
  6P GAIN MUTATED     1   4   0
  6P GAIN WILD-TYPE 149 202   5
D11V3, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  T2               1               149
  T3               4               202
  T4               0                 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"
D11V4, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     3   2
  6P GAIN WILD-TYPE 260  42
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      3    2
  6P GAIN WILD-TYPE  260   42
   clus
vv  6P GAIN MUTATED 6P GAIN WILD-TYPE
  0               3               260
  1               2                42
[1] 2 2
[1] FALSE
D11V5, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     1   4
  6P GAIN WILD-TYPE  12 346
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      1    4
  6P GAIN WILD-TYPE   12  346
                                        clus
vv                                       6P GAIN MUTATED 6P GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE               1                12
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  4               346
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  6P GAIN MUTATED     2   3   0   0
  6P GAIN WILD-TYPE 241  87   5  11
D11V6, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  R0               2               241
  R1               3                87
  R2               0                 5
  RX               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"
D11V7, continuous
D11V8, continuous
D11V9, continuous
D11V10, continuous
D11V11, continuous
D11V12, continuous
D11V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6P GAIN MUTATED       0                         0     1
  6P GAIN WILD-TYPE     2                         7   145
D11V14, multiclass
[1] "Remove cluster labels:" "6P GAIN MUTATED"       
clus
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                1               154 
       TCGA-CH-5737        TCGA-CH-5738        TCGA-CH-5739        TCGA-CH-5740 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CH-5741        TCGA-CH-5743        TCGA-CH-5744        TCGA-CH-5746 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CH-5748        TCGA-CH-5750        TCGA-CH-5751        TCGA-CH-5752 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CH-5753        TCGA-CH-5754        TCGA-CH-5761        TCGA-CH-5762 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CH-5763        TCGA-CH-5764        TCGA-CH-5765        TCGA-CH-5766 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CH-5767        TCGA-CH-5768        TCGA-CH-5769        TCGA-CH-5771 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CH-5772        TCGA-CH-5788        TCGA-CH-5789        TCGA-CH-5790 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-CH-5791        TCGA-CH-5792        TCGA-CH-5794        TCGA-EJ-5494 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EJ-5495        TCGA-EJ-5496        TCGA-EJ-5497        TCGA-EJ-5498 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EJ-5499        TCGA-EJ-5501        TCGA-EJ-5503        TCGA-EJ-5504 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EJ-5505        TCGA-EJ-5506        TCGA-EJ-5507        TCGA-EJ-5508 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EJ-5509        TCGA-EJ-5510        TCGA-EJ-5511        TCGA-EJ-5512 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EJ-5514        TCGA-EJ-5515        TCGA-EJ-5516        TCGA-EJ-5517 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EJ-5518        TCGA-EJ-5519        TCGA-EJ-5521        TCGA-EJ-5522 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EJ-5524        TCGA-EJ-5525        TCGA-EJ-5526        TCGA-EJ-5527 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EJ-5530        TCGA-EJ-5531        TCGA-EJ-5532        TCGA-EJ-5542 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EJ-7115        TCGA-EJ-7123        TCGA-EJ-7125        TCGA-EJ-7314 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EJ-7315        TCGA-EJ-7317        TCGA-EJ-7321        TCGA-EJ-7327 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EJ-7328        TCGA-EJ-7330        TCGA-EJ-7331        TCGA-EJ-7781 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EJ-7782        TCGA-EJ-7783        TCGA-EJ-7784        TCGA-EJ-7785 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EJ-7786        TCGA-EJ-7788        TCGA-EJ-7789        TCGA-EJ-7791 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EJ-7792        TCGA-EJ-7793        TCGA-EJ-7794        TCGA-EJ-7797 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-FC-7708        TCGA-FC-7961        TCGA-G9-6329        TCGA-G9-6332 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-G9-6333        TCGA-G9-6336        TCGA-G9-6338        TCGA-G9-6342 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-G9-6343        TCGA-G9-6348        TCGA-G9-6351        TCGA-G9-6353 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-G9-6356        TCGA-G9-6361        TCGA-G9-6362        TCGA-G9-6363 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-G9-6364        TCGA-G9-6365        TCGA-G9-6366        TCGA-G9-6367 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-G9-6369        TCGA-G9-6370        TCGA-G9-6371        TCGA-G9-6373 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-G9-6377        TCGA-G9-6378        TCGA-G9-6384        TCGA-G9-6385 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-G9-6494        TCGA-G9-6496        TCGA-G9-6499        TCGA-H9-7775 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HC-7075        TCGA-HC-7077        TCGA-HC-7078        TCGA-HC-7079 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HC-7080        TCGA-HC-7081        TCGA-HC-7209        TCGA-HC-7210 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HC-7211        TCGA-HC-7212        TCGA-HC-7213        TCGA-HC-7230 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HC-7231        TCGA-HC-7232        TCGA-HC-7233        TCGA-HC-7736 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HC-7737        TCGA-HC-7738        TCGA-HC-7740        TCGA-HC-7742 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HC-7744        TCGA-HC-7745        TCGA-HC-7747        TCGA-HC-7748 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HC-7749        TCGA-HC-7750        TCGA-HC-7752        TCGA-HC-7818 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HC-7819        TCGA-HC-7820        TCGA-HC-7821        TCGA-HI-7169 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HI-7170        TCGA-HI-7171 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 

Clustering(12) Variable = 6Q GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                 0   1
  6Q GAIN MUTATED     4   0
  6Q GAIN WILD-TYPE 351   6
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                4               357 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                0                 6 
$`6Q GAIN MUTATED`
TCGA-HI-7168 TCGA-KK-A59Z TCGA-XJ-A9DX TCGA-XK-AAJT 
       78.61        61.78        25.97        37.02 

$`6Q GAIN WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 
        1.02         2.04         0.92        44.02        12.00         1.02 
TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 
       23.01         1.02        15.06        24.03         2.04        13.02 
TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 
       15.98        26.99         9.99        32.02        33.01         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        27.16        33.11        19.56        13.32        29.79 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        26.30        45.73        28.93        30.31 
TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 
       27.19        23.90        38.93        48.13        36.69        48.53 
TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 
       38.53        36.23        60.23        46.55        47.80        52.27 
TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 
       64.50        51.88        68.35        43.07        36.66        38.76 
TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 
       39.75        60.23        41.85        47.87        29.06        27.02 
TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 
       49.02        61.15        83.57        21.80         9.70         9.50 
TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 
        9.37        16.77         7.66        17.52         5.75        27.68 
TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 
        6.28         0.30        23.90        38.37        25.87        25.68 
TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 
       20.55        14.53        14.14        18.15        19.59        17.29 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 
        3.75        23.05        19.92        64.47        63.98        26.99 
TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G 
       10.32         5.33         4.24        17.49         9.83         3.06 
TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F 
        7.53        21.96        17.62        12.92        13.71        18.41 
TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI 
        9.14         2.99         7.56        28.41        15.42        13.45 
TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 
        8.98        17.23        16.24         1.78        41.62        87.35 
TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 
       81.04        67.99        66.67        69.37        55.76        18.21 
TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 
       68.68        49.81        46.16        50.70        49.35        47.15 
TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 
       46.52        47.44        45.30        39.39        44.81         3.32 
TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 
       40.18        39.95        38.01        40.31        26.66        31.50 
TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 
       37.97        45.80        25.15        27.29        58.22        56.75 
TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 
       52.87        50.73        38.27        38.96        27.91        30.97 
TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 
       35.34        28.18        32.68        26.01        21.14         6.08 
TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 
       30.94         3.68        19.76         5.33         2.93         2.01 
TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 
        2.37        14.47        28.54         0.79        28.60         1.97 
TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 
        1.68         2.37         2.93         1.71         0.72         2.10 
TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 
        2.66         1.74         1.48         1.68         2.07        24.59 
TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 
       26.04         1.97         1.12         3.22        30.51         1.48 
TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 
       17.85        24.56         1.84        19.36        22.42         3.12 
TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 
       23.87         2.17         2.27         1.94        17.95        22.32 
TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 
        1.58        15.88         1.15        22.36         0.76         1.78 
TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ 
        2.01         2.20         1.61         5.49         2.33         3.48 
TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
        1.45         1.25         4.41        88.24        82.92        43.69 
TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N 
       20.19        12.30        21.76        17.03        16.04        16.54 
TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 
       16.14        20.52        14.93        17.19         6.02        13.32 
TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L 
       17.36         9.17         9.17        10.19         6.77        10.39 
TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-KK-A59V 
       14.37        20.28        13.87         5.85        10.62        93.99 
TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 
       56.28        44.68       115.86        30.02        54.54       151.36 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 
       67.59        90.51        49.25       113.33        67.07        58.19 
TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IB TCGA-KK-A8IF TCGA-KK-A8IL 
       27.62        34.95        22.75         2.73        26.43        20.65 
TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 
        5.19         6.87         9.93        13.15        27.02        25.08 
TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO 
       15.88        18.84         3.19        41.00       114.64        47.21 
TCGA-QU-A6IP TCGA-TP-A8TT TCGA-TP-A8TV TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L 
       86.14        11.90         8.19         8.84        25.51        12.95 
TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R 
        6.02        15.52        15.81        30.15        32.91        15.09 
TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 
        4.34       106.95        26.47        84.69        94.65        23.93 
TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J 
       75.91        55.56        60.92        66.97        21.80        48.85 
TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR 
       21.53        17.82         5.79        37.18        27.81         3.91 
TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XK-AAIR TCGA-XK-AAIV 
       38.04        48.03         9.04         2.99        31.96        31.50 
TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJU 
       31.96        28.54        30.58        29.23        27.09        39.65 
TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO 
       25.48        52.96        49.02        38.56        36.95        71.77 
TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF 
       62.14        60.56        16.83        45.50        41.46        45.14 
TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO 
       28.77        47.38        45.86        37.97        26.24       106.75 
TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ 
       71.34        62.79         7.00        14.04        41.39        60.99 
TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX 
       62.37        24.33        49.91        28.34         1.64         4.93 
TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9ND 
        1.12         7.86         6.02 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            25.97              0.30 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            78.61            151.36 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
             49.4              23.9 
[1] "26.0 - 78.6 (49.4)" "0.3 - 151.4 (23.9)"
[1] "hr="     "2.5e+07"
D12V2, continuous
                   vv
clus                 T2  T3  T4
  6Q GAIN MUTATED     1   3   0
  6Q GAIN WILD-TYPE 149 203   5
D12V3, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  T2               1               149
  T3               3               203
  T4               0                 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"
D12V4, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     3   1
  6Q GAIN WILD-TYPE 260  43
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      3    1
  6Q GAIN WILD-TYPE  260   43
   clus
vv  6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  0               3               260
  1               1                43
[1] 2 2
[1] FALSE
D12V5, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     1   3
  6Q GAIN WILD-TYPE  12 347
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      1    3
  6Q GAIN WILD-TYPE   12  347
                                        clus
vv                                       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE               1                12
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  3               347
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  6Q GAIN MUTATED     2   2   0   0
  6Q GAIN WILD-TYPE 241  88   5  11
D12V6, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  R0               2               241
  R1               2                88
  R2               0                 5
  RX               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"
D12V7, continuous
D12V8, continuous
D12V9, continuous
D12V10, continuous
D12V11, continuous
D12V12, continuous
D12V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6Q GAIN MUTATED       0                         0     1
  6Q GAIN WILD-TYPE     2                         7   145
D12V14, multiclass
[1] "Remove cluster labels:" "6Q GAIN MUTATED"       
clus
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                1               154 
       TCGA-CH-5737        TCGA-CH-5738        TCGA-CH-5739        TCGA-CH-5740 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CH-5741        TCGA-CH-5743        TCGA-CH-5744        TCGA-CH-5746 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CH-5748        TCGA-CH-5750        TCGA-CH-5751        TCGA-CH-5752 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CH-5753        TCGA-CH-5754        TCGA-CH-5761        TCGA-CH-5762 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CH-5763        TCGA-CH-5764        TCGA-CH-5765        TCGA-CH-5766 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CH-5767        TCGA-CH-5768        TCGA-CH-5769        TCGA-CH-5771 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CH-5772        TCGA-CH-5788        TCGA-CH-5789        TCGA-CH-5790 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-CH-5791        TCGA-CH-5792        TCGA-CH-5794        TCGA-EJ-5494 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EJ-5495        TCGA-EJ-5496        TCGA-EJ-5497        TCGA-EJ-5498 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EJ-5499        TCGA-EJ-5501        TCGA-EJ-5503        TCGA-EJ-5504 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EJ-5505        TCGA-EJ-5506        TCGA-EJ-5507        TCGA-EJ-5508 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EJ-5509        TCGA-EJ-5510        TCGA-EJ-5511        TCGA-EJ-5512 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EJ-5514        TCGA-EJ-5515        TCGA-EJ-5516        TCGA-EJ-5517 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EJ-5518        TCGA-EJ-5519        TCGA-EJ-5521        TCGA-EJ-5522 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EJ-5524        TCGA-EJ-5525        TCGA-EJ-5526        TCGA-EJ-5527 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EJ-5530        TCGA-EJ-5531        TCGA-EJ-5532        TCGA-EJ-5542 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EJ-7115        TCGA-EJ-7123        TCGA-EJ-7125        TCGA-EJ-7314 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EJ-7315        TCGA-EJ-7317        TCGA-EJ-7321        TCGA-EJ-7327 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EJ-7328        TCGA-EJ-7330        TCGA-EJ-7331        TCGA-EJ-7781 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EJ-7782        TCGA-EJ-7783        TCGA-EJ-7784        TCGA-EJ-7785 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EJ-7786        TCGA-EJ-7788        TCGA-EJ-7789        TCGA-EJ-7791 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EJ-7792        TCGA-EJ-7793        TCGA-EJ-7794        TCGA-EJ-7797 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FC-7708        TCGA-FC-7961        TCGA-G9-6329        TCGA-G9-6332 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G9-6333        TCGA-G9-6336        TCGA-G9-6338        TCGA-G9-6342 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G9-6343        TCGA-G9-6348        TCGA-G9-6351        TCGA-G9-6353 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G9-6356        TCGA-G9-6361        TCGA-G9-6362        TCGA-G9-6363 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G9-6364        TCGA-G9-6365        TCGA-G9-6366        TCGA-G9-6367 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G9-6369        TCGA-G9-6370        TCGA-G9-6371        TCGA-G9-6373 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G9-6377        TCGA-G9-6378        TCGA-G9-6384        TCGA-G9-6385 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G9-6494        TCGA-G9-6496        TCGA-G9-6499        TCGA-H9-7775 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-HC-7075        TCGA-HC-7077        TCGA-HC-7078        TCGA-HC-7079 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-HC-7080        TCGA-HC-7081        TCGA-HC-7209        TCGA-HC-7210 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-HC-7211        TCGA-HC-7212        TCGA-HC-7213        TCGA-HC-7230 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-HC-7231        TCGA-HC-7232        TCGA-HC-7233        TCGA-HC-7736 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-HC-7737        TCGA-HC-7738        TCGA-HC-7740        TCGA-HC-7742 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-HC-7744        TCGA-HC-7745        TCGA-HC-7747        TCGA-HC-7748 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-HC-7749        TCGA-HC-7750        TCGA-HC-7752        TCGA-HC-7818 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-HC-7819        TCGA-HC-7820        TCGA-HC-7821        TCGA-HI-7169 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-HI-7170        TCGA-HI-7171 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 

Clustering(13) Variable = 7P GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                 0   1
  7P GAIN MUTATED    68   0
  7P GAIN WILD-TYPE 287   6
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               68               293 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                0                 6 
$`7P GAIN MUTATED`
TCGA-CH-5751 TCGA-CH-5754 TCGA-CH-5768 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 
       35.01         2.04        24.03        13.02        15.98        26.99 
TCGA-CH-5791 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5509 TCGA-EJ-5525 TCGA-EJ-5542 
       33.01        27.16        33.11        48.13        36.66        29.06 
TCGA-EJ-7125 TCGA-EJ-7314 TCGA-EJ-7330 TCGA-EJ-7784 TCGA-EJ-7786 TCGA-EJ-7789 
       61.15         9.70         6.28        25.68        14.53        18.15 
TCGA-EJ-A46F TCGA-EJ-A65M TCGA-FC-7961 TCGA-FC-A4JI TCGA-G9-6338 TCGA-G9-6366 
        9.83         7.56        15.42        13.45        66.67         3.32 
TCGA-G9-6371 TCGA-G9-6377 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7523 
       40.31        31.50        56.75        52.87        50.73        28.18 
TCGA-HC-7742 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8265 TCGA-HC-A4ZV TCGA-HC-A631 
        1.48         1.94        17.95        15.88         0.76         1.78 
TCGA-HC-A6AP TCGA-HI-7168 TCGA-J4-8198 TCGA-J9-A52E TCGA-KK-A59Z TCGA-KK-A6E8 
        2.33        78.61        20.19        10.62        61.78        58.19 
TCGA-KK-A8IB TCGA-KK-A8IF TCGA-M7-A721 TCGA-QU-A6IM TCGA-TP-A8TV TCGA-VN-A88P 
        2.73        26.43        13.15        41.00         8.19        30.15 
TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A87B TCGA-VP-A87H TCGA-VP-AA1N TCGA-X4-A8KQ 
      106.95        26.47        75.91        21.80        17.82        37.18 
TCGA-XK-AAIV TCGA-XK-AAJ3 TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8SB 
       31.50        28.54        36.95        71.77        62.14        45.50 
TCGA-YL-A8SF TCGA-YL-A8SO TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI 
       45.14       106.75        62.79         7.00        14.04        41.39 
TCGA-YL-A9WK TCGA-ZG-A8QX 
       62.37         4.93 

$`7P GAIN WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5753 
        1.97        24.03         1.02        13.02        31.00         1.02 
TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 
        0.92        44.02        12.00         1.02        23.01         1.02 
TCGA-CH-5767 TCGA-CH-5769 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5792 TCGA-CH-5794 
       15.06         2.04         9.99        32.02         2.99        29.00 
TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 
       19.56        13.32        29.79        46.52        44.88        26.30 
TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 
       45.73        28.93        30.31        27.19        23.90        38.93 
TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 
       36.69        48.53        38.53        36.23        60.23        46.55 
TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 
       47.80        52.27        64.50        51.88        68.35        43.07 
TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 
       38.76        39.75        60.23        41.85        47.87        27.02 
TCGA-EJ-7123 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 
       49.02        83.57        21.80         9.50         9.37        16.77 
TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7331 TCGA-EJ-7781 
        7.66        17.52         5.75        27.68         0.30        23.90 
TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7785 TCGA-EJ-7788 TCGA-EJ-7791 TCGA-EJ-7792 
       38.37        25.87        20.55        14.14        19.59        17.29 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 
        3.75        23.05        19.92        64.47        63.98        26.99 
TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46G TCGA-EJ-A46H 
       10.32         5.33         4.24        17.49         3.06         7.53 
TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G 
       21.96        17.62        12.92        13.71        18.41         9.14 
TCGA-EJ-A65J TCGA-FC-7708 TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 
        2.99        28.41         8.98        17.23        16.24         1.78 
TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6339 TCGA-G9-6342 
       41.62        87.35        81.04        67.99        69.37        55.76 
TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 
       18.21        68.68        49.81        46.16        50.70        49.35 
TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 
       47.15        46.52        47.44        45.30        39.39        44.81 
TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6373 TCGA-G9-6378 TCGA-G9-6379 
       40.18        39.95        38.01        26.66        37.97        45.80 
TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 
       25.15        27.29        58.22        38.27        38.96        27.91 
TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 
       30.97        35.34        32.68        26.01        21.14         6.08 
TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 
       30.94         3.68        19.76         5.33         2.93         2.01 
TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 
        2.37        14.47        28.54         0.79        28.60         1.97 
TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 
        1.68         2.37         2.93         1.71         0.72         2.10 
TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 
        2.66         1.74         1.68         2.07        24.59        26.04 
TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 
        1.97         1.12         3.22        30.51         1.48        17.85 
TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 
       24.56         1.84        19.36        22.42         3.12        23.87 
TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8266 TCGA-HC-A48F 
        2.17         2.27        22.32         1.58         1.15        22.36 
TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AQ TCGA-HC-A6AS 
        2.01         2.20         1.61         5.49         3.48         1.45 
TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8200 
        1.25         4.41        88.24        82.92        43.69        12.30 
TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q 
       21.76        17.03        16.04        16.54        16.14        20.52 
TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 
       14.93        17.19         6.02        13.32        17.36         9.17 
TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N 
        9.17        10.19         6.77        10.39        14.37        20.28 
TCGA-J9-A52B TCGA-J9-A52C TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A6DY 
       13.87         5.85        93.99        56.28        44.68       115.86 
TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 
       30.02        54.54       151.36        67.59        90.51        49.25 
TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IL 
      113.33        67.07        27.62        34.95        22.75        20.65 
TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 
        5.19         6.87         9.93        27.02        25.08        15.88 
TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-TP-A8TT 
       18.84         3.19       114.64        47.21        86.14        11.90 
TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O 
        8.84        25.51        12.95         6.02        15.52        15.81 
TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 
       32.91        15.09         4.34        84.69        94.65        23.93 
TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI 
       55.56        60.92        66.97        48.85        21.53         5.79 
TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ 
       27.81         3.91        38.04        48.03         9.04         2.99 
TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIW TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR 
       25.97        31.96        31.96        30.58        29.23        27.09 
TCGA-XK-AAJT TCGA-XK-AAJU TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL 
       37.02        39.65        25.48        52.96        49.02        38.56 
TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SC TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ 
       60.56        16.83        41.46        28.77        47.38        45.86 
TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SP TCGA-YL-A9WJ TCGA-YL-A9WL TCGA-YL-A9WX 
       37.97        26.24        71.34        60.99        24.33        49.91 
TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9ND 
       28.34         1.64         1.12         7.86         6.02 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             0.76              0.30 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           106.95            151.36 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           27.075            23.010 
[1] "0.8 - 107.0 (27.1)" "0.3 - 151.4 (23.0)"
[1] "hr="     "2.7e+08"
D13V2, continuous
                   vv
clus                 T2  T3  T4
  7P GAIN MUTATED    22  45   1
  7P GAIN WILD-TYPE 128 161   4
D13V3, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  T2              22               128
  T3              45               161
  T4               1                 4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V4, binary
                   cls
clus                  0   1
  7P GAIN MUTATED    51   8
  7P GAIN WILD-TYPE 212  36
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     51    8
  7P GAIN WILD-TYPE  212   36
   clus
vv  7P GAIN MUTATED 7P GAIN WILD-TYPE
  0              51               212
  1               8                36
[1] 2 2
[1] FALSE
D13V5, binary
                   cls
clus                  0   1
  7P GAIN MUTATED     1  67
  7P GAIN WILD-TYPE  12 283
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      1   67
  7P GAIN WILD-TYPE   12  283
                                        clus
vv                                       7P GAIN MUTATED 7P GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE               1                12
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 67               283
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  7P GAIN MUTATED    35  26   1   3
  7P GAIN WILD-TYPE 208  64   4   8
D13V6, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  R0              35               208
  R1              26                64
  R2               1                 4
  RX               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"
D13V7, continuous
D13V8, continuous
D13V9, continuous
D13V10, continuous
D13V11, continuous
D13V12, continuous
D13V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7P GAIN MUTATED       0                         1    26
  7P GAIN WILD-TYPE     2                         6   120
D13V14, multiclass
                           clus
vv                          7P GAIN MUTATED 7P GAIN WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               1                 6
  WHITE                                  26               120
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(14) Variable = 7Q GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                 0   1
  7Q GAIN MUTATED    62   0
  7Q GAIN WILD-TYPE 293   6
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               62               299 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                0                 6 
$`7Q GAIN MUTATED`
TCGA-CH-5751 TCGA-CH-5768 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5791 TCGA-EJ-5494 
       35.01        24.03        13.02        15.98        33.01        27.16 
TCGA-EJ-5495 TCGA-EJ-5509 TCGA-EJ-5525 TCGA-EJ-5542 TCGA-EJ-7125 TCGA-EJ-7314 
       33.11        48.13        36.66        29.06        61.15         9.70 
TCGA-EJ-7330 TCGA-EJ-7784 TCGA-EJ-7789 TCGA-EJ-A46F TCGA-EJ-A65M TCGA-FC-7961 
        6.28        25.68        18.15         9.83         7.56        15.42 
TCGA-FC-A4JI TCGA-G9-6338 TCGA-G9-6366 TCGA-G9-6371 TCGA-G9-6377 TCGA-G9-6496 
       13.45        66.67         3.32        40.31        31.50        56.75 
TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7523 TCGA-HC-7742 TCGA-HC-8260 TCGA-HC-8261 
       52.87        50.73        28.18         1.48         1.94        17.95 
TCGA-HC-8265 TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A6AP TCGA-HI-7168 TCGA-J4-8198 
       15.88         0.76         1.78         2.33        78.61        20.19 
TCGA-J9-A52E TCGA-KK-A59Z TCGA-KK-A6E8 TCGA-KK-A8IB TCGA-KK-A8IF TCGA-M7-A721 
       10.62        61.78        58.19         2.73        26.43        13.15 
TCGA-QU-A6IM TCGA-TP-A8TV TCGA-VN-A88P TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A87B 
       41.00         8.19        30.15       106.95        26.47        75.91 
TCGA-VP-A87H TCGA-VP-AA1N TCGA-X4-A8KQ TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 
       21.80        17.82        37.18        36.95        71.77        62.14 
TCGA-YL-A8SB TCGA-YL-A8SF TCGA-YL-A8SO TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH 
       45.50        45.14       106.75        62.79         7.00        14.04 
TCGA-YL-A9WK TCGA-ZG-A8QX 
       62.37         4.93 

$`7Q GAIN WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5753 
        1.97        24.03         1.02        13.02        31.00         1.02 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 
        2.04         0.92        44.02        12.00         1.02        23.01 
TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5769 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 
        1.02        15.06         2.04        26.99         9.99        32.02 
TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
        2.99        29.00        19.56        13.32        29.79        46.52 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       44.88        26.30        45.73        28.93        30.31        27.19 
TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 
       23.90        38.93        36.69        48.53        38.53        36.23 
TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 
       60.23        46.55        47.80        52.27        64.50        51.88 
TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 
       68.35        43.07        38.76        39.75        60.23        41.85 
TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7315 
       47.87        27.02        49.02        83.57        21.80         9.50 
TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 
        9.37        16.77         7.66        17.52         5.75        27.68 
TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7785 TCGA-EJ-7786 
        0.30        23.90        38.37        25.87        20.55        14.53 
TCGA-EJ-7788 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 
       14.14        19.59        17.29         3.75        23.05        19.92 
TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D 
       64.47        63.98        26.99        10.32         5.33         4.24 
TCGA-EJ-A46E TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D 
       17.49         3.06         7.53        21.96        17.62        12.92 
TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-FC-7708 TCGA-FC-A5OB 
       13.71        18.41         9.14         2.99        28.41         8.98 
TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 
       17.23        16.24         1.78        41.62        87.35        81.04 
TCGA-G9-6336 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 
       67.99        69.37        55.76        18.21        68.68        49.81 
TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 
       46.16        50.70        49.35        47.15        46.52        47.44 
TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 
       45.30        39.39        44.81        40.18        39.95        38.01 
TCGA-G9-6373 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 
       26.66        37.97        45.80        25.15        27.29        58.22 
TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7525 
       38.27        38.96        27.91        30.97        35.34        32.68 
TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 
       26.01        21.14         6.08        30.94         3.68        19.76 
TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 
        5.33         2.93         2.01         2.37        14.47        28.54 
TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 
        0.79        28.60         1.97         1.68         2.37         2.93 
TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7744 
        1.71         0.72         2.10         2.66         1.74         1.68 
TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 
        2.07        24.59        26.04         1.97         1.12         3.22 
TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 
       30.51         1.48        17.85        24.56         1.84        19.36 
TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8262 
       22.42         3.12        23.87         2.17         2.27        22.32 
TCGA-HC-8264 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN 
        1.58         1.15        22.36         2.01         2.20         1.61 
TCGA-HC-A6AO TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HI-7169 
        5.49         3.48         1.45         1.25         4.41        88.24 
TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M 
       82.92        43.69        12.30        21.76        17.03        16.04 
TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T 
       16.54        16.14        20.52        14.93        17.19         6.02 
TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K 
       13.32        17.36         9.17         9.17        10.19         6.77 
TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52C TCGA-KK-A59V 
       10.39        14.37        20.28        13.87         5.85        93.99 
TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 
       56.28        44.68       115.86        30.02        54.54       151.36 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A7AZ 
       67.59        90.51        49.25       113.33        67.07        27.62 
TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 
       34.95        22.75        20.65         5.19         6.87         9.93 
TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IN 
       27.02        25.08        15.88        18.84         3.19       114.64 
TCGA-QU-A6IO TCGA-QU-A6IP TCGA-TP-A8TT TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L 
       47.21        86.14        11.90         8.84        25.51        12.95 
TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 
        6.02        15.52        15.81        32.91        15.09         4.34 
TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E 
       84.69        94.65        23.93        55.56        60.92        66.97 
TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83G 
       48.85        21.53         5.79        27.81         3.91        38.04 
TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV 
       48.03         9.04         2.99        25.97        31.96        31.50 
TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT 
       31.96        28.54        30.58        29.23        27.09        37.02 
TCGA-XK-AAJU TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8S9 
       39.65        25.48        52.96        49.02        38.56        60.56 
TCGA-YL-A8SA TCGA-YL-A8SC TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK 
       16.83        41.46        28.77        47.38        45.86        37.97 
TCGA-YL-A8SL TCGA-YL-A8SP TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WL TCGA-YL-A9WX 
       26.24        71.34        41.39        60.99        24.33        49.91 
TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9ND 
       28.34         1.64         1.12         7.86         6.02 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             0.76              0.30 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           106.95            151.36 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           26.815            23.050 
[1] "0.8 - 107.0 (26.8)" "0.3 - 151.4 (23.1)"
[1] "hr="     "2.7e+08"
D14V2, continuous
                   vv
clus                 T2  T3  T4
  7Q GAIN MUTATED    21  40   1
  7Q GAIN WILD-TYPE 129 166   4
D14V3, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T2              21               129
  T3              40               166
  T4               1                 4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V4, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED    49   4
  7Q GAIN WILD-TYPE 214  40
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     49    4
  7Q GAIN WILD-TYPE  214   40
   clus
vv  7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  0              49               214
  1               4                40
[1] 2 2
[1] FALSE
D14V5, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED     1  61
  7Q GAIN WILD-TYPE  12 289
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      1   61
  7Q GAIN WILD-TYPE   12  289
                                        clus
vv                                       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE               1                12
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 61               289
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  7Q GAIN MUTATED    31  24   1   3
  7Q GAIN WILD-TYPE 212  66   4   8
D14V6, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  R0              31               212
  R1              24                66
  R2               1                 4
  RX               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"
D14V7, continuous
D14V8, continuous
D14V9, continuous
D14V10, continuous
D14V11, continuous
D14V12, continuous
D14V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7Q GAIN MUTATED       0                         1    23
  7Q GAIN WILD-TYPE     2                         6   123
D14V14, multiclass
                           clus
vv                          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               1                 6
  WHITE                                  23               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"

Clustering(15) Variable = 8P GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                 0   1
  8P GAIN MUTATED    47   1
  8P GAIN WILD-TYPE 308   5
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               48               313 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                1                 5 
$`8P GAIN MUTATED`
TCGA-CH-5751 TCGA-CH-5761 TCGA-EJ-5504 TCGA-EJ-5509 TCGA-EJ-5514 TCGA-EJ-5521 
       35.01         0.92        28.93        48.13        36.23        51.88 
TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7312 TCGA-EJ-7784 
       36.66        38.76        49.02        61.15        21.80        25.68 
TCGA-EJ-7789 TCGA-EJ-A65J TCGA-EJ-A65M TCGA-FC-7961 TCGA-FC-A4JI TCGA-G9-6499 
       18.15         2.99         7.56        15.42        13.45        50.73 
TCGA-G9-7510 TCGA-G9-7521 TCGA-HC-7078 TCGA-HC-7742 TCGA-HC-7745 TCGA-HC-8265 
       38.96        30.97         5.33         1.48         2.07        15.88 
TCGA-HC-8266 TCGA-HC-A4ZV TCGA-HC-A6AO TCGA-J9-A52B TCGA-KK-A59V TCGA-KK-A59Z 
        1.15         0.76         5.49        13.87        93.99        61.78 
TCGA-KK-A6DY TCGA-KK-A6E8 TCGA-KK-A8IB TCGA-M7-A724 TCGA-QU-A6IL TCGA-VN-A88M 
      115.86        58.19         2.73        15.88         3.19         6.02 
TCGA-VN-A943 TCGA-VP-A87H TCGA-VP-AA1N TCGA-XK-AAJT TCGA-YL-A8HM TCGA-YL-A8HO 
        4.34        21.80        17.82        37.02        36.95        71.77 
TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SK TCGA-YL-A8SQ TCGA-YL-A9WJ TCGA-YL-A9WK 
       62.14        60.56        37.97        62.79        60.99        62.37 

$`8P GAIN WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5753 
        1.97        24.03         1.02        13.02        31.00         1.02 
TCGA-CH-5754 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 
        2.04        44.02        12.00         1.02        23.01         1.02 
TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 
       15.06        24.03         2.04        13.02        15.98        26.99 
TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 
        9.99        32.02        33.01         2.99        29.00        27.16 
TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 
       33.11        19.56        13.32        29.79        46.52        44.88 
TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 
       26.30        45.73        30.31        27.19        23.90        38.93 
TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 
       36.69        48.53        38.53        60.23        46.55        47.80 
TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5527 TCGA-EJ-5530 
       52.27        64.50        68.35        43.07        39.75        60.23 
TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7218 TCGA-EJ-7314 
       41.85        47.87        29.06        27.02        83.57         9.70 
TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 
        9.50         9.37        16.77         7.66        17.52         5.75 
TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 
       27.68         6.28         0.30        23.90        38.37        25.87 
TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 
       20.55        14.53        14.14        19.59        17.29         3.75 
TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8474 
       23.05        19.92        64.47        63.98        26.99        10.32 
TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H 
        5.33         4.24        17.49         9.83         3.06         7.53 
TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G 
       21.96        17.62        12.92        13.71        18.41         9.14 
TCGA-FC-7708 TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 
       28.41         8.98        17.23        16.24         1.78        41.62 
TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 
       87.35        81.04        67.99        66.67        69.37        55.76 
TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 
       18.21        68.68        49.81        46.16        50.70        49.35 
TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 
       47.15        46.52        47.44        45.30        39.39        44.81 
TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 
        3.32        40.18        39.95        38.01        40.31        26.66 
TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 
       31.50        37.97        45.80        25.15        27.29        58.22 
TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-7509 TCGA-G9-7519 TCGA-G9-7522 TCGA-G9-7523 
       56.75        52.87        38.27        27.91        35.34        28.18 
TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY 
       32.68        26.01        21.14         6.08        30.94         3.68 
TCGA-HC-7075 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 
       19.76         2.93         2.01         2.37        14.47        28.54 
TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 
        0.79        28.60         1.97         1.68         2.37         2.93 
TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7744 
        1.71         0.72         2.10         2.66         1.74         1.68 
TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 
       24.59        26.04         1.97         1.12         3.22        30.51 
TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 
        1.48        17.85        24.56         1.84        19.36        22.42 
TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 
        3.12        23.87         2.17         2.27         1.94        17.95 
TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-A48F TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL 
       22.32         1.58        22.36         1.78         2.01         2.20 
TCGA-HC-A6AN TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY 
        1.61         2.33         3.48         1.45         1.25         4.41 
TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 
       78.61        88.24        82.92        43.69        20.19        12.30 
TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q 
       21.76        17.03        16.04        16.54        16.14        20.52 
TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 
       14.93        17.19         6.02        13.32        17.36         9.17 
TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N 
        9.17        10.19         6.77        10.39        14.37        20.28 
TCGA-J9-A52C TCGA-J9-A52E TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A6E0 TCGA-KK-A6E1 
        5.85        10.62        56.28        44.68        30.02        54.54 
TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 
      151.36        67.59        90.51        49.25       113.33        67.07 
TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IF TCGA-KK-A8IL TCGA-M7-A71Y 
       27.62        34.95        22.75        26.43        20.65         5.19 
TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A725 
        6.87         9.93        13.15        27.02        25.08        18.84 
TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-TP-A8TT TCGA-TP-A8TV 
       41.00       114.64        47.21        86.14        11.90         8.19 
TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P 
        8.84        25.51        12.95        15.52        15.81        30.15 
TCGA-VN-A88Q TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 
       32.91        15.09       106.95        26.47        84.69        94.65 
TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87J 
       23.93        75.91        55.56        60.92        66.97        48.85 
TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83G 
       21.53         5.79        37.18        27.81         3.91        38.04 
TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV 
       48.03         9.04         2.99        25.97        31.96        31.50 
TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJU 
       31.96        28.54        30.58        29.23        27.09        39.65 
TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8SA TCGA-YL-A8SB 
       25.48        52.96        49.02        38.56        16.83        45.50 
TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SL 
       41.46        45.14        28.77        47.38        45.86        26.24 
TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WL 
      106.75        71.34         7.00        14.04        41.39        24.33 
TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       49.91        28.34         1.64         4.93         1.12         7.86 
TCGA-ZG-A9ND 
        6.02 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             0.76              0.30 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           115.86            151.36 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            29.95             23.90 
[1] "0.8 - 115.9 (29.9)" "0.3 - 151.4 (23.9)"
[1] "hr=" "1"  
D15V2, continuous
                   vv
clus                 T2  T3  T4
  8P GAIN MUTATED    14  33   1
  8P GAIN WILD-TYPE 136 173   4
D15V3, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  T2              14               136
  T3              33               173
  T4               1                 4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V4, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    40   6
  8P GAIN WILD-TYPE 223  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     40    6
  8P GAIN WILD-TYPE  223   38
   clus
vv  8P GAIN MUTATED 8P GAIN WILD-TYPE
  0              40               223
  1               6                38
[1] 2 2
[1] FALSE
D15V5, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     0  48
  8P GAIN WILD-TYPE  13 302
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      0   48
  8P GAIN WILD-TYPE   13  302
                                        clus
vv                                       8P GAIN MUTATED 8P GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE               0                13
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 48               302
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  8P GAIN MUTATED    26  18   1   1
  8P GAIN WILD-TYPE 217  72   4  10
D15V6, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  R0              26               217
  R1              18                72
  R2               1                 4
  RX               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"
D15V7, continuous
D15V8, continuous
D15V9, continuous
D15V10, continuous
D15V11, continuous
D15V12, continuous
D15V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8P GAIN MUTATED       0                         1    16
  8P GAIN WILD-TYPE     2                         6   130
D15V14, multiclass
                           clus
vv                          8P GAIN MUTATED 8P GAIN WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               1                 6
  WHITE                                  16               130
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(16) Variable = 8Q GAIN MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                 0   1
  8Q GAIN MUTATED    77   1
  8Q GAIN WILD-TYPE 278   5
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               78               283 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                1                 5 
$`8Q GAIN MUTATED`
TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-CH-5751 TCGA-CH-5761 TCGA-CH-5771 
       22.06        33.96         3.68        35.01         0.92        13.02 
TCGA-EJ-5504 TCGA-EJ-5509 TCGA-EJ-5511 TCGA-EJ-5514 TCGA-EJ-5517 TCGA-EJ-5521 
       28.93        48.13        48.53        36.23        47.80        51.88 
TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5532 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7312 
       36.66        38.76        47.87        49.02        61.15        21.80 
TCGA-EJ-7781 TCGA-EJ-7784 TCGA-EJ-7789 TCGA-EJ-8469 TCGA-EJ-A46F TCGA-EJ-A46G 
       23.90        25.68        18.15        63.98         9.83         3.06 
TCGA-EJ-A65J TCGA-EJ-A65M TCGA-FC-7961 TCGA-FC-A4JI TCGA-G9-6366 TCGA-G9-6373 
        2.99         7.56        15.42        13.45         3.32        26.66 
TCGA-G9-6377 TCGA-G9-6499 TCGA-G9-7510 TCGA-G9-7521 TCGA-G9-A9S7 TCGA-HC-7078 
       31.50        50.73        38.96        30.97        21.14         5.33 
TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7742 TCGA-HC-7745 TCGA-HC-8216 TCGA-HC-8265 
       28.60         1.97         1.48         2.07        22.42        15.88 
TCGA-HC-8266 TCGA-HC-A4ZV TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AO TCGA-J4-A67M 
        1.15         0.76         2.01         2.20         5.49        16.04 
TCGA-J9-A52B TCGA-KK-A59V TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E8 TCGA-KK-A7AZ 
       13.87        93.99        61.78       115.86        58.19        27.62 
TCGA-KK-A8IB TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IO TCGA-VN-A88M 
        2.73        15.88        18.84         3.19        47.21         6.02 
TCGA-VN-A88P TCGA-VN-A943 TCGA-VP-A875 TCGA-VP-A87H TCGA-VP-AA1N TCGA-XJ-A83G 
       30.15         4.34        26.47        21.80        17.82        38.04 
TCGA-XK-AAIV TCGA-XK-AAJT TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 
       31.50        37.02        36.95        71.77        62.14        60.56 
TCGA-YL-A8SK TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WY 
       37.97        62.79         7.00        60.99        62.37        28.34 

$`8Q GAIN WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8W3 TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 
       20.42        43.79        25.35         2.99         6.97        22.06 
TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 
        1.02        12.99        13.97         1.97        24.03         1.02 
TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5762 TCGA-CH-5763 
       13.02        31.00         1.02         2.04        44.02        12.00 
TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 
        1.02        23.01         1.02        15.06        24.03         2.04 
TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 
       15.98        26.99         9.99        32.02        33.01         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        27.16        33.11        19.56        13.32        29.79 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5505 TCGA-EJ-5506 
       46.52        44.88        26.30        45.73        30.31        27.19 
TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5510 TCGA-EJ-5512 TCGA-EJ-5515 TCGA-EJ-5516 
       23.90        38.93        36.69        38.53        60.23        46.55 
TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5527 TCGA-EJ-5530 
       52.27        64.50        68.35        43.07        39.75        60.23 
TCGA-EJ-5531 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7218 TCGA-EJ-7314 TCGA-EJ-7315 
       41.85        29.06        27.02        83.57         9.70         9.50 
TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 
        9.37        16.77         7.66        17.52         5.75        27.68 
TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7785 TCGA-EJ-7786 
        6.28         0.30        38.37        25.87        20.55        14.53 
TCGA-EJ-7788 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 
       14.14        19.59        17.29         3.75        23.05        19.92 
TCGA-EJ-8468 TCGA-EJ-8470 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E 
       64.47        26.99        10.32         5.33         4.24        17.49 
TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F 
        7.53        21.96        17.62        12.92        13.71        18.41 
TCGA-EJ-A65G TCGA-FC-7708 TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 
        9.14        28.41         8.98        17.23        16.24         1.78 
TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 
       41.62        87.35        81.04        67.99        66.67        69.37 
TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 
       55.76        18.21        68.68        49.81        46.16        50.70 
TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 
       49.35        47.15        46.52        47.44        45.30        39.39 
TCGA-G9-6365 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6378 
       44.81        40.18        39.95        38.01        40.31        37.97 
TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 
       45.80        25.15        27.29        58.22        56.75        52.87 
TCGA-G9-7509 TCGA-G9-7519 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 
       38.27        27.91        35.34        28.18        32.68        26.01 
TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7079 TCGA-HC-7080 
        6.08        30.94         3.68        19.76         2.93         2.01 
TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7230 TCGA-HC-7231 
        2.37        14.47        28.54         0.79         1.68         2.37 
TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 
        2.93         1.71         0.72         2.10         2.66         1.74 
TCGA-HC-7744 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 
        1.68        24.59        26.04         1.97         1.12         3.22 
TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 
       30.51         1.48        17.85        24.56         1.84        19.36 
TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 
        3.12        23.87         2.17         2.27         1.94        17.95 
TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-A48F TCGA-HC-A631 TCGA-HC-A6AN TCGA-HC-A6AP 
       22.32         1.58        22.36         1.78         1.61         2.33 
TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HI-7168 TCGA-HI-7169 
        3.48         1.45         1.25         4.41        78.61        88.24 
TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L 
       82.92        43.69        20.19        12.30        21.76        17.03 
TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T 
       16.54        16.14        20.52        14.93        17.19         6.02 
TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K 
       13.32        17.36         9.17         9.17        10.19         6.77 
TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52C TCGA-J9-A52E TCGA-KK-A59X 
       10.39        14.37        20.28         5.85        10.62        56.28 
TCGA-KK-A59Y TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 
       44.68        30.02        54.54       151.36        67.59        90.51 
TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IF 
       49.25       113.33        67.07        34.95        22.75        26.43 
TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 
       20.65         5.19         6.87         9.93        13.15        27.02 
TCGA-M7-A723 TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IP TCGA-TP-A8TT TCGA-TP-A8TV 
       25.08        41.00       114.64        86.14        11.90         8.19 
TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88Q 
        8.84        25.51        12.95        15.52        15.81        32.91 
TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B 
       15.09       106.95        84.69        94.65        23.93        75.91 
TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI 
       55.56        60.92        66.97        48.85        21.53         5.79 
TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ 
       37.18        27.81         3.91        48.03         9.04         2.99 
TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP 
       25.97        31.96        31.96        28.54        30.58        29.23 
TCGA-XK-AAJR TCGA-XK-AAJU TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL 
       27.09        39.65        25.48        52.96        49.02        38.56 
TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI 
       16.83        45.50        41.46        45.14        28.77        47.38 
TCGA-YL-A8SJ TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A9WH TCGA-YL-A9WI 
       45.86        26.24       106.75        71.34        14.04        41.39 
TCGA-YL-A9WL TCGA-YL-A9WX TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       24.33        49.91         1.64         4.93         1.12         7.86 
TCGA-ZG-A9ND 
        6.02 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.76              0.30 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           115.86            151.36 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           26.565            23.870 
[1] "0.8 - 115.9 (26.6)" "0.3 - 151.4 (23.9)"
[1] "hr=" "1.6"
D16V2, continuous
                   vv
clus                 T2  T3  T4
  8Q GAIN MUTATED    23  54   1
  8Q GAIN WILD-TYPE 127 152   4
D16V3, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T2              23               127
  T3              54               152
  T4               1                 4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V4, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED    65   9
  8Q GAIN WILD-TYPE 198  35
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     65    9
  8Q GAIN WILD-TYPE  198   35
   clus
vv  8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  0              65               198
  1               9                35
[1] 2 2
[1] FALSE
D16V5, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED     1  77
  8Q GAIN WILD-TYPE  12 273
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      1   77
  8Q GAIN WILD-TYPE   12  273
                                        clus
vv                                       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE               1                12
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 77               273
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  8Q GAIN MUTATED    47  24   1   2
  8Q GAIN WILD-TYPE 196  66   4   9
D16V6, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  R0              47               196
  R1              24                66
  R2               1                 4
  RX               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"
D16V7, continuous
D16V8, continuous
D16V9, continuous
D16V10, continuous
D16V11, continuous
D16V12, continuous
D16V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8Q GAIN MUTATED       0                         2    25
  8Q GAIN WILD-TYPE     2                         5   121
D16V14, multiclass
                           clus
vv                          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               2                 5
  WHITE                                  25               121
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(17) Variable = 9P GAIN MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                 0   1
  9P GAIN MUTATED    19   0
  9P GAIN WILD-TYPE 336   6
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               19               342 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                0                 6 
$`9P GAIN MUTATED`
TCGA-CH-5771 TCGA-CH-5791 TCGA-EJ-5495 TCGA-EJ-5514 TCGA-EJ-5526 TCGA-EJ-7789 
       13.02        33.01        33.11        36.23        38.76        18.15 
TCGA-EJ-A65F TCGA-FC-A4JI TCGA-HC-7821 TCGA-HC-8266 TCGA-VP-A872 TCGA-VP-A875 
       18.41        13.45         1.84         1.15       106.95        26.47 
TCGA-VP-A87H TCGA-XK-AAIV TCGA-YL-A8HO TCGA-YL-A8SC TCGA-YL-A8SL TCGA-YL-A8SQ 
       21.80        31.50        71.77        41.46        26.24        62.79 
TCGA-YL-A9WK 
       62.37 

$`9P GAIN WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 
        1.02         2.04         0.92        44.02        12.00         1.02 
TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5772 
       23.01         1.02        15.06        24.03         2.04        15.98 
TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 
       26.99         9.99        32.02         2.99        29.00        27.16 
TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 
       19.56        13.32        29.79        46.52        44.88        26.30 
TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 
       45.73        28.93        30.31        27.19        23.90        38.93 
TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5515 TCGA-EJ-5516 
       48.13        36.69        48.53        38.53        60.23        46.55 
TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 
       47.80        52.27        64.50        51.88        68.35        43.07 
TCGA-EJ-5525 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 
       36.66        39.75        60.23        41.85        47.87        29.06 
TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 
       27.02        49.02        61.15        83.57        21.80         9.70 
TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 
        9.50         9.37        16.77         7.66        17.52         5.75 
TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 
       27.68         6.28         0.30        23.90        38.37        25.87 
TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7791 TCGA-EJ-7792 
       25.68        20.55        14.53        14.14        19.59        17.29 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 
        3.75        23.05        19.92        64.47        63.98        26.99 
TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G 
       10.32         5.33         4.24        17.49         9.83         3.06 
TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65G 
        7.53        21.96        17.62        12.92        13.71         9.14 
TCGA-EJ-A65J TCGA-EJ-A65M TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A5OB TCGA-FC-A66V 
        2.99         7.56        28.41        15.42         8.98        17.23 
TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 
       16.24         1.78        41.62        87.35        81.04        67.99 
TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 
       66.67        69.37        55.76        18.21        68.68        49.81 
TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 
       46.16        50.70        49.35        47.15        46.52        47.44 
TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 
       45.30        39.39        44.81         3.32        40.18        39.95 
TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 
       38.01        40.31        26.66        31.50        37.97        45.80 
TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 
       25.15        27.29        58.22        56.75        52.87        50.73 
TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 
       38.27        38.96        27.91        30.97        35.34        28.18 
TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY 
       32.68        26.01        21.14         6.08        30.94         3.68 
TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 
       19.76         5.33         2.93         2.01         2.37        14.47 
TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 
       28.54         0.79        28.60         1.97         1.68         2.37 
TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 
        2.93         1.71         0.72         2.10         2.66         1.74 
TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 
        1.48         1.68         2.07        24.59        26.04         1.97 
TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 
        1.12         3.22        30.51         1.48        17.85        24.56 
TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 
       19.36        22.42         3.12        23.87         2.17         2.27 
TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-A48F 
        1.94        17.95        22.32         1.58        15.88        22.36 
TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO 
        0.76         1.78         2.01         2.20         1.61         5.49 
TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HI-7168 
        2.33         3.48         1.45         1.25         4.41        78.61 
TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K 
       88.24        82.92        43.69        20.19        12.30        21.76 
TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R 
       17.03        16.04        16.54        16.14        20.52        14.93 
TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I 
       17.19         6.02        13.32        17.36         9.17         9.17 
TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B 
       10.19         6.77        10.39        14.37        20.28        13.87 
TCGA-J9-A52C TCGA-J9-A52E TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z 
        5.85        10.62        93.99        56.28        44.68        61.78 
TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 
      115.86        30.02        54.54       151.36        67.59        90.51 
TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AZ TCGA-KK-A7B1 
       49.25       113.33        67.07        58.19        27.62        34.95 
TCGA-KK-A7B2 TCGA-KK-A8IB TCGA-KK-A8IF TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z 
       22.75         2.73        26.43        20.65         5.19         6.87 
TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 
        9.93        13.15        27.02        25.08        15.88        18.84 
TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-TP-A8TT 
        3.19        41.00       114.64        47.21        86.14        11.90 
TCGA-TP-A8TV TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N 
        8.19         8.84        25.51        12.95         6.02        15.52 
TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A876 
       15.81        30.15        32.91        15.09         4.34        84.69 
TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E 
       94.65        23.93        75.91        55.56        60.92        66.97 
TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS 
       48.85        21.53        17.82         5.79        37.18        27.81 
TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX 
        3.91        38.04        48.03         9.04         2.99        25.97 
TCGA-XK-AAIR TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR 
       31.96        31.96        28.54        30.58        29.23        27.09 
TCGA-XK-AAJT TCGA-XK-AAJU TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL 
       37.02        39.65        25.48        52.96        49.02        38.56 
TCGA-YL-A8HM TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SF 
       36.95        62.14        60.56        16.83        45.50        45.14 
TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SO TCGA-YL-A8SP 
       28.77        47.38        45.86        37.97       106.75        71.34 
TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WL TCGA-YL-A9WX 
        7.00        14.04        41.39        60.99        24.33        49.91 
TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9ND 
       28.34         1.64         4.93         1.12         7.86         6.02 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
             1.15              0.30 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           106.95            151.36 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           31.500            23.885 
[1] "1.1 - 107.0 (31.5)" "0.3 - 151.4 (23.9)"
[1] "hr="     "7.5e+07"
D17V2, continuous
                   vv
clus                 T2  T3  T4
  9P GAIN MUTATED     2  17   0
  9P GAIN WILD-TYPE 148 189   5
D17V3, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  T2               2               148
  T3              17               189
  T4               0                 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"
D17V4, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    13   5
  9P GAIN WILD-TYPE 250  39
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     13    5
  9P GAIN WILD-TYPE  250   39
   clus
vv  9P GAIN MUTATED 9P GAIN WILD-TYPE
  0              13               250
  1               5                39
[1] 2 2
[1] FALSE
D17V5, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     2  17
  9P GAIN WILD-TYPE  11 333
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      2   17
  9P GAIN WILD-TYPE   11  333
                                        clus
vv                                       9P GAIN MUTATED 9P GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE               2                11
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 17               333
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  9P GAIN MUTATED    10   7   1   0
  9P GAIN WILD-TYPE 233  83   4  11
D17V6, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  R0              10               233
  R1               7                83
  R2               1                 4
  RX               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"
D17V7, continuous
D17V8, continuous
D17V9, continuous
D17V10, continuous
D17V11, continuous
D17V12, continuous
D17V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9P GAIN MUTATED       0                         1     6
  9P GAIN WILD-TYPE     2                         6   140
D17V14, multiclass
                           clus
vv                          9P GAIN MUTATED 9P GAIN WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               1                 6
  WHITE                                   6               140
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(18) Variable = 9Q GAIN MUTATION ANALYSIS
D18V1, survival
                   sevent
clus2                 0   1
  9Q GAIN MUTATED    31   0
  9Q GAIN WILD-TYPE 324   6
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               31               330 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                0                 6 
$`9Q GAIN MUTATED`
TCGA-CH-5751 TCGA-CH-5771 TCGA-CH-5791 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5526 
       35.01        13.02        33.01        33.11        19.56        38.76 
TCGA-EJ-7789 TCGA-EJ-A46G TCGA-EJ-A65F TCGA-FC-A4JI TCGA-G9-6356 TCGA-G9-6373 
       18.15         3.06        18.41        13.45        47.15        26.66 
TCGA-G9-7521 TCGA-HC-7821 TCGA-HC-8216 TCGA-HC-8266 TCGA-HC-A4ZV TCGA-HC-A631 
       30.97         1.84        22.42         1.15         0.76         1.78 
TCGA-KK-A59Z TCGA-VN-A88K TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A87D TCGA-VP-A87H 
       61.78        25.51       106.95        26.47        60.92        21.80 
TCGA-X4-A8KQ TCGA-XK-AAIV TCGA-YL-A8HO TCGA-YL-A8SC TCGA-YL-A8SL TCGA-YL-A8SQ 
       37.18        31.50        71.77        41.46        26.24        62.79 
TCGA-YL-A9WK 
       62.37 

$`9Q GAIN WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5753 
        1.97        24.03         1.02        13.02        31.00         1.02 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 
        2.04         0.92        44.02        12.00         1.02        23.01 
TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5772 TCGA-CH-5788 
        1.02        15.06        24.03         2.04        15.98        26.99 
TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5497 
        9.99        32.02         2.99        29.00        27.16        13.32 
TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 
       29.79        46.52        44.88        26.30        45.73        28.93 
TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 
       30.31        27.19        23.90        38.93        48.13        36.69 
TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 
       48.53        38.53        36.23        60.23        46.55        47.80 
TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 
       52.27        64.50        51.88        68.35        43.07        36.66 
TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 
       39.75        60.23        41.85        47.87        29.06        27.02 
TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 
       49.02        61.15        83.57        21.80         9.70         9.50 
TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 
        9.37        16.77         7.66        17.52         5.75        27.68 
TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 
        6.28         0.30        23.90        38.37        25.87        25.68 
TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 
       20.55        14.53        14.14        19.59        17.29         3.75 
TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8474 
       23.05        19.92        64.47        63.98        26.99        10.32 
TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46H TCGA-EJ-A46I 
        5.33         4.24        17.49         9.83         7.53        21.96 
TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M 
       17.62        12.92        13.71         9.14         2.99         7.56 
TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 
       28.41        15.42         8.98        17.23        16.24         1.78 
TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 
       41.62        87.35        81.04        67.99        66.67        69.37 
TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 
       55.76        18.21        68.68        49.81        46.16        50.70 
TCGA-G9-6354 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 
       49.35        46.52        47.44        45.30        39.39        44.81 
TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6377 
        3.32        40.18        39.95        38.01        40.31        31.50 
TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 
       37.97        45.80        25.15        27.29        58.22        56.75 
TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7522 
       52.87        50.73        38.27        38.96        27.91        35.34 
TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX 
       28.18        32.68        26.01        21.14         6.08        30.94 
TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 
        3.68        19.76         5.33         2.93         2.01         2.37 
TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 
       14.47        28.54         0.79        28.60         1.97         1.68 
TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 
        2.37         2.93         1.71         0.72         2.10         2.66 
TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 
        1.74         1.48         1.68         2.07        24.59        26.04 
TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 
        1.97         1.12         3.22        30.51         1.48        17.85 
TCGA-HC-7820 TCGA-HC-8213 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 
       24.56        19.36         3.12        23.87         2.17         2.27 
TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-A48F 
        1.94        17.95        22.32         1.58        15.88        22.36 
TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ 
        2.01         2.20         1.61         5.49         2.33         3.48 
TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 
        1.45         1.25         4.41        78.61        88.24        82.92 
TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M 
       43.69        20.19        12.30        21.76        17.03        16.04 
TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T 
       16.54        16.14        20.52        14.93        17.19         6.02 
TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K 
       13.32        17.36         9.17         9.17        10.19         6.77 
TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E 
       10.39        14.37        20.28        13.87         5.85        10.62 
TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 
       93.99        56.28        44.68       115.86        30.02        54.54 
TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 
      151.36        67.59        90.51        49.25       113.33        67.07 
TCGA-KK-A6E8 TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IB TCGA-KK-A8IF 
       58.19        27.62        34.95        22.75         2.73        26.43 
TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 
       20.65         5.19         6.87         9.93        13.15        27.02 
TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN 
       25.08        15.88        18.84         3.19        41.00       114.64 
TCGA-QU-A6IO TCGA-QU-A6IP TCGA-TP-A8TT TCGA-TP-A8TV TCGA-VN-A88I TCGA-VN-A88L 
       47.21        86.14        11.90         8.19         8.84        12.95 
TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R 
        6.02        15.52        15.81        30.15        32.91        15.09 
TCGA-VN-A943 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C 
        4.34        84.69        94.65        23.93        75.91        55.56 
TCGA-VP-A87E TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KS 
       66.97        48.85        21.53        17.82         5.79        27.81 
TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX 
        3.91        38.04        48.03         9.04         2.99        25.97 
TCGA-XK-AAIR TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR 
       31.96        31.96        28.54        30.58        29.23        27.09 
TCGA-XK-AAJT TCGA-XK-AAJU TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL 
       37.02        39.65        25.48        52.96        49.02        38.56 
TCGA-YL-A8HM TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SF 
       36.95        62.14        60.56        16.83        45.50        45.14 
TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SO TCGA-YL-A8SP 
       28.77        47.38        45.86        37.97       106.75        71.34 
TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WL TCGA-YL-A9WX 
        7.00        14.04        41.39        60.99        24.33        49.91 
TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9ND 
       28.34         1.64         4.93         1.12         7.86         6.02 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             0.76              0.30 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           106.95            151.36 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            26.66             23.46 
[1] "0.8 - 107.0 (26.7)" "0.3 - 151.4 (23.5)"
[1] "hr="     "7.9e+07"
D18V2, continuous
                   vv
clus                 T2  T3  T4
  9Q GAIN MUTATED     4  27   1
  9Q GAIN WILD-TYPE 146 179   4
D18V3, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  T2               4               146
  T3              27               179
  T4               1                 4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V4, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    21   9
  9Q GAIN WILD-TYPE 242  35
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     21    9
  9Q GAIN WILD-TYPE  242   35
   clus
vv  9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  0              21               242
  1               9                35
[1] 2 2
[1] FALSE
D18V5, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     3  29
  9Q GAIN WILD-TYPE  10 321
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      3   29
  9Q GAIN WILD-TYPE   10  321
                                        clus
vv                                       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE               3                10
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 29               321
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  9Q GAIN MUTATED    18  11   1   1
  9Q GAIN WILD-TYPE 225  79   4  10
D18V6, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  R0              18               225
  R1              11                79
  R2               1                 4
  RX               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"
D18V7, continuous
D18V8, continuous
D18V9, continuous
D18V10, continuous
D18V11, continuous
D18V12, continuous
D18V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9Q GAIN MUTATED       0                         1     9
  9Q GAIN WILD-TYPE     2                         6   137
D18V14, multiclass
                           clus
vv                          9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               1                 6
  WHITE                                   9               137
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(19) Variable = 10P GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                  0   1
  10P GAIN MUTATED     9   0
  10P GAIN WILD-TYPE 346   6
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 9                352 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 0                  6 
$`10P GAIN MUTATED`
TCGA-EJ-5514 TCGA-EJ-8469 TCGA-G9-6499 TCGA-HC-7078 TCGA-HC-7231 TCGA-HC-7742 
       36.23        63.98        50.73         5.33         2.37         1.48 
TCGA-VP-A872 TCGA-YL-A9WH TCGA-YL-A9WY 
      106.95        14.04        28.34 

$`10P GAIN WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 
        1.02         2.04         0.92        44.02        12.00         1.02 
TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 
       23.01         1.02        15.06        24.03         2.04        13.02 
TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 
       15.98        26.99         9.99        32.02        33.01         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        27.16        33.11        19.56        13.32        29.79 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        26.30        45.73        28.93        30.31 
TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 
       27.19        23.90        38.93        48.13        36.69        48.53 
TCGA-EJ-5512 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 
       38.53        60.23        46.55        47.80        52.27        64.50 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 
       51.88        68.35        43.07        36.66        38.76        39.75 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 
       60.23        41.85        47.87        29.06        27.02        49.02 
TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 
       61.15        83.57        21.80         9.70         9.50         9.37 
TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 
       16.77         7.66        17.52         5.75        27.68         6.28 
TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 
        0.30        23.90        38.37        25.87        25.68        20.55 
TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 
       14.53        14.14        18.15        19.59        17.29         3.75 
TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8470 TCGA-EJ-8474 TCGA-EJ-A46B 
       23.05        19.92        64.47        26.99        10.32         5.33 
TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I 
        4.24        17.49         9.83         3.06         7.53        21.96 
TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J 
       17.62        12.92        13.71        18.41         9.14         2.99 
TCGA-EJ-A65M TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V 
        7.56        28.41        15.42        13.45         8.98        17.23 
TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 
       16.24         1.78        41.62        87.35        81.04        67.99 
TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 
       66.67        69.37        55.76        18.21        68.68        49.81 
TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 
       46.16        50.70        49.35        47.15        46.52        47.44 
TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 
       45.30        39.39        44.81         3.32        40.18        39.95 
TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 
       38.01        40.31        26.66        31.50        37.97        45.80 
TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-7509 
       25.15        27.29        58.22        56.75        52.87        38.27 
TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 
       38.96        27.91        30.97        35.34        28.18        32.68 
TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 
       26.01        21.14         6.08        30.94         3.68        19.76 
TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 
        2.93         2.01         2.37        14.47        28.54         0.79 
TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 
       28.60         1.97         1.68         2.93         1.71         0.72 
TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 
        2.10         2.66         1.74         1.68         2.07        24.59 
TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 
       26.04         1.97         1.12         3.22        30.51         1.48 
TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 
       17.85        24.56         1.84        19.36        22.42         3.12 
TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 
       23.87         2.17         2.27         1.94        17.95        22.32 
TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 
        1.58        15.88         1.15        22.36         0.76         1.78 
TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ 
        2.01         2.20         1.61         5.49         2.33         3.48 
TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 
        1.45         1.25         4.41        78.61        88.24        82.92 
TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M 
       43.69        20.19        12.30        21.76        17.03        16.04 
TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T 
       16.54        16.14        20.52        14.93        17.19         6.02 
TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K 
       13.32        17.36         9.17         9.17        10.19         6.77 
TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E 
       10.39        14.37        20.28        13.87         5.85        10.62 
TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 
       93.99        56.28        44.68        61.78       115.86        30.02 
TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 
       54.54       151.36        67.59        90.51        49.25       113.33 
TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IB 
       67.07        58.19        27.62        34.95        22.75         2.73 
TCGA-KK-A8IF TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 
       26.43        20.65         5.19         6.87         9.93        13.15 
TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM 
       27.02        25.08        15.88        18.84         3.19        41.00 
TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-TP-A8TT TCGA-TP-A8TV TCGA-VN-A88I 
      114.64        47.21        86.14        11.90         8.19         8.84 
TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P 
       25.51        12.95         6.02        15.52        15.81        30.15 
TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 
       32.91        15.09         4.34        26.47        84.69        94.65 
TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H 
       23.93        75.91        55.56        60.92        66.97        21.80 
TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS 
       48.85        21.53        17.82         5.79        37.18        27.81 
TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX 
        3.91        38.04        48.03         9.04         2.99        25.97 
TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP 
       31.96        31.50        31.96        28.54        30.58        29.23 
TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK 
       27.09        37.02        39.65        25.48        52.96        49.02 
TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA 
       38.56        36.95        71.77        62.14        60.56        16.83 
TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ 
       45.50        41.46        45.14        28.77        47.38        45.86 
TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR 
       37.97        26.24       106.75        71.34        62.79         7.00 
TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-ZG-A8QW 
       41.39        60.99        62.37        24.33        49.91         1.64 
TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9ND 
        4.93         1.12         7.86         6.02 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              1.48               0.30 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
            106.95             151.36 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
            28.340             23.915 
[1] "1.5 - 107.0 (28.3)" "0.3 - 151.4 (23.9)"
[1] "hr="     "2.6e+07"
D19V2, continuous
                    vv
clus                  T2  T3  T4
  10P GAIN MUTATED     2   7   0
  10P GAIN WILD-TYPE 148 199   5
D19V3, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  T2                2                148
  T3                7                199
  T4                0                  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"
D19V4, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     6   2
  10P GAIN WILD-TYPE 257  42
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      6    2
  10P GAIN WILD-TYPE  257   42
   clus
vv  10P GAIN MUTATED 10P GAIN WILD-TYPE
  0                6                257
  1                2                 42
[1] 2 2
[1] FALSE
D19V5, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     1   8
  10P GAIN WILD-TYPE  12 342
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      1    8
  10P GAIN WILD-TYPE   12  342
                                        clus
vv                                       10P GAIN MUTATED 10P GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                1                 12
  PROSTATE ADENOCARCINOMA ACINAR TYPE                   8                342
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  10P GAIN MUTATED     6   2   0   1
  10P GAIN WILD-TYPE 237  88   5  10
D19V6, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  R0                6                237
  R1                2                 88
  R2                0                  5
  RX                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"
D19V7, continuous
D19V8, continuous
D19V9, continuous
D19V10, continuous
D19V11, continuous
D19V12, continuous
D19V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10P GAIN MUTATED       0                         0     5
  10P GAIN WILD-TYPE     2                         7   141
D19V14, multiclass
                           clus
vv                          10P GAIN MUTATED 10P GAIN WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  7
  WHITE                                    5                141
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(20) Variable = 10Q GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                  0   1
  10Q GAIN MUTATED    10   0
  10Q GAIN WILD-TYPE 345   6
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                10                351 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 0                  6 
$`10Q GAIN MUTATED`
TCGA-CH-5761 TCGA-CH-5788 TCGA-EJ-5514 TCGA-EJ-8469 TCGA-HC-7078 TCGA-HC-7231 
        0.92        26.99        36.23        63.98         5.33         2.37 
TCGA-HC-7742 TCGA-VP-A872 TCGA-YL-A8SQ TCGA-YL-A9WY 
        1.48       106.95        62.79        28.34 

$`10Q GAIN WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 
        1.02         2.04        44.02        12.00         1.02        23.01 
TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 
        1.02        15.06        24.03         2.04        13.02        15.98 
TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 
        9.99        32.02        33.01         2.99        29.00        27.16 
TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 
       33.11        19.56        13.32        29.79        46.52        44.88 
TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 
       26.30        45.73        28.93        30.31        27.19        23.90 
TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5515 
       38.93        48.13        36.69        48.53        38.53        60.23 
TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 
       46.55        47.80        52.27        64.50        51.88        68.35 
TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 
       43.07        36.66        38.76        39.75        60.23        41.85 
TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 
       47.87        29.06        27.02        49.02        61.15        83.57 
TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 
       21.80         9.70         9.50         9.37        16.77         7.66 
TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 
       17.52         5.75        27.68         6.28         0.30        23.90 
TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 
       38.37        25.87        25.68        20.55        14.53        14.14 
TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 
       18.15        19.59        17.29         3.75        23.05        19.92 
TCGA-EJ-8468 TCGA-EJ-8470 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E 
       64.47        26.99        10.32         5.33         4.24        17.49 
TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D 
        9.83         3.06         7.53        21.96        17.62        12.92 
TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-FC-7708 
       13.71        18.41         9.14         2.99         7.56        28.41 
TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 
       15.42        13.45         8.98        17.23        16.24         1.78 
TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 
       41.62        87.35        81.04        67.99        66.67        69.37 
TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 
       55.76        18.21        68.68        49.81        46.16        50.70 
TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 
       49.35        47.15        46.52        47.44        45.30        39.39 
TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 
       44.81         3.32        40.18        39.95        38.01        40.31 
TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 
       26.66        31.50        37.97        45.80        25.15        27.29 
TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 
       58.22        56.75        52.87        50.73        38.27        38.96 
TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 
       27.91        30.97        35.34        28.18        32.68        26.01 
TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7079 
       21.14         6.08        30.94         3.68        19.76         2.93 
TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 
        2.01         2.37        14.47        28.54         0.79        28.60 
TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 
        1.97         1.68         2.93         1.71         0.72         2.10 
TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 
        2.66         1.74         1.68         2.07        24.59        26.04 
TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 
        1.97         1.12         3.22        30.51         1.48        17.85 
TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 
       24.56         1.84        19.36        22.42         3.12        23.87 
TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 
        2.17         2.27         1.94        17.95        22.32         1.58 
TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 
       15.88         1.15        22.36         0.76         1.78         2.01 
TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS 
        2.20         1.61         5.49         2.33         3.48         1.45 
TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
        1.25         4.41        78.61        88.24        82.92        43.69 
TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N 
       20.19        12.30        21.76        17.03        16.04        16.54 
TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 
       16.14        20.52        14.93        17.19         6.02        13.32 
TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L 
       17.36         9.17         9.17        10.19         6.77        10.39 
TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-KK-A59V 
       14.37        20.28        13.87         5.85        10.62        93.99 
TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 
       56.28        44.68        61.78       115.86        30.02        54.54 
TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 
      151.36        67.59        90.51        49.25       113.33        67.07 
TCGA-KK-A6E8 TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IB TCGA-KK-A8IF 
       58.19        27.62        34.95        22.75         2.73        26.43 
TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 
       20.65         5.19         6.87         9.93        13.15        27.02 
TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN 
       25.08        15.88        18.84         3.19        41.00       114.64 
TCGA-QU-A6IO TCGA-QU-A6IP TCGA-TP-A8TT TCGA-TP-A8TV TCGA-VN-A88I TCGA-VN-A88K 
       47.21        86.14        11.90         8.19         8.84        25.51 
TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q 
       12.95         6.02        15.52        15.81        30.15        32.91 
TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 
       15.09         4.34        26.47        84.69        94.65        23.93 
TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J 
       75.91        55.56        60.92        66.97        21.80        48.85 
TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR 
       21.53        17.82         5.79        37.18        27.81         3.91 
TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR 
       38.04        48.03         9.04         2.99        25.97        31.96 
TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR 
       31.50        31.96        28.54        30.58        29.23        27.09 
TCGA-XK-AAJT TCGA-XK-AAJU TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL 
       37.02        39.65        25.48        52.96        49.02        38.56 
TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB 
       36.95        71.77        62.14        60.56        16.83        45.50 
TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK 
       41.46        45.14        28.77        47.38        45.86        37.97 
TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI 
       26.24       106.75        71.34         7.00        14.04        41.39 
TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-ZG-A8QW TCGA-ZG-A8QX 
       60.99        62.37        24.33        49.91         1.64         4.93 
TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9ND 
        1.12         7.86         6.02 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              0.92               0.30 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
            106.95             151.36 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
            27.665             23.900 
[1] "0.9 - 107.0 (27.7)" "0.3 - 151.4 (23.9)"
[1] "hr="     "2.6e+07"
D20V2, continuous
                    vv
clus                  T2  T3  T4
  10Q GAIN MUTATED     2   8   0
  10Q GAIN WILD-TYPE 148 198   5
D20V3, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  T2                2                148
  T3                8                198
  T4                0                  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"
D20V4, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     7   2
  10Q GAIN WILD-TYPE 256  42
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      7    2
  10Q GAIN WILD-TYPE  256   42
   clus
vv  10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  0                7                256
  1                2                 42
[1] 2 2
[1] FALSE
D20V5, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     1   9
  10Q GAIN WILD-TYPE  12 341
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      1    9
  10Q GAIN WILD-TYPE   12  341
                                        clus
vv                                       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                1                 12
  PROSTATE ADENOCARCINOMA ACINAR TYPE                   9                341
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  10Q GAIN MUTATED     7   2   0   1
  10Q GAIN WILD-TYPE 236  88   5  10
D20V6, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  R0                7                236
  R1                2                 88
  R2                0                  5
  RX                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"
D20V7, continuous
D20V8, continuous
D20V9, continuous
D20V10, continuous
D20V11, continuous
D20V12, continuous
D20V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10Q GAIN MUTATED       0                         0     6
  10Q GAIN WILD-TYPE     2                         7   140
D20V14, multiclass
                           clus
vv                          10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  7
  WHITE                                    6                140
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(21) Variable = 11P GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                  0   1
  11P GAIN MUTATED    13   0
  11P GAIN WILD-TYPE 342   6
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                13                348 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 0                  6 
$`11P GAIN MUTATED`
TCGA-CH-5751 TCGA-EJ-5495 TCGA-EJ-5511 TCGA-EJ-7784 TCGA-G9-7523 TCGA-HC-8216 
       35.01        33.11        48.53        25.68        28.18        22.42 
TCGA-HI-7168 TCGA-KK-A6E8 TCGA-X4-A8KS TCGA-YL-A8HM TCGA-YL-A8SQ TCGA-YL-A9WH 
       78.61        58.19        27.81        36.95        62.79        14.04 
TCGA-YL-A9WI 
       41.39 

$`11P GAIN WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5753 
        1.97        24.03         1.02        13.02        31.00         1.02 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 
        2.04         0.92        44.02        12.00         1.02        23.01 
TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 
        1.02        15.06        24.03         2.04        13.02        15.98 
TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 
       26.99         9.99        32.02        33.01         2.99        29.00 
TCGA-EJ-5494 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 
       27.16        19.56        13.32        29.79        46.52        44.88 
TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 
       26.30        45.73        28.93        30.31        27.19        23.90 
TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 
       38.93        48.13        36.69        38.53        36.23        60.23 
TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 
       46.55        47.80        52.27        64.50        51.88        68.35 
TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 
       43.07        36.66        38.76        39.75        60.23        41.85 
TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 
       47.87        29.06        27.02        49.02        61.15        83.57 
TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 
       21.80         9.70         9.50         9.37        16.77         7.66 
TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 
       17.52         5.75        27.68         6.28         0.30        23.90 
TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 
       38.37        25.87        20.55        14.53        14.14        18.15 
TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 
       19.59        17.29         3.75        23.05        19.92        64.47 
TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E 
       63.98        26.99        10.32         5.33         4.24        17.49 
TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D 
        9.83         3.06         7.53        21.96        17.62        12.92 
TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-FC-7708 
       13.71        18.41         9.14         2.99         7.56        28.41 
TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 
       15.42        13.45         8.98        17.23        16.24         1.78 
TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 
       41.62        87.35        81.04        67.99        66.67        69.37 
TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 
       55.76        18.21        68.68        49.81        46.16        50.70 
TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 
       49.35        47.15        46.52        47.44        45.30        39.39 
TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 
       44.81         3.32        40.18        39.95        38.01        40.31 
TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 
       26.66        31.50        37.97        45.80        25.15        27.29 
TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 
       58.22        56.75        52.87        50.73        38.27        38.96 
TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 
       27.91        30.97        35.34        32.68        26.01        21.14 
TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 
        6.08        30.94         3.68        19.76         5.33         2.93 
TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 
        2.01         2.37        14.47        28.54         0.79        28.60 
TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 
        1.97         1.68         2.37         2.93         1.71         0.72 
TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 
        2.10         2.66         1.74         1.48         1.68         2.07 
TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 
       24.59        26.04         1.97         1.12         3.22        30.51 
TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8256 
        1.48        17.85        24.56         1.84        19.36         3.12 
TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 
       23.87         2.17         2.27         1.94        17.95        22.32 
TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 
        1.58        15.88         1.15        22.36         0.76         1.78 
TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ 
        2.01         2.20         1.61         5.49         2.33         3.48 
TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
        1.45         1.25         4.41        88.24        82.92        43.69 
TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N 
       20.19        12.30        21.76        17.03        16.04        16.54 
TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 
       16.14        20.52        14.93        17.19         6.02        13.32 
TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L 
       17.36         9.17         9.17        10.19         6.77        10.39 
TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-KK-A59V 
       14.37        20.28        13.87         5.85        10.62        93.99 
TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 
       56.28        44.68        61.78       115.86        30.02        54.54 
TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 
      151.36        67.59        90.51        49.25       113.33        67.07 
TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IB TCGA-KK-A8IF TCGA-KK-A8IL 
       27.62        34.95        22.75         2.73        26.43        20.65 
TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 
        5.19         6.87         9.93        13.15        27.02        25.08 
TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO 
       15.88        18.84         3.19        41.00       114.64        47.21 
TCGA-QU-A6IP TCGA-TP-A8TT TCGA-TP-A8TV TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L 
       86.14        11.90         8.19         8.84        25.51        12.95 
TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R 
        6.02        15.52        15.81        30.15        32.91        15.09 
TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 
        4.34       106.95        26.47        84.69        94.65        23.93 
TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J 
       75.91        55.56        60.92        66.97        21.80        48.85 
TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-XA-A8JR TCGA-XJ-A83G 
       21.53        17.82         5.79        37.18         3.91        38.04 
TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV 
       48.03         9.04         2.99        25.97        31.96        31.50 
TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT 
       31.96        28.54        30.58        29.23        27.09        37.02 
TCGA-XK-AAJU TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HO 
       39.65        25.48        52.96        49.02        38.56        71.77 
TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF 
       62.14        60.56        16.83        45.50        41.46        45.14 
TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO 
       28.77        47.38        45.86        37.97        26.24       106.75 
TCGA-YL-A8SP TCGA-YL-A8SR TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX 
       71.34         7.00        60.99        62.37        24.33        49.91 
TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9ND 
       28.34         1.64         4.93         1.12         7.86         6.02 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             14.04               0.30 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             78.61             151.36 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             35.01              23.03 
[1] "14.0 - 78.6 (35.0)" "0.3 - 151.4 (23.0)"
[1] "hr="     "2.7e+07"
D21V2, continuous
                    vv
clus                  T2  T3  T4
  11P GAIN MUTATED     3   9   1
  11P GAIN WILD-TYPE 147 197   4
D21V3, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  T2                3                147
  T3                9                197
  T4                1                  4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V4, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     8   4
  11P GAIN WILD-TYPE 255  40
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      8    4
  11P GAIN WILD-TYPE  255   40
   clus
vv  11P GAIN MUTATED 11P GAIN WILD-TYPE
  0                8                255
  1                4                 40
[1] 2 2
[1] FALSE
D21V5, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     0  13
  11P GAIN WILD-TYPE  13 337
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      0   13
  11P GAIN WILD-TYPE   13  337
                                        clus
vv                                       11P GAIN MUTATED 11P GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                0                 13
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  13                337
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  11P GAIN MUTATED     7   4   0   2
  11P GAIN WILD-TYPE 236  86   5   9
D21V6, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  R0                7                236
  R1                4                 86
  R2                0                  5
  RX                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"
D21V7, continuous
D21V8, continuous
D21V9, continuous
D21V10, continuous
D21V11, continuous
D21V12, continuous
D21V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11P GAIN MUTATED       0                         1     4
  11P GAIN WILD-TYPE     2                         6   142
D21V14, multiclass
                           clus
vv                          11P GAIN MUTATED 11P GAIN WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                1                  6
  WHITE                                    4                142
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(22) Variable = 11Q GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                  0   1
  11Q GAIN MUTATED    14   0
  11Q GAIN WILD-TYPE 341   6
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                14                347 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 0                  6 
$`11Q GAIN MUTATED`
TCGA-CH-5751 TCGA-EJ-5495 TCGA-EJ-5511 TCGA-EJ-7784 TCGA-G9-7523 TCGA-HC-8216 
       35.01        33.11        48.53        25.68        28.18        22.42 
TCGA-HI-7168 TCGA-KK-A6E8 TCGA-X4-A8KS TCGA-YL-A8HM TCGA-YL-A8SB TCGA-YL-A8SQ 
       78.61        58.19        27.81        36.95        45.50        62.79 
TCGA-YL-A9WH TCGA-YL-A9WI 
       14.04        41.39 

$`11Q GAIN WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5753 
        1.97        24.03         1.02        13.02        31.00         1.02 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 
        2.04         0.92        44.02        12.00         1.02        23.01 
TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 
        1.02        15.06        24.03         2.04        13.02        15.98 
TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 
       26.99         9.99        32.02        33.01         2.99        29.00 
TCGA-EJ-5494 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 
       27.16        19.56        13.32        29.79        46.52        44.88 
TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 
       26.30        45.73        28.93        30.31        27.19        23.90 
TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 
       38.93        48.13        36.69        38.53        36.23        60.23 
TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 
       46.55        47.80        52.27        64.50        51.88        68.35 
TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 
       43.07        36.66        38.76        39.75        60.23        41.85 
TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 
       47.87        29.06        27.02        49.02        61.15        83.57 
TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 
       21.80         9.70         9.50         9.37        16.77         7.66 
TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 
       17.52         5.75        27.68         6.28         0.30        23.90 
TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 
       38.37        25.87        20.55        14.53        14.14        18.15 
TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 
       19.59        17.29         3.75        23.05        19.92        64.47 
TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E 
       63.98        26.99        10.32         5.33         4.24        17.49 
TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D 
        9.83         3.06         7.53        21.96        17.62        12.92 
TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-FC-7708 
       13.71        18.41         9.14         2.99         7.56        28.41 
TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 
       15.42        13.45         8.98        17.23        16.24         1.78 
TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 
       41.62        87.35        81.04        67.99        66.67        69.37 
TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 
       55.76        18.21        68.68        49.81        46.16        50.70 
TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 
       49.35        47.15        46.52        47.44        45.30        39.39 
TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 
       44.81         3.32        40.18        39.95        38.01        40.31 
TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 
       26.66        31.50        37.97        45.80        25.15        27.29 
TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 
       58.22        56.75        52.87        50.73        38.27        38.96 
TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 
       27.91        30.97        35.34        32.68        26.01        21.14 
TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 
        6.08        30.94         3.68        19.76         5.33         2.93 
TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 
        2.01         2.37        14.47        28.54         0.79        28.60 
TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 
        1.97         1.68         2.37         2.93         1.71         0.72 
TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 
        2.10         2.66         1.74         1.48         1.68         2.07 
TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 
       24.59        26.04         1.97         1.12         3.22        30.51 
TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8256 
        1.48        17.85        24.56         1.84        19.36         3.12 
TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 
       23.87         2.17         2.27         1.94        17.95        22.32 
TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 
        1.58        15.88         1.15        22.36         0.76         1.78 
TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ 
        2.01         2.20         1.61         5.49         2.33         3.48 
TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
        1.45         1.25         4.41        88.24        82.92        43.69 
TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N 
       20.19        12.30        21.76        17.03        16.04        16.54 
TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 
       16.14        20.52        14.93        17.19         6.02        13.32 
TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L 
       17.36         9.17         9.17        10.19         6.77        10.39 
TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-KK-A59V 
       14.37        20.28        13.87         5.85        10.62        93.99 
TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 
       56.28        44.68        61.78       115.86        30.02        54.54 
TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 
      151.36        67.59        90.51        49.25       113.33        67.07 
TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IB TCGA-KK-A8IF TCGA-KK-A8IL 
       27.62        34.95        22.75         2.73        26.43        20.65 
TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 
        5.19         6.87         9.93        13.15        27.02        25.08 
TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO 
       15.88        18.84         3.19        41.00       114.64        47.21 
TCGA-QU-A6IP TCGA-TP-A8TT TCGA-TP-A8TV TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L 
       86.14        11.90         8.19         8.84        25.51        12.95 
TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R 
        6.02        15.52        15.81        30.15        32.91        15.09 
TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 
        4.34       106.95        26.47        84.69        94.65        23.93 
TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J 
       75.91        55.56        60.92        66.97        21.80        48.85 
TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-XA-A8JR TCGA-XJ-A83G 
       21.53        17.82         5.79        37.18         3.91        38.04 
TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV 
       48.03         9.04         2.99        25.97        31.96        31.50 
TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT 
       31.96        28.54        30.58        29.23        27.09        37.02 
TCGA-XK-AAJU TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HO 
       39.65        25.48        52.96        49.02        38.56        71.77 
TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH 
       62.14        60.56        16.83        41.46        45.14        28.77 
TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP 
       47.38        45.86        37.97        26.24       106.75        71.34 
TCGA-YL-A8SR TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY 
        7.00        60.99        62.37        24.33        49.91        28.34 
TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9ND 
        1.64         4.93         1.12         7.86         6.02 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             14.04               0.30 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             78.61             151.36 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             35.98              23.01 
[1] "14.0 - 78.6 (36.0)" "0.3 - 151.4 (23.0)"
[1] "hr="     "2.7e+07"
D22V2, continuous
                    vv
clus                  T2  T3  T4
  11Q GAIN MUTATED     3  11   1
  11Q GAIN WILD-TYPE 147 195   4
D22V3, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T2                3                147
  T3               11                195
  T4                1                  4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V4, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    10   4
  11Q GAIN WILD-TYPE 253  40
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     10    4
  11Q GAIN WILD-TYPE  253   40
   clus
vv  11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  0               10                253
  1                4                 40
[1] 2 2
[1] FALSE
D22V5, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     0  15
  11Q GAIN WILD-TYPE  13 335
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      0   15
  11Q GAIN WILD-TYPE   13  335
                                        clus
vv                                       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                0                 13
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  15                335
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  11Q GAIN MUTATED     8   5   0   2
  11Q GAIN WILD-TYPE 235  85   5   9
D22V6, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  R0                8                235
  R1                5                 85
  R2                0                  5
  RX                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"
D22V7, continuous
D22V8, continuous
D22V9, continuous
D22V10, continuous
D22V11, continuous
D22V12, continuous
D22V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11Q GAIN MUTATED       0                         1     4
  11Q GAIN WILD-TYPE     2                         6   142
D22V14, multiclass
                           clus
vv                          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                1                  6
  WHITE                                    4                142
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(23) Variable = 12P GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                  0   1
  12P GAIN MUTATED     8   0
  12P GAIN WILD-TYPE 347   6
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 8                353 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 0                  6 
$`12P GAIN MUTATED`
TCGA-FC-A4JI TCGA-HC-8264 TCGA-VP-A875 TCGA-VP-A87H TCGA-XK-AAIV TCGA-YL-A8SO 
       13.45         1.58        26.47        21.80        31.50       106.75 
TCGA-YL-A8SQ TCGA-YL-A9WH 
       62.79        14.04 

$`12P GAIN WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 
        1.02         2.04         0.92        44.02        12.00         1.02 
TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 
       23.01         1.02        15.06        24.03         2.04        13.02 
TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 
       15.98        26.99         9.99        32.02        33.01         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        27.16        33.11        19.56        13.32        29.79 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        26.30        45.73        28.93        30.31 
TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 
       27.19        23.90        38.93        48.13        36.69        48.53 
TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 
       38.53        36.23        60.23        46.55        47.80        52.27 
TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 
       64.50        51.88        68.35        43.07        36.66        38.76 
TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 
       39.75        60.23        41.85        47.87        29.06        27.02 
TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 
       49.02        61.15        83.57        21.80         9.70         9.50 
TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 
        9.37        16.77         7.66        17.52         5.75        27.68 
TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 
        6.28         0.30        23.90        38.37        25.87        25.68 
TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 
       20.55        14.53        14.14        18.15        19.59        17.29 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 
        3.75        23.05        19.92        64.47        63.98        26.99 
TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G 
       10.32         5.33         4.24        17.49         9.83         3.06 
TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F 
        7.53        21.96        17.62        12.92        13.71        18.41 
TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A5OB 
        9.14         2.99         7.56        28.41        15.42         8.98 
TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 
       17.23        16.24         1.78        41.62        87.35        81.04 
TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 
       67.99        66.67        69.37        55.76        18.21        68.68 
TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 
       49.81        46.16        50.70        49.35        47.15        46.52 
TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 
       47.44        45.30        39.39        44.81         3.32        40.18 
TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 
       39.95        38.01        40.31        26.66        31.50        37.97 
TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 
       45.80        25.15        27.29        58.22        56.75        52.87 
TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 
       50.73        38.27        38.96        27.91        30.97        35.34 
TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX 
       28.18        32.68        26.01        21.14         6.08        30.94 
TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 
        3.68        19.76         5.33         2.93         2.01         2.37 
TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 
       14.47        28.54         0.79        28.60         1.97         1.68 
TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 
        2.37         2.93         1.71         0.72         2.10         2.66 
TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 
        1.74         1.48         1.68         2.07        24.59        26.04 
TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 
        1.97         1.12         3.22        30.51         1.48        17.85 
TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 
       24.56         1.84        19.36        22.42         3.12        23.87 
TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8265 
        2.17         2.27         1.94        17.95        22.32        15.88 
TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL 
        1.15        22.36         0.76         1.78         2.01         2.20 
TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX 
        1.61         5.49         2.33         3.48         1.45         1.25 
TCGA-HC-A6HY TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 
        4.41        78.61        88.24        82.92        43.69        20.19 
TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O 
       12.30        21.76        17.03        16.04        16.54        16.14 
TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 
       20.52        14.93        17.19         6.02        13.32        17.36 
TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M 
        9.17         9.17        10.19         6.77        10.39        14.37 
TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-KK-A59V TCGA-KK-A59X 
       20.28        13.87         5.85        10.62        93.99        56.28 
TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 
       44.68        61.78       115.86        30.02        54.54       151.36 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 
       67.59        90.51        49.25       113.33        67.07        58.19 
TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IB TCGA-KK-A8IF TCGA-KK-A8IL 
       27.62        34.95        22.75         2.73        26.43        20.65 
TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 
        5.19         6.87         9.93        13.15        27.02        25.08 
TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO 
       15.88        18.84         3.19        41.00       114.64        47.21 
TCGA-QU-A6IP TCGA-TP-A8TT TCGA-TP-A8TV TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L 
       86.14        11.90         8.19         8.84        25.51        12.95 
TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R 
        6.02        15.52        15.81        30.15        32.91        15.09 
TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B 
        4.34       106.95        84.69        94.65        23.93        75.91 
TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N 
       55.56        60.92        66.97        48.85        21.53        17.82 
TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DI 
        5.79        37.18        27.81         3.91        38.04        48.03 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIW TCGA-XK-AAJ3 
        9.04         2.99        25.97        31.96        31.96        28.54 
TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-Y6-A8TL 
       30.58        29.23        27.09        37.02        39.65        25.48 
TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 
       52.96        49.02        38.56        36.95        71.77        62.14 
TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH 
       60.56        16.83        45.50        41.46        45.14        28.77 
TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SP TCGA-YL-A8SR 
       47.38        45.86        37.97        26.24        71.34         7.00 
TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY 
       41.39        60.99        62.37        24.33        49.91        28.34 
TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9ND 
        1.64         4.93         1.12         7.86         6.02 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              1.58               0.30 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            106.75             151.36 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            24.135             23.930 
[1] "1.6 - 106.8 (24.1)" "0.3 - 151.4 (23.9)"
[1] "hr="     "2.5e+07"
D23V2, continuous
                    vv
clus                  T2  T3  T4
  12P GAIN MUTATED     0   8   0
  12P GAIN WILD-TYPE 150 198   5
D23V3, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  T2                0                150
  T3                8                198
  T4                0                  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"
D23V4, binary
                    cls
clus                   0   1
  12P GAIN MUTATED     3   3
  12P GAIN WILD-TYPE 260  41
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      3    3
  12P GAIN WILD-TYPE  260   41
   clus
vv  12P GAIN MUTATED 12P GAIN WILD-TYPE
  0                3                260
  1                3                 41
[1] 2 2
[1] FALSE
D23V5, binary
                    cls
clus                   0   1
  12P GAIN MUTATED     0   8
  12P GAIN WILD-TYPE  13 342
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      0    8
  12P GAIN WILD-TYPE   13  342
                                        clus
vv                                       12P GAIN MUTATED 12P GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                0                 13
  PROSTATE ADENOCARCINOMA ACINAR TYPE                   8                342
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  12P GAIN MUTATED     2   5   1   0
  12P GAIN WILD-TYPE 241  85   4  11
D23V6, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  R0                2                241
  R1                5                 85
  R2                1                  4
  RX                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"
D23V7, continuous
D23V8, continuous
D23V9, continuous
D23V10, continuous
D23V11, continuous
D23V12, continuous
D23V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12P GAIN MUTATED       0                         0     0
  12P GAIN WILD-TYPE     2                         7   146
D23V14, multiclass

Clustering(24) Variable = 12Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                  0   1
  12Q GAIN MUTATED     8   0
  12Q GAIN WILD-TYPE 347   6
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 8                353 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 0                  6 
$`12Q GAIN MUTATED`
TCGA-CH-5762 TCGA-FC-A4JI TCGA-HC-8264 TCGA-VP-A87H TCGA-XK-AAIV TCGA-YL-A8SO 
       44.02        13.45         1.58        21.80        31.50       106.75 
TCGA-YL-A8SQ TCGA-YL-A9WH 
       62.79        14.04 

$`12Q GAIN WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 
        1.02         2.04         0.92        12.00         1.02        23.01 
TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 
        1.02        15.06        24.03         2.04        13.02        15.98 
TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 
       26.99         9.99        32.02        33.01         2.99        29.00 
TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
       27.16        33.11        19.56        13.32        29.79        46.52 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       44.88        26.30        45.73        28.93        30.31        27.19 
TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       23.90        38.93        48.13        36.69        48.53        38.53 
TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 
       36.23        60.23        46.55        47.80        52.27        64.50 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 
       51.88        68.35        43.07        36.66        38.76        39.75 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 
       60.23        41.85        47.87        29.06        27.02        49.02 
TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 
       61.15        83.57        21.80         9.70         9.50         9.37 
TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 
       16.77         7.66        17.52         5.75        27.68         6.28 
TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 
        0.30        23.90        38.37        25.87        25.68        20.55 
TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 
       14.53        14.14        18.15        19.59        17.29         3.75 
TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8474 
       23.05        19.92        64.47        63.98        26.99        10.32 
TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H 
        5.33         4.24        17.49         9.83         3.06         7.53 
TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G 
       21.96        17.62        12.92        13.71        18.41         9.14 
TCGA-EJ-A65J TCGA-EJ-A65M TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A5OB TCGA-FC-A66V 
        2.99         7.56        28.41        15.42         8.98        17.23 
TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 
       16.24         1.78        41.62        87.35        81.04        67.99 
TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 
       66.67        69.37        55.76        18.21        68.68        49.81 
TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 
       46.16        50.70        49.35        47.15        46.52        47.44 
TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 
       45.30        39.39        44.81         3.32        40.18        39.95 
TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 
       38.01        40.31        26.66        31.50        37.97        45.80 
TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 
       25.15        27.29        58.22        56.75        52.87        50.73 
TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 
       38.27        38.96        27.91        30.97        35.34        28.18 
TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY 
       32.68        26.01        21.14         6.08        30.94         3.68 
TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 
       19.76         5.33         2.93         2.01         2.37        14.47 
TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 
       28.54         0.79        28.60         1.97         1.68         2.37 
TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 
        2.93         1.71         0.72         2.10         2.66         1.74 
TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 
        1.48         1.68         2.07        24.59        26.04         1.97 
TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 
        1.12         3.22        30.51         1.48        17.85        24.56 
TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 
        1.84        19.36        22.42         3.12        23.87         2.17 
TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8265 TCGA-HC-8266 
        2.27         1.94        17.95        22.32        15.88         1.15 
TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN 
       22.36         0.76         1.78         2.01         2.20         1.61 
TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY 
        5.49         2.33         3.48         1.45         1.25         4.41 
TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 
       78.61        88.24        82.92        43.69        20.19        12.30 
TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q 
       21.76        17.03        16.04        16.54        16.14        20.52 
TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 
       14.93        17.19         6.02        13.32        17.36         9.17 
TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N 
        9.17        10.19         6.77        10.39        14.37        20.28 
TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y 
       13.87         5.85        10.62        93.99        56.28        44.68 
TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 
       61.78       115.86        30.02        54.54       151.36        67.59 
TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AZ 
       90.51        49.25       113.33        67.07        58.19        27.62 
TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IB TCGA-KK-A8IF TCGA-KK-A8IL TCGA-M7-A71Y 
       34.95        22.75         2.73        26.43        20.65         5.19 
TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 
        6.87         9.93        13.15        27.02        25.08        15.88 
TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP 
       18.84         3.19        41.00       114.64        47.21        86.14 
TCGA-TP-A8TT TCGA-TP-A8TV TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M 
       11.90         8.19         8.84        25.51        12.95         6.02 
TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 
       15.52        15.81        30.15        32.91        15.09         4.34 
TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B 
      106.95        26.47        84.69        94.65        23.93        75.91 
TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N 
       55.56        60.92        66.97        48.85        21.53        17.82 
TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DI 
        5.79        37.18        27.81         3.91        38.04        48.03 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIW TCGA-XK-AAJ3 
        9.04         2.99        25.97        31.96        31.96        28.54 
TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-Y6-A8TL 
       30.58        29.23        27.09        37.02        39.65        25.48 
TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 
       52.96        49.02        38.56        36.95        71.77        62.14 
TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH 
       60.56        16.83        45.50        41.46        45.14        28.77 
TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SP TCGA-YL-A8SR 
       47.38        45.86        37.97        26.24        71.34         7.00 
TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY 
       41.39        60.99        62.37        24.33        49.91        28.34 
TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9ND 
        1.64         4.93         1.12         7.86         6.02 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              1.58               0.30 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            106.75             151.36 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             26.65              23.93 
[1] "1.6 - 106.8 (26.6)" "0.3 - 151.4 (23.9)"
[1] "hr="     "2.6e+07"
D24V2, continuous
                    vv
clus                  T2  T3  T4
  12Q GAIN MUTATED     0   8   0
  12Q GAIN WILD-TYPE 150 198   5
D24V3, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T2                0                150
  T3                8                198
  T4                0                  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"
D24V4, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED     3   3
  12Q GAIN WILD-TYPE 260  41
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      3    3
  12Q GAIN WILD-TYPE  260   41
   clus
vv  12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  0                3                260
  1                3                 41
[1] 2 2
[1] FALSE
D24V5, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED     0   8
  12Q GAIN WILD-TYPE  13 342
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      0    8
  12Q GAIN WILD-TYPE   13  342
                                        clus
vv                                       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                0                 13
  PROSTATE ADENOCARCINOMA ACINAR TYPE                   8                342
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  12Q GAIN MUTATED     1   6   1   0
  12Q GAIN WILD-TYPE 242  84   4  11
D24V6, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  R0                1                242
  R1                6                 84
  R2                1                  4
  RX                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"
D24V7, continuous
D24V8, continuous
D24V9, continuous
D24V10, continuous
D24V11, continuous
D24V12, continuous
D24V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12Q GAIN MUTATED       0                         0     1
  12Q GAIN WILD-TYPE     2                         7   145
D24V14, multiclass
[1] "Remove cluster labels:" "12Q GAIN MUTATED"      
clus
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 1                154 
        TCGA-CH-5737         TCGA-CH-5738         TCGA-CH-5739 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CH-5740         TCGA-CH-5741         TCGA-CH-5743 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CH-5744         TCGA-CH-5746         TCGA-CH-5748 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CH-5750         TCGA-CH-5751         TCGA-CH-5752 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CH-5753         TCGA-CH-5754         TCGA-CH-5761 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CH-5763         TCGA-CH-5764         TCGA-CH-5765 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CH-5766         TCGA-CH-5767         TCGA-CH-5768 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CH-5769         TCGA-CH-5771         TCGA-CH-5772 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CH-5788         TCGA-CH-5789         TCGA-CH-5790 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CH-5791         TCGA-CH-5792         TCGA-CH-5794 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-5494         TCGA-EJ-5495         TCGA-EJ-5496 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-5497         TCGA-EJ-5498         TCGA-EJ-5499 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-5501         TCGA-EJ-5503         TCGA-EJ-5504 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-5505         TCGA-EJ-5506         TCGA-EJ-5507 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-5508         TCGA-EJ-5509         TCGA-EJ-5510 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-5511         TCGA-EJ-5512         TCGA-EJ-5514 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-5515         TCGA-EJ-5516         TCGA-EJ-5517 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-5518         TCGA-EJ-5519         TCGA-EJ-5521 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-5522         TCGA-EJ-5524         TCGA-EJ-5525 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-5526         TCGA-EJ-5527         TCGA-EJ-5530 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-5531         TCGA-EJ-5532         TCGA-EJ-5542 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-7115         TCGA-EJ-7123         TCGA-EJ-7125 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-7314         TCGA-EJ-7315         TCGA-EJ-7317 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-7321         TCGA-EJ-7327         TCGA-EJ-7328 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-7330         TCGA-EJ-7331         TCGA-EJ-7781 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-7782         TCGA-EJ-7783         TCGA-EJ-7784 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-7785         TCGA-EJ-7786         TCGA-EJ-7788 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-7789         TCGA-EJ-7791         TCGA-EJ-7792 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EJ-7793         TCGA-EJ-7794         TCGA-EJ-7797 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FC-7708         TCGA-FC-7961         TCGA-G9-6329 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G9-6332         TCGA-G9-6333         TCGA-G9-6336 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G9-6338         TCGA-G9-6342         TCGA-G9-6343 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G9-6348         TCGA-G9-6351         TCGA-G9-6353 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G9-6356         TCGA-G9-6361         TCGA-G9-6362 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G9-6363         TCGA-G9-6364         TCGA-G9-6365 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G9-6366         TCGA-G9-6367         TCGA-G9-6369 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G9-6370         TCGA-G9-6371         TCGA-G9-6373 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G9-6377         TCGA-G9-6378         TCGA-G9-6384 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G9-6385         TCGA-G9-6494         TCGA-G9-6496 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G9-6499         TCGA-H9-7775         TCGA-HC-7075 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-HC-7077         TCGA-HC-7078         TCGA-HC-7079 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-HC-7080         TCGA-HC-7081         TCGA-HC-7209 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-HC-7210         TCGA-HC-7211         TCGA-HC-7212 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-HC-7213         TCGA-HC-7230         TCGA-HC-7231 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-HC-7232         TCGA-HC-7233         TCGA-HC-7736 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-HC-7737         TCGA-HC-7738         TCGA-HC-7740 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-HC-7742         TCGA-HC-7744         TCGA-HC-7745 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-HC-7747         TCGA-HC-7748         TCGA-HC-7749 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-HC-7750         TCGA-HC-7752         TCGA-HC-7818 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-HC-7819         TCGA-HC-7820         TCGA-HC-7821 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-HI-7168         TCGA-HI-7169         TCGA-HI-7170 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-HI-7171 
"12Q GAIN WILD-TYPE" 

Clustering(25) Variable = 13Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                  0   1
  13Q GAIN MUTATED     5   0
  13Q GAIN WILD-TYPE 350   6
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 5                356 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 0                  6 
$`13Q GAIN MUTATED`
TCGA-EJ-7784 TCGA-G9-7509 TCGA-VP-A872 TCGA-YL-A8HO TCGA-YL-A8S8 
       25.68        38.27       106.95        71.77        62.14 

$`13Q GAIN WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 
        1.02         2.04         0.92        44.02        12.00         1.02 
TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 
       23.01         1.02        15.06        24.03         2.04        13.02 
TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 
       15.98        26.99         9.99        32.02        33.01         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        27.16        33.11        19.56        13.32        29.79 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        26.30        45.73        28.93        30.31 
TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 
       27.19        23.90        38.93        48.13        36.69        48.53 
TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 
       38.53        36.23        60.23        46.55        47.80        52.27 
TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 
       64.50        51.88        68.35        43.07        36.66        38.76 
TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 
       39.75        60.23        41.85        47.87        29.06        27.02 
TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 
       49.02        61.15        83.57        21.80         9.70         9.50 
TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 
        9.37        16.77         7.66        17.52         5.75        27.68 
TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7785 
        6.28         0.30        23.90        38.37        25.87        20.55 
TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 
       14.53        14.14        18.15        19.59        17.29         3.75 
TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8474 
       23.05        19.92        64.47        63.98        26.99        10.32 
TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H 
        5.33         4.24        17.49         9.83         3.06         7.53 
TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G 
       21.96        17.62        12.92        13.71        18.41         9.14 
TCGA-EJ-A65J TCGA-EJ-A65M TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB 
        2.99         7.56        28.41        15.42        13.45         8.98 
TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 
       17.23        16.24         1.78        41.62        87.35        81.04 
TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 
       67.99        66.67        69.37        55.76        18.21        68.68 
TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 
       49.81        46.16        50.70        49.35        47.15        46.52 
TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 
       47.44        45.30        39.39        44.81         3.32        40.18 
TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 
       39.95        38.01        40.31        26.66        31.50        37.97 
TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 
       45.80        25.15        27.29        58.22        56.75        52.87 
TCGA-G9-6499 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 
       50.73        38.96        27.91        30.97        35.34        28.18 
TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY 
       32.68        26.01        21.14         6.08        30.94         3.68 
TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 
       19.76         5.33         2.93         2.01         2.37        14.47 
TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 
       28.54         0.79        28.60         1.97         1.68         2.37 
TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 
        2.93         1.71         0.72         2.10         2.66         1.74 
TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 
        1.48         1.68         2.07        24.59        26.04         1.97 
TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 
        1.12         3.22        30.51         1.48        17.85        24.56 
TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 
        1.84        19.36        22.42         3.12        23.87         2.17 
TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 
        2.27         1.94        17.95        22.32         1.58        15.88 
TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL 
        1.15        22.36         0.76         1.78         2.01         2.20 
TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX 
        1.61         5.49         2.33         3.48         1.45         1.25 
TCGA-HC-A6HY TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 
        4.41        78.61        88.24        82.92        43.69        20.19 
TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O 
       12.30        21.76        17.03        16.04        16.54        16.14 
TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 
       20.52        14.93        17.19         6.02        13.32        17.36 
TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M 
        9.17         9.17        10.19         6.77        10.39        14.37 
TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-KK-A59V TCGA-KK-A59X 
       20.28        13.87         5.85        10.62        93.99        56.28 
TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 
       44.68        61.78       115.86        30.02        54.54       151.36 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 
       67.59        90.51        49.25       113.33        67.07        58.19 
TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IB TCGA-KK-A8IF TCGA-KK-A8IL 
       27.62        34.95        22.75         2.73        26.43        20.65 
TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 
        5.19         6.87         9.93        13.15        27.02        25.08 
TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO 
       15.88        18.84         3.19        41.00       114.64        47.21 
TCGA-QU-A6IP TCGA-TP-A8TT TCGA-TP-A8TV TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L 
       86.14        11.90         8.19         8.84        25.51        12.95 
TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R 
        6.02        15.52        15.81        30.15        32.91        15.09 
TCGA-VN-A943 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B 
        4.34        26.47        84.69        94.65        23.93        75.91 
TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K 
       55.56        60.92        66.97        21.80        48.85        21.53 
TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83G 
       17.82         5.79        37.18        27.81         3.91        38.04 
TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV 
       48.03         9.04         2.99        25.97        31.96        31.50 
TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT 
       31.96        28.54        30.58        29.23        27.09        37.02 
TCGA-XK-AAJU TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM 
       39.65        25.48        52.96        49.02        38.56        36.95 
TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH 
       60.56        16.83        45.50        41.46        45.14        28.77 
TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP 
       47.38        45.86        37.97        26.24       106.75        71.34 
TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK 
       62.79         7.00        14.04        41.39        60.99        62.37 
TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY 
       24.33        49.91        28.34         1.64         4.93         1.12 
TCGA-ZG-A8QZ TCGA-ZG-A9ND 
        7.86         6.02 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             25.68               0.30 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
            106.95             151.36 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
            62.140             23.885 
[1] "25.7 - 107.0 (62.1)" "0.3 - 151.4 (23.9)" 
[1] "hr="     "2.6e+07"
D25V2, continuous
                    vv
clus                  T2  T3  T4
  13Q GAIN MUTATED     2   3   0
  13Q GAIN WILD-TYPE 148 203   5
D25V3, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  T2                2                148
  T3                3                203
  T4                0                  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"
D25V4, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     4   0
  13Q GAIN WILD-TYPE 259  44
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      4    0
  13Q GAIN WILD-TYPE  259   44
   clus
vv  13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  0                4                259
  1                0                 44
[1] 2 2
[1] FALSE
D25V5, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     1   4
  13Q GAIN WILD-TYPE  12 346
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      1    4
  13Q GAIN WILD-TYPE   12  346
                                        clus
vv                                       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                1                 12
  PROSTATE ADENOCARCINOMA ACINAR TYPE                   4                346
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  13Q GAIN MUTATED     3   2   0   0
  13Q GAIN WILD-TYPE 240  88   5  11
D25V6, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  R0                3                240
  R1                2                 88
  R2                0                  5
  RX                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"
D25V7, continuous
D25V8, continuous
D25V9, continuous
D25V10, continuous
D25V11, continuous
D25V12, continuous
D25V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  13Q GAIN MUTATED       0                         0     1
  13Q GAIN WILD-TYPE     2                         7   145
D25V14, multiclass
[1] "Remove cluster labels:" "13Q GAIN MUTATED"      
clus
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 1                154 
        TCGA-CH-5737         TCGA-CH-5738         TCGA-CH-5739 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CH-5740         TCGA-CH-5741         TCGA-CH-5743 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CH-5744         TCGA-CH-5746         TCGA-CH-5748 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CH-5750         TCGA-CH-5751         TCGA-CH-5752 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CH-5753         TCGA-CH-5754         TCGA-CH-5761 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CH-5762         TCGA-CH-5763         TCGA-CH-5764 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CH-5765         TCGA-CH-5766         TCGA-CH-5767 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CH-5768         TCGA-CH-5769         TCGA-CH-5771 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CH-5772         TCGA-CH-5788         TCGA-CH-5789 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CH-5790         TCGA-CH-5791         TCGA-CH-5792 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-CH-5794         TCGA-EJ-5494         TCGA-EJ-5495 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EJ-5496         TCGA-EJ-5497         TCGA-EJ-5498 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EJ-5499         TCGA-EJ-5501         TCGA-EJ-5503 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EJ-5504         TCGA-EJ-5505         TCGA-EJ-5506 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EJ-5507         TCGA-EJ-5508         TCGA-EJ-5509 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EJ-5510         TCGA-EJ-5511         TCGA-EJ-5512 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EJ-5514         TCGA-EJ-5515         TCGA-EJ-5516 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EJ-5517         TCGA-EJ-5518         TCGA-EJ-5519 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EJ-5521         TCGA-EJ-5522         TCGA-EJ-5524 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EJ-5525         TCGA-EJ-5526         TCGA-EJ-5527 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EJ-5530         TCGA-EJ-5531         TCGA-EJ-5532 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EJ-5542         TCGA-EJ-7115         TCGA-EJ-7123 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EJ-7125         TCGA-EJ-7314         TCGA-EJ-7315 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EJ-7317         TCGA-EJ-7321         TCGA-EJ-7327 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EJ-7328         TCGA-EJ-7330         TCGA-EJ-7331 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EJ-7781         TCGA-EJ-7782         TCGA-EJ-7783 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EJ-7785         TCGA-EJ-7786         TCGA-EJ-7788 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EJ-7789         TCGA-EJ-7791         TCGA-EJ-7792 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EJ-7793         TCGA-EJ-7794         TCGA-EJ-7797 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FC-7708         TCGA-FC-7961         TCGA-G9-6329 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-G9-6332         TCGA-G9-6333         TCGA-G9-6336 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-G9-6338         TCGA-G9-6342         TCGA-G9-6343 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-G9-6348         TCGA-G9-6351         TCGA-G9-6353 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-G9-6356         TCGA-G9-6361         TCGA-G9-6362 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-G9-6363         TCGA-G9-6364         TCGA-G9-6365 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-G9-6366         TCGA-G9-6367         TCGA-G9-6369 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-G9-6370         TCGA-G9-6371         TCGA-G9-6373 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-G9-6377         TCGA-G9-6378         TCGA-G9-6384 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-G9-6385         TCGA-G9-6494         TCGA-G9-6496 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-G9-6499         TCGA-H9-7775         TCGA-HC-7075 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-HC-7077         TCGA-HC-7078         TCGA-HC-7079 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-HC-7080         TCGA-HC-7081         TCGA-HC-7209 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-HC-7210         TCGA-HC-7211         TCGA-HC-7212 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-HC-7213         TCGA-HC-7230         TCGA-HC-7231 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-HC-7232         TCGA-HC-7233         TCGA-HC-7736 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-HC-7737         TCGA-HC-7738         TCGA-HC-7740 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-HC-7742         TCGA-HC-7744         TCGA-HC-7745 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-HC-7747         TCGA-HC-7748         TCGA-HC-7749 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-HC-7750         TCGA-HC-7752         TCGA-HC-7818 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-HC-7819         TCGA-HC-7820         TCGA-HC-7821 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-HI-7168         TCGA-HI-7169         TCGA-HI-7170 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-HI-7171 
"13Q GAIN WILD-TYPE" 

Clustering(26) Variable = 14Q GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                  0   1
  14Q GAIN MUTATED     7   1
  14Q GAIN WILD-TYPE 348   5
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 8                353 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 1                  5 
$`14Q GAIN MUTATED`
TCGA-CH-5772 TCGA-FC-A4JI TCGA-G9-A9S0 TCGA-HC-A631 TCGA-KK-A59Z TCGA-KK-A6E8 
       15.98        13.45        26.01         1.78        61.78        58.19 
TCGA-VP-A872 TCGA-YL-A8SK 
      106.95        37.97 

$`14Q GAIN WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 
        1.02         2.04         0.92        44.02        12.00         1.02 
TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 
       23.01         1.02        15.06        24.03         2.04        13.02 
TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 
       26.99         9.99        32.02        33.01         2.99        29.00 
TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
       27.16        33.11        19.56        13.32        29.79        46.52 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       44.88        26.30        45.73        28.93        30.31        27.19 
TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       23.90        38.93        48.13        36.69        48.53        38.53 
TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 
       36.23        60.23        46.55        47.80        52.27        64.50 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 
       51.88        68.35        43.07        36.66        38.76        39.75 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 
       60.23        41.85        47.87        29.06        27.02        49.02 
TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 
       61.15        83.57        21.80         9.70         9.50         9.37 
TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 
       16.77         7.66        17.52         5.75        27.68         6.28 
TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 
        0.30        23.90        38.37        25.87        25.68        20.55 
TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 
       14.53        14.14        18.15        19.59        17.29         3.75 
TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8474 
       23.05        19.92        64.47        63.98        26.99        10.32 
TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H 
        5.33         4.24        17.49         9.83         3.06         7.53 
TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G 
       21.96        17.62        12.92        13.71        18.41         9.14 
TCGA-EJ-A65J TCGA-EJ-A65M TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A5OB TCGA-FC-A66V 
        2.99         7.56        28.41        15.42         8.98        17.23 
TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 
       16.24         1.78        41.62        87.35        81.04        67.99 
TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 
       66.67        69.37        55.76        18.21        68.68        49.81 
TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 
       46.16        50.70        49.35        47.15        46.52        47.44 
TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 
       45.30        39.39        44.81         3.32        40.18        39.95 
TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 
       38.01        40.31        26.66        31.50        37.97        45.80 
TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 
       25.15        27.29        58.22        56.75        52.87        50.73 
TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 
       38.27        38.96        27.91        30.97        35.34        28.18 
TCGA-G9-7525 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 
       32.68        21.14         6.08        30.94         3.68        19.76 
TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 
        5.33         2.93         2.01         2.37        14.47        28.54 
TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 
        0.79        28.60         1.97         1.68         2.37         2.93 
TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 
        1.71         0.72         2.10         2.66         1.74         1.48 
TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 
        1.68         2.07        24.59        26.04         1.97         1.12 
TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 
        3.22        30.51         1.48        17.85        24.56         1.84 
TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 
       19.36        22.42         3.12        23.87         2.17         2.27 
TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 
        1.94        17.95        22.32         1.58        15.88         1.15 
TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO 
       22.36         0.76         2.01         2.20         1.61         5.49 
TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HI-7168 
        2.33         3.48         1.45         1.25         4.41        78.61 
TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K 
       88.24        82.92        43.69        20.19        12.30        21.76 
TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R 
       17.03        16.04        16.54        16.14        20.52        14.93 
TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I 
       17.19         6.02        13.32        17.36         9.17         9.17 
TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B 
       10.19         6.77        10.39        14.37        20.28        13.87 
TCGA-J9-A52C TCGA-J9-A52E TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A6DY 
        5.85        10.62        93.99        56.28        44.68       115.86 
TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 
       30.02        54.54       151.36        67.59        90.51        49.25 
TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IB 
      113.33        67.07        27.62        34.95        22.75         2.73 
TCGA-KK-A8IF TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 
       26.43        20.65         5.19         6.87         9.93        13.15 
TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM 
       27.02        25.08        15.88        18.84         3.19        41.00 
TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-TP-A8TT TCGA-TP-A8TV TCGA-VN-A88I 
      114.64        47.21        86.14        11.90         8.19         8.84 
TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P 
       25.51        12.95         6.02        15.52        15.81        30.15 
TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 
       32.91        15.09         4.34        26.47        84.69        94.65 
TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H 
       23.93        75.91        55.56        60.92        66.97        21.80 
TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS 
       48.85        21.53        17.82         5.79        37.18        27.81 
TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX 
        3.91        38.04        48.03         9.04         2.99        25.97 
TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP 
       31.96        31.50        31.96        28.54        30.58        29.23 
TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK 
       27.09        37.02        39.65        25.48        52.96        49.02 
TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA 
       38.56        36.95        71.77        62.14        60.56        16.83 
TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ 
       45.50        41.46        45.14        28.77        47.38        45.86 
TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH 
       26.24       106.75        71.34        62.79         7.00        14.04 
TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY 
       41.39        60.99        62.37        24.33        49.91        28.34 
TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9ND 
        1.64         4.93         1.12         7.86         6.02 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              1.78               0.30 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
            106.95             151.36 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             31.99              23.90 
[1] "1.8 - 107.0 (32.0)" "0.3 - 151.4 (23.9)"
[1] "hr=" "5.9"
D26V2, continuous
                    vv
clus                  T2  T3  T4
  14Q GAIN MUTATED     3   5   0
  14Q GAIN WILD-TYPE 147 201   5
D26V3, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  T2                3                147
  T3                5                201
  T4                0                  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"
D26V4, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     5   2
  14Q GAIN WILD-TYPE 258  42
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      5    2
  14Q GAIN WILD-TYPE  258   42
   clus
vv  14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  0                5                258
  1                2                 42
[1] 2 2
[1] FALSE
D26V5, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     1   7
  14Q GAIN WILD-TYPE  12 343
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      1    7
  14Q GAIN WILD-TYPE   12  343
                                        clus
vv                                       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                1                 12
  PROSTATE ADENOCARCINOMA ACINAR TYPE                   7                343
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  14Q GAIN MUTATED     3   4   0   1
  14Q GAIN WILD-TYPE 240  86   5  10
D26V6, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  R0                3                240
  R1                4                 86
  R2                0                  5
  RX                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"
D26V7, continuous
D26V8, continuous
D26V9, continuous
D26V10, continuous
D26V11, continuous
D26V12, continuous
D26V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  14Q GAIN MUTATED       0                         0     1
  14Q GAIN WILD-TYPE     2                         7   145
D26V14, multiclass
[1] "Remove cluster labels:" "14Q GAIN MUTATED"      
clus
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 1                154 
        TCGA-CH-5737         TCGA-CH-5738         TCGA-CH-5739 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CH-5740         TCGA-CH-5741         TCGA-CH-5743 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CH-5744         TCGA-CH-5746         TCGA-CH-5748 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CH-5750         TCGA-CH-5751         TCGA-CH-5752 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CH-5753         TCGA-CH-5754         TCGA-CH-5761 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CH-5762         TCGA-CH-5763         TCGA-CH-5764 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CH-5765         TCGA-CH-5766         TCGA-CH-5767 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CH-5768         TCGA-CH-5769         TCGA-CH-5771 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CH-5788         TCGA-CH-5789         TCGA-CH-5790 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-CH-5791         TCGA-CH-5792         TCGA-CH-5794 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EJ-5494         TCGA-EJ-5495         TCGA-EJ-5496 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EJ-5497         TCGA-EJ-5498         TCGA-EJ-5499 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EJ-5501         TCGA-EJ-5503         TCGA-EJ-5504 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EJ-5505         TCGA-EJ-5506         TCGA-EJ-5507 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EJ-5508         TCGA-EJ-5509         TCGA-EJ-5510 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EJ-5511         TCGA-EJ-5512         TCGA-EJ-5514 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EJ-5515         TCGA-EJ-5516         TCGA-EJ-5517 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EJ-5518         TCGA-EJ-5519         TCGA-EJ-5521 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EJ-5522         TCGA-EJ-5524         TCGA-EJ-5525 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EJ-5526         TCGA-EJ-5527         TCGA-EJ-5530 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EJ-5531         TCGA-EJ-5532         TCGA-EJ-5542 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EJ-7115         TCGA-EJ-7123         TCGA-EJ-7125 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EJ-7314         TCGA-EJ-7315         TCGA-EJ-7317 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EJ-7321         TCGA-EJ-7327         TCGA-EJ-7328 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EJ-7330         TCGA-EJ-7331         TCGA-EJ-7781 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EJ-7782         TCGA-EJ-7783         TCGA-EJ-7784 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EJ-7785         TCGA-EJ-7786         TCGA-EJ-7788 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EJ-7789         TCGA-EJ-7791         TCGA-EJ-7792 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-EJ-7793         TCGA-EJ-7794         TCGA-EJ-7797 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-FC-7708         TCGA-FC-7961         TCGA-G9-6329 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G9-6332         TCGA-G9-6333         TCGA-G9-6336 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G9-6338         TCGA-G9-6342         TCGA-G9-6343 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G9-6348         TCGA-G9-6351         TCGA-G9-6353 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G9-6356         TCGA-G9-6361         TCGA-G9-6362 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G9-6363         TCGA-G9-6364         TCGA-G9-6365 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G9-6366         TCGA-G9-6367         TCGA-G9-6369 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G9-6370         TCGA-G9-6371         TCGA-G9-6373 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G9-6377         TCGA-G9-6378         TCGA-G9-6384 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G9-6385         TCGA-G9-6494         TCGA-G9-6496 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-G9-6499         TCGA-H9-7775         TCGA-HC-7075 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HC-7077         TCGA-HC-7078         TCGA-HC-7079 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HC-7080         TCGA-HC-7081         TCGA-HC-7209 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HC-7210         TCGA-HC-7211         TCGA-HC-7212 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HC-7213         TCGA-HC-7230         TCGA-HC-7231 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HC-7232         TCGA-HC-7233         TCGA-HC-7736 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HC-7737         TCGA-HC-7738         TCGA-HC-7740 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HC-7742         TCGA-HC-7744         TCGA-HC-7745 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HC-7747         TCGA-HC-7748         TCGA-HC-7749 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HC-7750         TCGA-HC-7752         TCGA-HC-7818 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HC-7819         TCGA-HC-7820         TCGA-HC-7821 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HI-7168         TCGA-HI-7169         TCGA-HI-7170 
"14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" "14Q GAIN WILD-TYPE" 
        TCGA-HI-7171 
"14Q GAIN WILD-TYPE" 

Clustering(27) Variable = 15Q GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                  0   1
  15Q GAIN MUTATED     5   0
  15Q GAIN WILD-TYPE 350   6
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 5                356 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 0                  6 
$`15Q GAIN MUTATED`
TCGA-EJ-5514 TCGA-G9-7525 TCGA-HC-8266 TCGA-VP-A875 TCGA-XK-AAIV 
       36.23        32.68         1.15        26.47        31.50 

$`15Q GAIN WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 
        1.02         2.04         0.92        44.02        12.00         1.02 
TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 
       23.01         1.02        15.06        24.03         2.04        13.02 
TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 
       15.98        26.99         9.99        32.02        33.01         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        27.16        33.11        19.56        13.32        29.79 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        26.30        45.73        28.93        30.31 
TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 
       27.19        23.90        38.93        48.13        36.69        48.53 
TCGA-EJ-5512 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 
       38.53        60.23        46.55        47.80        52.27        64.50 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 
       51.88        68.35        43.07        36.66        38.76        39.75 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 
       60.23        41.85        47.87        29.06        27.02        49.02 
TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 
       61.15        83.57        21.80         9.70         9.50         9.37 
TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 
       16.77         7.66        17.52         5.75        27.68         6.28 
TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 
        0.30        23.90        38.37        25.87        25.68        20.55 
TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 
       14.53        14.14        18.15        19.59        17.29         3.75 
TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8474 
       23.05        19.92        64.47        63.98        26.99        10.32 
TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H 
        5.33         4.24        17.49         9.83         3.06         7.53 
TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G 
       21.96        17.62        12.92        13.71        18.41         9.14 
TCGA-EJ-A65J TCGA-EJ-A65M TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB 
        2.99         7.56        28.41        15.42        13.45         8.98 
TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 
       17.23        16.24         1.78        41.62        87.35        81.04 
TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 
       67.99        66.67        69.37        55.76        18.21        68.68 
TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 
       49.81        46.16        50.70        49.35        47.15        46.52 
TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 
       47.44        45.30        39.39        44.81         3.32        40.18 
TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 
       39.95        38.01        40.31        26.66        31.50        37.97 
TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 
       45.80        25.15        27.29        58.22        56.75        52.87 
TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 
       50.73        38.27        38.96        27.91        30.97        35.34 
TCGA-G9-7523 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY 
       28.18        26.01        21.14         6.08        30.94         3.68 
TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 
       19.76         5.33         2.93         2.01         2.37        14.47 
TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 
       28.54         0.79        28.60         1.97         1.68         2.37 
TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 
        2.93         1.71         0.72         2.10         2.66         1.74 
TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 
        1.48         1.68         2.07        24.59        26.04         1.97 
TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 
        1.12         3.22        30.51         1.48        17.85        24.56 
TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 
        1.84        19.36        22.42         3.12        23.87         2.17 
TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 
        2.27         1.94        17.95        22.32         1.58        15.88 
TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN 
       22.36         0.76         1.78         2.01         2.20         1.61 
TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY 
        5.49         2.33         3.48         1.45         1.25         4.41 
TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 
       78.61        88.24        82.92        43.69        20.19        12.30 
TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q 
       21.76        17.03        16.04        16.54        16.14        20.52 
TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 
       14.93        17.19         6.02        13.32        17.36         9.17 
TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N 
        9.17        10.19         6.77        10.39        14.37        20.28 
TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y 
       13.87         5.85        10.62        93.99        56.28        44.68 
TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 
       61.78       115.86        30.02        54.54       151.36        67.59 
TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AZ 
       90.51        49.25       113.33        67.07        58.19        27.62 
TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IB TCGA-KK-A8IF TCGA-KK-A8IL TCGA-M7-A71Y 
       34.95        22.75         2.73        26.43        20.65         5.19 
TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 
        6.87         9.93        13.15        27.02        25.08        15.88 
TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP 
       18.84         3.19        41.00       114.64        47.21        86.14 
TCGA-TP-A8TT TCGA-TP-A8TV TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M 
       11.90         8.19         8.84        25.51        12.95         6.02 
TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 
       15.52        15.81        30.15        32.91        15.09         4.34 
TCGA-VP-A872 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C 
      106.95        84.69        94.65        23.93        75.91        55.56 
TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N 
       60.92        66.97        21.80        48.85        21.53        17.82 
TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DI 
        5.79        37.18        27.81         3.91        38.04        48.03 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIW TCGA-XK-AAJ3 
        9.04         2.99        25.97        31.96        31.96        28.54 
TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-Y6-A8TL 
       30.58        29.23        27.09        37.02        39.65        25.48 
TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 
       52.96        49.02        38.56        36.95        71.77        62.14 
TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH 
       60.56        16.83        45.50        41.46        45.14        28.77 
TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP 
       47.38        45.86        37.97        26.24       106.75        71.34 
TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK 
       62.79         7.00        14.04        41.39        60.99        62.37 
TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY 
       24.33        49.91        28.34         1.64         4.93         1.12 
TCGA-ZG-A8QZ TCGA-ZG-A9ND 
        7.86         6.02 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              1.15               0.30 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             36.23             151.36 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              31.5               23.9 
[1] "1.1 - 36.2 (31.5)"  "0.3 - 151.4 (23.9)"
[1] "hr="     "9200000"
D27V2, continuous
                    vv
clus                  T2  T3  T4
  15Q GAIN MUTATED     2   3   0
  15Q GAIN WILD-TYPE 148 203   5
D27V3, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  T2                2                148
  T3                3                203
  T4                0                  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"
D27V4, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     4   1
  15Q GAIN WILD-TYPE 259  43
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      4    1
  15Q GAIN WILD-TYPE  259   43
   clus
vv  15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  0                4                259
  1                1                 43
[1] 2 2
[1] FALSE
D27V5, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     0   5
  15Q GAIN WILD-TYPE  13 345
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      0    5
  15Q GAIN WILD-TYPE   13  345
                                        clus
vv                                       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                0                 13
  PROSTATE ADENOCARCINOMA ACINAR TYPE                   5                345
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  15Q GAIN MUTATED     3   2   0   0
  15Q GAIN WILD-TYPE 240  88   5  11
D27V6, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  R0                3                240
  R1                2                 88
  R2                0                  5
  RX                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"
D27V7, continuous
D27V8, continuous
D27V9, continuous
D27V10, continuous
D27V11, continuous
D27V12, continuous
D27V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  15Q GAIN MUTATED       0                         0     1
  15Q GAIN WILD-TYPE     2                         7   145
D27V14, multiclass
[1] "Remove cluster labels:" "15Q GAIN MUTATED"      
clus
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 1                154 
        TCGA-CH-5737         TCGA-CH-5738         TCGA-CH-5739 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CH-5740         TCGA-CH-5741         TCGA-CH-5743 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CH-5744         TCGA-CH-5746         TCGA-CH-5748 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CH-5750         TCGA-CH-5751         TCGA-CH-5752 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CH-5753         TCGA-CH-5754         TCGA-CH-5761 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CH-5762         TCGA-CH-5763         TCGA-CH-5764 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CH-5765         TCGA-CH-5766         TCGA-CH-5767 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CH-5768         TCGA-CH-5769         TCGA-CH-5771 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CH-5772         TCGA-CH-5788         TCGA-CH-5789 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CH-5790         TCGA-CH-5791         TCGA-CH-5792 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CH-5794         TCGA-EJ-5494         TCGA-EJ-5495 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EJ-5496         TCGA-EJ-5497         TCGA-EJ-5498 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EJ-5499         TCGA-EJ-5501         TCGA-EJ-5503 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EJ-5504         TCGA-EJ-5505         TCGA-EJ-5506 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EJ-5507         TCGA-EJ-5508         TCGA-EJ-5509 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EJ-5510         TCGA-EJ-5511         TCGA-EJ-5512 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EJ-5515         TCGA-EJ-5516         TCGA-EJ-5517 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EJ-5518         TCGA-EJ-5519         TCGA-EJ-5521 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EJ-5522         TCGA-EJ-5524         TCGA-EJ-5525 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EJ-5526         TCGA-EJ-5527         TCGA-EJ-5530 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EJ-5531         TCGA-EJ-5532         TCGA-EJ-5542 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EJ-7115         TCGA-EJ-7123         TCGA-EJ-7125 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EJ-7314         TCGA-EJ-7315         TCGA-EJ-7317 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EJ-7321         TCGA-EJ-7327         TCGA-EJ-7328 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EJ-7330         TCGA-EJ-7331         TCGA-EJ-7781 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EJ-7782         TCGA-EJ-7783         TCGA-EJ-7784 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EJ-7785         TCGA-EJ-7786         TCGA-EJ-7788 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EJ-7789         TCGA-EJ-7791         TCGA-EJ-7792 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EJ-7793         TCGA-EJ-7794         TCGA-EJ-7797 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FC-7708         TCGA-FC-7961         TCGA-G9-6329 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G9-6332         TCGA-G9-6333         TCGA-G9-6336 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G9-6338         TCGA-G9-6342         TCGA-G9-6343 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G9-6348         TCGA-G9-6351         TCGA-G9-6353 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G9-6356         TCGA-G9-6361         TCGA-G9-6362 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G9-6363         TCGA-G9-6364         TCGA-G9-6365 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G9-6366         TCGA-G9-6367         TCGA-G9-6369 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G9-6370         TCGA-G9-6371         TCGA-G9-6373 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G9-6377         TCGA-G9-6378         TCGA-G9-6384 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G9-6385         TCGA-G9-6494         TCGA-G9-6496 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G9-6499         TCGA-H9-7775         TCGA-HC-7075 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-HC-7077         TCGA-HC-7078         TCGA-HC-7079 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-HC-7080         TCGA-HC-7081         TCGA-HC-7209 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-HC-7210         TCGA-HC-7211         TCGA-HC-7212 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-HC-7213         TCGA-HC-7230         TCGA-HC-7231 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-HC-7232         TCGA-HC-7233         TCGA-HC-7736 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-HC-7737         TCGA-HC-7738         TCGA-HC-7740 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-HC-7742         TCGA-HC-7744         TCGA-HC-7745 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-HC-7747         TCGA-HC-7748         TCGA-HC-7749 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-HC-7750         TCGA-HC-7752         TCGA-HC-7818 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-HC-7819         TCGA-HC-7820         TCGA-HC-7821 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-HI-7168         TCGA-HI-7169         TCGA-HI-7170 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-HI-7171 
"15Q GAIN WILD-TYPE" 

Clustering(28) Variable = 16P GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                  0   1
  16P GAIN MUTATED    20   0
  16P GAIN WILD-TYPE 335   6
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                20                341 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 0                  6 
$`16P GAIN MUTATED`
TCGA-CH-5751 TCGA-CH-5761 TCGA-EJ-7328 TCGA-EJ-7783 TCGA-G9-6373 TCGA-G9-7521 
       35.01         0.92        27.68        25.87        26.66        30.97 
TCGA-HC-7213 TCGA-HC-7232 TCGA-HC-7742 TCGA-HI-7168 TCGA-J9-A52B TCGA-KK-A8IF 
        1.97         2.93         1.48        78.61        13.87        26.43 
TCGA-QU-A6IL TCGA-QU-A6IO TCGA-VP-A872 TCGA-XK-AAIV TCGA-YL-A8HM TCGA-YL-A8SP 
        3.19        47.21       106.95        31.50        36.95        71.34 
TCGA-YL-A9WH TCGA-YL-A9WX 
       14.04        49.91 

$`16P GAIN WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5753 
        1.97        24.03         1.02        13.02        31.00         1.02 
TCGA-CH-5754 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 
        2.04        44.02        12.00         1.02        23.01         1.02 
TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 
       15.06        24.03         2.04        13.02        15.98        26.99 
TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 
        9.99        32.02        33.01         2.99        29.00        27.16 
TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 
       33.11        19.56        13.32        29.79        46.52        44.88 
TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 
       26.30        45.73        28.93        30.31        27.19        23.90 
TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 
       38.93        48.13        36.69        48.53        38.53        36.23 
TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 
       60.23        46.55        47.80        52.27        64.50        51.88 
TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 
       68.35        43.07        36.66        38.76        39.75        60.23 
TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 
       41.85        47.87        29.06        27.02        49.02        61.15 
TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 
       83.57        21.80         9.70         9.50         9.37        16.77 
TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 
        7.66        17.52         5.75         6.28         0.30        23.90 
TCGA-EJ-7782 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 
       38.37        25.68        20.55        14.53        14.14        18.15 
TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 
       19.59        17.29         3.75        23.05        19.92        64.47 
TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E 
       63.98        26.99        10.32         5.33         4.24        17.49 
TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D 
        9.83         3.06         7.53        21.96        17.62        12.92 
TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-FC-7708 
       13.71        18.41         9.14         2.99         7.56        28.41 
TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 
       15.42        13.45         8.98        17.23        16.24         1.78 
TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 
       41.62        87.35        81.04        67.99        66.67        69.37 
TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 
       55.76        18.21        68.68        49.81        46.16        50.70 
TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 
       49.35        47.15        46.52        47.44        45.30        39.39 
TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 
       44.81         3.32        40.18        39.95        38.01        40.31 
TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 
       31.50        37.97        45.80        25.15        27.29        58.22 
TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 
       56.75        52.87        50.73        38.27        38.96        27.91 
TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 
       35.34        28.18        32.68        26.01        21.14         6.08 
TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 
       30.94         3.68        19.76         5.33         2.93         2.01 
TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7230 
        2.37        14.47        28.54         0.79        28.60         1.68 
TCGA-HC-7231 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 
        2.37         1.71         0.72         2.10         2.66         1.74 
TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 
        1.68         2.07        24.59        26.04         1.97         1.12 
TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 
        3.22        30.51         1.48        17.85        24.56         1.84 
TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 
       19.36        22.42         3.12        23.87         2.17         2.27 
TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 
        1.94        17.95        22.32         1.58        15.88         1.15 
TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN 
       22.36         0.76         1.78         2.01         2.20         1.61 
TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY 
        5.49         2.33         3.48         1.45         1.25         4.41 
TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K 
       88.24        82.92        43.69        20.19        12.30        21.76 
TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R 
       17.03        16.04        16.54        16.14        20.52        14.93 
TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I 
       17.19         6.02        13.32        17.36         9.17         9.17 
TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52C 
       10.19         6.77        10.39        14.37        20.28         5.85 
TCGA-J9-A52E TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY 
       10.62        93.99        56.28        44.68        61.78       115.86 
TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 
       30.02        54.54       151.36        67.59        90.51        49.25 
TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 
      113.33        67.07        58.19        27.62        34.95        22.75 
TCGA-KK-A8IB TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 
        2.73        20.65         5.19         6.87         9.93        13.15 
TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IM TCGA-QU-A6IN 
       27.02        25.08        15.88        18.84        41.00       114.64 
TCGA-QU-A6IP TCGA-TP-A8TT TCGA-TP-A8TV TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L 
       86.14        11.90         8.19         8.84        25.51        12.95 
TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R 
        6.02        15.52        15.81        30.15        32.91        15.09 
TCGA-VN-A943 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B 
        4.34        26.47        84.69        94.65        23.93        75.91 
TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K 
       55.56        60.92        66.97        21.80        48.85        21.53 
TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83G 
       17.82         5.79        37.18        27.81         3.91        38.04 
TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIW 
       48.03         9.04         2.99        25.97        31.96        31.96 
TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU 
       28.54        30.58        29.23        27.09        37.02        39.65 
TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HO TCGA-YL-A8S8 
       25.48        52.96        49.02        38.56        71.77        62.14 
TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH 
       60.56        16.83        45.50        41.46        45.14        28.77 
TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SQ 
       47.38        45.86        37.97        26.24       106.75        62.79 
TCGA-YL-A8SR TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WY 
        7.00        41.39        60.99        62.37        24.33        28.34 
TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9ND 
        1.64         4.93         1.12         7.86         6.02 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              0.92               0.30 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            106.95             151.36 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             27.17              23.87 
[1] "0.9 - 107.0 (27.2)" "0.3 - 151.4 (23.9)"
[1] "hr="     "2.7e+07"
D28V2, continuous
                    vv
clus                  T2  T3  T4
  16P GAIN MUTATED     2  17   1
  16P GAIN WILD-TYPE 148 189   4
D28V3, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  T2                2                148
  T3               17                189
  T4                1                  4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V4, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    12   5
  16P GAIN WILD-TYPE 251  39
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     12    5
  16P GAIN WILD-TYPE  251   39
   clus
vv  16P GAIN MUTATED 16P GAIN WILD-TYPE
  0               12                251
  1                5                 39
[1] 2 2
[1] FALSE
D28V5, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     1  19
  16P GAIN WILD-TYPE  12 331
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      1   19
  16P GAIN WILD-TYPE   12  331
                                        clus
vv                                       16P GAIN MUTATED 16P GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                1                 12
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  19                331
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  16P GAIN MUTATED    13   7   0   0
  16P GAIN WILD-TYPE 230  83   5  11
D28V6, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  R0               13                230
  R1                7                 83
  R2                0                  5
  RX                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"
D28V7, continuous
D28V8, continuous
D28V9, continuous
D28V10, continuous
D28V11, continuous
D28V12, continuous
D28V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16P GAIN MUTATED       0                         0     9
  16P GAIN WILD-TYPE     2                         7   137
D28V14, multiclass
                           clus
vv                          16P GAIN MUTATED 16P GAIN WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  7
  WHITE                                    9                137
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(29) Variable = 16Q GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                  0   1
  16Q GAIN MUTATED     7   0
  16Q GAIN WILD-TYPE 348   6
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 7                354 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 0                  6 
$`16Q GAIN MUTATED`
TCGA-CH-5761 TCGA-EJ-7328 TCGA-G9-6373 TCGA-HC-7232 TCGA-QU-A6IL TCGA-YL-A8HM 
        0.92        27.68        26.66         2.93         3.19        36.95 
TCGA-YL-A9WH 
       14.04 

$`16Q GAIN WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 
        1.02         2.04        44.02        12.00         1.02        23.01 
TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 
        1.02        15.06        24.03         2.04        13.02        15.98 
TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 
       26.99         9.99        32.02        33.01         2.99        29.00 
TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
       27.16        33.11        19.56        13.32        29.79        46.52 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       44.88        26.30        45.73        28.93        30.31        27.19 
TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       23.90        38.93        48.13        36.69        48.53        38.53 
TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 
       36.23        60.23        46.55        47.80        52.27        64.50 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 
       51.88        68.35        43.07        36.66        38.76        39.75 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 
       60.23        41.85        47.87        29.06        27.02        49.02 
TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 
       61.15        83.57        21.80         9.70         9.50         9.37 
TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7330 TCGA-EJ-7331 
       16.77         7.66        17.52         5.75         6.28         0.30 
TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 
       23.90        38.37        25.87        25.68        20.55        14.53 
TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 
       14.14        18.15        19.59        17.29         3.75        23.05 
TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8474 TCGA-EJ-A46B 
       19.92        64.47        63.98        26.99        10.32         5.33 
TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I 
        4.24        17.49         9.83         3.06         7.53        21.96 
TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J 
       17.62        12.92        13.71        18.41         9.14         2.99 
TCGA-EJ-A65M TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V 
        7.56        28.41        15.42        13.45         8.98        17.23 
TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 
       16.24         1.78        41.62        87.35        81.04        67.99 
TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 
       66.67        69.37        55.76        18.21        68.68        49.81 
TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 
       46.16        50.70        49.35        47.15        46.52        47.44 
TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 
       45.30        39.39        44.81         3.32        40.18        39.95 
TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 
       38.01        40.31        31.50        37.97        45.80        25.15 
TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 
       27.29        58.22        56.75        52.87        50.73        38.27 
TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 
       38.96        27.91        30.97        35.34        28.18        32.68 
TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 
       26.01        21.14         6.08        30.94         3.68        19.76 
TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 
        5.33         2.93         2.01         2.37        14.47        28.54 
TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7233 
        0.79        28.60         1.97         1.68         2.37         1.71 
TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 
        0.72         2.10         2.66         1.74         1.48         1.68 
TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 
        2.07        24.59        26.04         1.97         1.12         3.22 
TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 
       30.51         1.48        17.85        24.56         1.84        19.36 
TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 
       22.42         3.12        23.87         2.17         2.27         1.94 
TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F 
       17.95        22.32         1.58        15.88         1.15        22.36 
TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO 
        0.76         1.78         2.01         2.20         1.61         5.49 
TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HI-7168 
        2.33         3.48         1.45         1.25         4.41        78.61 
TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K 
       88.24        82.92        43.69        20.19        12.30        21.76 
TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R 
       17.03        16.04        16.54        16.14        20.52        14.93 
TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I 
       17.19         6.02        13.32        17.36         9.17         9.17 
TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B 
       10.19         6.77        10.39        14.37        20.28        13.87 
TCGA-J9-A52C TCGA-J9-A52E TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z 
        5.85        10.62        93.99        56.28        44.68        61.78 
TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 
      115.86        30.02        54.54       151.36        67.59        90.51 
TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AZ TCGA-KK-A7B1 
       49.25       113.33        67.07        58.19        27.62        34.95 
TCGA-KK-A7B2 TCGA-KK-A8IB TCGA-KK-A8IF TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z 
       22.75         2.73        26.43        20.65         5.19         6.87 
TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 
        9.93        13.15        27.02        25.08        15.88        18.84 
TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-TP-A8TT TCGA-TP-A8TV 
       41.00       114.64        47.21        86.14        11.90         8.19 
TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O 
        8.84        25.51        12.95         6.02        15.52        15.81 
TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 
       30.15        32.91        15.09         4.34       106.95        26.47 
TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D 
       84.69        94.65        23.93        75.91        55.56        60.92 
TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI 
       66.97        21.80        48.85        21.53        17.82         5.79 
TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK 
       37.18        27.81         3.91        38.04        48.03         9.04 
TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 
        2.99        25.97        31.96        31.50        31.96        28.54 
TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-Y6-A8TL 
       30.58        29.23        27.09        37.02        39.65        25.48 
TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 
       52.96        49.02        38.56        71.77        62.14        60.56 
TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI 
       16.83        45.50        41.46        45.14        28.77        47.38 
TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ 
       45.86        37.97        26.24       106.75        71.34        62.79 
TCGA-YL-A8SR TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX 
        7.00        41.39        60.99        62.37        24.33        49.91 
TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9ND 
       28.34         1.64         4.93         1.12         7.86         6.02 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              0.92               0.30 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             36.95             151.36 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             14.04              23.98 
[1] "0.9 - 37.0 (14.0)"  "0.3 - 151.4 (24.0)"
[1] "hr="     "9100000"
D29V2, continuous
                    vv
clus                  T2  T3  T4
  16Q GAIN MUTATED     1   6   0
  16Q GAIN WILD-TYPE 149 200   5
D29V3, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T2                1                149
  T3                6                200
  T4                0                  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"
D29V4, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     4   1
  16Q GAIN WILD-TYPE 259  43
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      4    1
  16Q GAIN WILD-TYPE  259   43
   clus
vv  16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  0                4                259
  1                1                 43
[1] 2 2
[1] FALSE
D29V5, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     0   7
  16Q GAIN WILD-TYPE  13 343
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      0    7
  16Q GAIN WILD-TYPE   13  343
                                        clus
vv                                       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                0                 13
  PROSTATE ADENOCARCINOMA ACINAR TYPE                   7                343
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  16Q GAIN MUTATED     6   1   0   0
  16Q GAIN WILD-TYPE 237  89   5  11
D29V6, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  R0                6                237
  R1                1                 89
  R2                0                  5
  RX                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"
D29V7, continuous
D29V8, continuous
D29V9, continuous
D29V10, continuous
D29V11, continuous
D29V12, continuous
D29V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16Q GAIN MUTATED       0                         0     4
  16Q GAIN WILD-TYPE     2                         7   142
D29V14, multiclass
                           clus
vv                          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  7
  WHITE                                    4                142
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(30) Variable = 17P GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                  0   1
  17P GAIN MUTATED     5   0
  17P GAIN WILD-TYPE 350   6
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 5                356 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 0                  6 
$`17P GAIN MUTATED`
TCGA-EJ-5527 TCGA-HC-8216 TCGA-TP-A8TT TCGA-XK-AAIV TCGA-YL-A9WY 
       39.75        22.42        11.90        31.50        28.34 

$`17P GAIN WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 
        1.02         2.04         0.92        44.02        12.00         1.02 
TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 
       23.01         1.02        15.06        24.03         2.04        13.02 
TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 
       15.98        26.99         9.99        32.02        33.01         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        27.16        33.11        19.56        13.32        29.79 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        26.30        45.73        28.93        30.31 
TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 
       27.19        23.90        38.93        48.13        36.69        48.53 
TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 
       38.53        36.23        60.23        46.55        47.80        52.27 
TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 
       64.50        51.88        68.35        43.07        36.66        38.76 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 
       60.23        41.85        47.87        29.06        27.02        49.02 
TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 
       61.15        83.57        21.80         9.70         9.50         9.37 
TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 
       16.77         7.66        17.52         5.75        27.68         6.28 
TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 
        0.30        23.90        38.37        25.87        25.68        20.55 
TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 
       14.53        14.14        18.15        19.59        17.29         3.75 
TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8474 
       23.05        19.92        64.47        63.98        26.99        10.32 
TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H 
        5.33         4.24        17.49         9.83         3.06         7.53 
TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G 
       21.96        17.62        12.92        13.71        18.41         9.14 
TCGA-EJ-A65J TCGA-EJ-A65M TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB 
        2.99         7.56        28.41        15.42        13.45         8.98 
TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 
       17.23        16.24         1.78        41.62        87.35        81.04 
TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 
       67.99        66.67        69.37        55.76        18.21        68.68 
TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 
       49.81        46.16        50.70        49.35        47.15        46.52 
TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 
       47.44        45.30        39.39        44.81         3.32        40.18 
TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 
       39.95        38.01        40.31        26.66        31.50        37.97 
TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 
       45.80        25.15        27.29        58.22        56.75        52.87 
TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 
       50.73        38.27        38.96        27.91        30.97        35.34 
TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX 
       28.18        32.68        26.01        21.14         6.08        30.94 
TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 
        3.68        19.76         5.33         2.93         2.01         2.37 
TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 
       14.47        28.54         0.79        28.60         1.97         1.68 
TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 
        2.37         2.93         1.71         0.72         2.10         2.66 
TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 
        1.74         1.48         1.68         2.07        24.59        26.04 
TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 
        1.97         1.12         3.22        30.51         1.48        17.85 
TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 
       24.56         1.84        19.36         3.12        23.87         2.17 
TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 
        2.27         1.94        17.95        22.32         1.58        15.88 
TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL 
        1.15        22.36         0.76         1.78         2.01         2.20 
TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX 
        1.61         5.49         2.33         3.48         1.45         1.25 
TCGA-HC-A6HY TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 
        4.41        78.61        88.24        82.92        43.69        20.19 
TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O 
       12.30        21.76        17.03        16.04        16.54        16.14 
TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 
       20.52        14.93        17.19         6.02        13.32        17.36 
TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M 
        9.17         9.17        10.19         6.77        10.39        14.37 
TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-KK-A59V TCGA-KK-A59X 
       20.28        13.87         5.85        10.62        93.99        56.28 
TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 
       44.68        61.78       115.86        30.02        54.54       151.36 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 
       67.59        90.51        49.25       113.33        67.07        58.19 
TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IB TCGA-KK-A8IF TCGA-KK-A8IL 
       27.62        34.95        22.75         2.73        26.43        20.65 
TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 
        5.19         6.87         9.93        13.15        27.02        25.08 
TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO 
       15.88        18.84         3.19        41.00       114.64        47.21 
TCGA-QU-A6IP TCGA-TP-A8TV TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M 
       86.14         8.19         8.84        25.51        12.95         6.02 
TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 
       15.52        15.81        30.15        32.91        15.09         4.34 
TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B 
      106.95        26.47        84.69        94.65        23.93        75.91 
TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K 
       55.56        60.92        66.97        21.80        48.85        21.53 
TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83G 
       17.82         5.79        37.18        27.81         3.91        38.04 
TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIW 
       48.03         9.04         2.99        25.97        31.96        31.96 
TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU 
       28.54        30.58        29.23        27.09        37.02        39.65 
TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO 
       25.48        52.96        49.02        38.56        36.95        71.77 
TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF 
       62.14        60.56        16.83        45.50        41.46        45.14 
TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO 
       28.77        47.38        45.86        37.97        26.24       106.75 
TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ 
       71.34        62.79         7.00        14.04        41.39        60.99 
TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY 
       62.37        24.33        49.91         1.64         4.93         1.12 
TCGA-ZG-A8QZ TCGA-ZG-A9ND 
        7.86         6.02 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              11.9                0.3 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             39.75             151.36 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
            28.340             23.915 
[1] "11.9 - 39.8 (28.3)" "0.3 - 151.4 (23.9)"
[1] "hr="     "9100000"
D30V2, continuous
                    vv
clus                  T2  T3  T4
  17P GAIN MUTATED     0   5   0
  17P GAIN WILD-TYPE 150 201   5
D30V3, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  T2                0                150
  T3                5                201
  T4                0                  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"
D30V4, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     3   2
  17P GAIN WILD-TYPE 260  42
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      3    2
  17P GAIN WILD-TYPE  260   42
   clus
vv  17P GAIN MUTATED 17P GAIN WILD-TYPE
  0                3                260
  1                2                 42
[1] 2 2
[1] FALSE
D30V5, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     0   5
  17P GAIN WILD-TYPE  13 345
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      0    5
  17P GAIN WILD-TYPE   13  345
                                        clus
vv                                       17P GAIN MUTATED 17P GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                0                 13
  PROSTATE ADENOCARCINOMA ACINAR TYPE                   5                345
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  17P GAIN MUTATED     3   2   0   0
  17P GAIN WILD-TYPE 240  88   5  11
D30V6, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  R0                3                240
  R1                2                 88
  R2                0                  5
  RX                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"
D30V7, continuous
D30V8, continuous
D30V9, continuous
D30V10, continuous
D30V11, continuous
D30V12, continuous
D30V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17P GAIN MUTATED       0                         0     1
  17P GAIN WILD-TYPE     2                         7   145
D30V14, multiclass
[1] "Remove cluster labels:" "17P GAIN MUTATED"      
clus
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 1                154 
        TCGA-CH-5737         TCGA-CH-5738         TCGA-CH-5739 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CH-5740         TCGA-CH-5741         TCGA-CH-5743 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CH-5744         TCGA-CH-5746         TCGA-CH-5748 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CH-5750         TCGA-CH-5751         TCGA-CH-5752 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CH-5753         TCGA-CH-5754         TCGA-CH-5761 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CH-5762         TCGA-CH-5763         TCGA-CH-5764 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CH-5765         TCGA-CH-5766         TCGA-CH-5767 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CH-5768         TCGA-CH-5769         TCGA-CH-5771 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CH-5772         TCGA-CH-5788         TCGA-CH-5789 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CH-5790         TCGA-CH-5791         TCGA-CH-5792 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CH-5794         TCGA-EJ-5494         TCGA-EJ-5495 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EJ-5496         TCGA-EJ-5497         TCGA-EJ-5498 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EJ-5499         TCGA-EJ-5501         TCGA-EJ-5503 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EJ-5504         TCGA-EJ-5505         TCGA-EJ-5506 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EJ-5507         TCGA-EJ-5508         TCGA-EJ-5509 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EJ-5510         TCGA-EJ-5511         TCGA-EJ-5512 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EJ-5514         TCGA-EJ-5515         TCGA-EJ-5516 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EJ-5517         TCGA-EJ-5518         TCGA-EJ-5519 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EJ-5521         TCGA-EJ-5522         TCGA-EJ-5524 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EJ-5525         TCGA-EJ-5526         TCGA-EJ-5530 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EJ-5531         TCGA-EJ-5532         TCGA-EJ-5542 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EJ-7115         TCGA-EJ-7123         TCGA-EJ-7125 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EJ-7314         TCGA-EJ-7315         TCGA-EJ-7317 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EJ-7321         TCGA-EJ-7327         TCGA-EJ-7328 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EJ-7330         TCGA-EJ-7331         TCGA-EJ-7781 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EJ-7782         TCGA-EJ-7783         TCGA-EJ-7784 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EJ-7785         TCGA-EJ-7786         TCGA-EJ-7788 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EJ-7789         TCGA-EJ-7791         TCGA-EJ-7792 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EJ-7793         TCGA-EJ-7794         TCGA-EJ-7797 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FC-7708         TCGA-FC-7961         TCGA-G9-6329 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G9-6332         TCGA-G9-6333         TCGA-G9-6336 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G9-6338         TCGA-G9-6342         TCGA-G9-6343 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G9-6348         TCGA-G9-6351         TCGA-G9-6353 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G9-6356         TCGA-G9-6361         TCGA-G9-6362 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G9-6363         TCGA-G9-6364         TCGA-G9-6365 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G9-6366         TCGA-G9-6367         TCGA-G9-6369 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G9-6370         TCGA-G9-6371         TCGA-G9-6373 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G9-6377         TCGA-G9-6378         TCGA-G9-6384 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G9-6385         TCGA-G9-6494         TCGA-G9-6496 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G9-6499         TCGA-H9-7775         TCGA-HC-7075 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-HC-7077         TCGA-HC-7078         TCGA-HC-7079 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-HC-7080         TCGA-HC-7081         TCGA-HC-7209 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-HC-7210         TCGA-HC-7211         TCGA-HC-7212 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-HC-7213         TCGA-HC-7230         TCGA-HC-7231 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-HC-7232         TCGA-HC-7233         TCGA-HC-7736 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-HC-7737         TCGA-HC-7738         TCGA-HC-7740 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-HC-7742         TCGA-HC-7744         TCGA-HC-7745 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-HC-7747         TCGA-HC-7748         TCGA-HC-7749 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-HC-7750         TCGA-HC-7752         TCGA-HC-7818 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-HC-7819         TCGA-HC-7820         TCGA-HC-7821 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-HI-7168         TCGA-HI-7169         TCGA-HI-7170 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-HI-7171 
"17P GAIN WILD-TYPE" 

Clustering(31) Variable = 17Q GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                  0   1
  17Q GAIN MUTATED     6   0
  17Q GAIN WILD-TYPE 349   6
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 6                355 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 0                  6 
$`17Q GAIN MUTATED`
TCGA-EJ-5527 TCGA-G9-7521 TCGA-HC-8216 TCGA-TP-A8TT TCGA-XK-AAIV TCGA-YL-A9WY 
       39.75        30.97        22.42        11.90        31.50        28.34 

$`17Q GAIN WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 
        1.02         2.04         0.92        44.02        12.00         1.02 
TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 
       23.01         1.02        15.06        24.03         2.04        13.02 
TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 
       15.98        26.99         9.99        32.02        33.01         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        27.16        33.11        19.56        13.32        29.79 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        26.30        45.73        28.93        30.31 
TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 
       27.19        23.90        38.93        48.13        36.69        48.53 
TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 
       38.53        36.23        60.23        46.55        47.80        52.27 
TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 
       64.50        51.88        68.35        43.07        36.66        38.76 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 
       60.23        41.85        47.87        29.06        27.02        49.02 
TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 
       61.15        83.57        21.80         9.70         9.50         9.37 
TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 
       16.77         7.66        17.52         5.75        27.68         6.28 
TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 
        0.30        23.90        38.37        25.87        25.68        20.55 
TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 
       14.53        14.14        18.15        19.59        17.29         3.75 
TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8474 
       23.05        19.92        64.47        63.98        26.99        10.32 
TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H 
        5.33         4.24        17.49         9.83         3.06         7.53 
TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G 
       21.96        17.62        12.92        13.71        18.41         9.14 
TCGA-EJ-A65J TCGA-EJ-A65M TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB 
        2.99         7.56        28.41        15.42        13.45         8.98 
TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 
       17.23        16.24         1.78        41.62        87.35        81.04 
TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 
       67.99        66.67        69.37        55.76        18.21        68.68 
TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 
       49.81        46.16        50.70        49.35        47.15        46.52 
TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 
       47.44        45.30        39.39        44.81         3.32        40.18 
TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 
       39.95        38.01        40.31        26.66        31.50        37.97 
TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 
       45.80        25.15        27.29        58.22        56.75        52.87 
TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7522 TCGA-G9-7523 
       50.73        38.27        38.96        27.91        35.34        28.18 
TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY 
       32.68        26.01        21.14         6.08        30.94         3.68 
TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 
       19.76         5.33         2.93         2.01         2.37        14.47 
TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 
       28.54         0.79        28.60         1.97         1.68         2.37 
TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 
        2.93         1.71         0.72         2.10         2.66         1.74 
TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 
        1.48         1.68         2.07        24.59        26.04         1.97 
TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 
        1.12         3.22        30.51         1.48        17.85        24.56 
TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 
        1.84        19.36         3.12        23.87         2.17         2.27 
TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 
        1.94        17.95        22.32         1.58        15.88         1.15 
TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN 
       22.36         0.76         1.78         2.01         2.20         1.61 
TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY 
        5.49         2.33         3.48         1.45         1.25         4.41 
TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 
       78.61        88.24        82.92        43.69        20.19        12.30 
TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q 
       21.76        17.03        16.04        16.54        16.14        20.52 
TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 
       14.93        17.19         6.02        13.32        17.36         9.17 
TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N 
        9.17        10.19         6.77        10.39        14.37        20.28 
TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y 
       13.87         5.85        10.62        93.99        56.28        44.68 
TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 
       61.78       115.86        30.02        54.54       151.36        67.59 
TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AZ 
       90.51        49.25       113.33        67.07        58.19        27.62 
TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IB TCGA-KK-A8IF TCGA-KK-A8IL TCGA-M7-A71Y 
       34.95        22.75         2.73        26.43        20.65         5.19 
TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 
        6.87         9.93        13.15        27.02        25.08        15.88 
TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP 
       18.84         3.19        41.00       114.64        47.21        86.14 
TCGA-TP-A8TV TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N 
        8.19         8.84        25.51        12.95         6.02        15.52 
TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 
       15.81        30.15        32.91        15.09         4.34       106.95 
TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C 
       26.47        84.69        94.65        23.93        75.91        55.56 
TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N 
       60.92        66.97        21.80        48.85        21.53        17.82 
TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DI 
        5.79        37.18        27.81         3.91        38.04        48.03 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIW TCGA-XK-AAJ3 
        9.04         2.99        25.97        31.96        31.96        28.54 
TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-Y6-A8TL 
       30.58        29.23        27.09        37.02        39.65        25.48 
TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 
       52.96        49.02        38.56        36.95        71.77        62.14 
TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH 
       60.56        16.83        45.50        41.46        45.14        28.77 
TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP 
       47.38        45.86        37.97        26.24       106.75        71.34 
TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK 
       62.79         7.00        14.04        41.39        60.99        62.37 
TCGA-YL-A9WL TCGA-YL-A9WX TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       24.33        49.91         1.64         4.93         1.12         7.86 
TCGA-ZG-A9ND 
        6.02 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              11.9                0.3 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             39.75             151.36 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
            29.655             23.900 
[1] "11.9 - 39.8 (29.7)" "0.3 - 151.4 (23.9)"
[1] "hr="     "9200000"
D31V2, continuous
                    vv
clus                  T2  T3  T4
  17Q GAIN MUTATED     0   6   0
  17Q GAIN WILD-TYPE 150 200   5
D31V3, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T2                0                150
  T3                6                200
  T4                0                  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"
D31V4, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     3   3
  17Q GAIN WILD-TYPE 260  41
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      3    3
  17Q GAIN WILD-TYPE  260   41
   clus
vv  17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  0                3                260
  1                3                 41
[1] 2 2
[1] FALSE
D31V5, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     0   6
  17Q GAIN WILD-TYPE  13 344
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      0    6
  17Q GAIN WILD-TYPE   13  344
                                        clus
vv                                       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                0                 13
  PROSTATE ADENOCARCINOMA ACINAR TYPE                   6                344
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  17Q GAIN MUTATED     4   2   0   0
  17Q GAIN WILD-TYPE 239  88   5  11
D31V6, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  R0                4                239
  R1                2                 88
  R2                0                  5
  RX                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"
D31V7, continuous
D31V8, continuous
D31V9, continuous
D31V10, continuous
D31V11, continuous
D31V12, continuous
D31V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17Q GAIN MUTATED       0                         0     1
  17Q GAIN WILD-TYPE     2                         7   145
D31V14, multiclass
[1] "Remove cluster labels:" "17Q GAIN MUTATED"      
clus
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 1                154 
        TCGA-CH-5737         TCGA-CH-5738         TCGA-CH-5739 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CH-5740         TCGA-CH-5741         TCGA-CH-5743 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CH-5744         TCGA-CH-5746         TCGA-CH-5748 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CH-5750         TCGA-CH-5751         TCGA-CH-5752 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CH-5753         TCGA-CH-5754         TCGA-CH-5761 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CH-5762         TCGA-CH-5763         TCGA-CH-5764 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CH-5765         TCGA-CH-5766         TCGA-CH-5767 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CH-5768         TCGA-CH-5769         TCGA-CH-5771 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CH-5772         TCGA-CH-5788         TCGA-CH-5789 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CH-5790         TCGA-CH-5791         TCGA-CH-5792 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CH-5794         TCGA-EJ-5494         TCGA-EJ-5495 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EJ-5496         TCGA-EJ-5497         TCGA-EJ-5498 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EJ-5499         TCGA-EJ-5501         TCGA-EJ-5503 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EJ-5504         TCGA-EJ-5505         TCGA-EJ-5506 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EJ-5507         TCGA-EJ-5508         TCGA-EJ-5509 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EJ-5510         TCGA-EJ-5511         TCGA-EJ-5512 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EJ-5514         TCGA-EJ-5515         TCGA-EJ-5516 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EJ-5517         TCGA-EJ-5518         TCGA-EJ-5519 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EJ-5521         TCGA-EJ-5522         TCGA-EJ-5524 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EJ-5525         TCGA-EJ-5526         TCGA-EJ-5530 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EJ-5531         TCGA-EJ-5532         TCGA-EJ-5542 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EJ-7115         TCGA-EJ-7123         TCGA-EJ-7125 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EJ-7314         TCGA-EJ-7315         TCGA-EJ-7317 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EJ-7321         TCGA-EJ-7327         TCGA-EJ-7328 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EJ-7330         TCGA-EJ-7331         TCGA-EJ-7781 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EJ-7782         TCGA-EJ-7783         TCGA-EJ-7784 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EJ-7785         TCGA-EJ-7786         TCGA-EJ-7788 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EJ-7789         TCGA-EJ-7791         TCGA-EJ-7792 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EJ-7793         TCGA-EJ-7794         TCGA-EJ-7797 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-FC-7708         TCGA-FC-7961         TCGA-G9-6329 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-G9-6332         TCGA-G9-6333         TCGA-G9-6336 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-G9-6338         TCGA-G9-6342         TCGA-G9-6343 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-G9-6348         TCGA-G9-6351         TCGA-G9-6353 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-G9-6356         TCGA-G9-6361         TCGA-G9-6362 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-G9-6363         TCGA-G9-6364         TCGA-G9-6365 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-G9-6366         TCGA-G9-6367         TCGA-G9-6369 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-G9-6370         TCGA-G9-6371         TCGA-G9-6373 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-G9-6377         TCGA-G9-6378         TCGA-G9-6384 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-G9-6385         TCGA-G9-6494         TCGA-G9-6496 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-G9-6499         TCGA-H9-7775         TCGA-HC-7075 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-HC-7077         TCGA-HC-7078         TCGA-HC-7079 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-HC-7080         TCGA-HC-7081         TCGA-HC-7209 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-HC-7210         TCGA-HC-7211         TCGA-HC-7212 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-HC-7213         TCGA-HC-7230         TCGA-HC-7231 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-HC-7232         TCGA-HC-7233         TCGA-HC-7736 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-HC-7737         TCGA-HC-7738         TCGA-HC-7740 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-HC-7742         TCGA-HC-7744         TCGA-HC-7745 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-HC-7747         TCGA-HC-7748         TCGA-HC-7749 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-HC-7750         TCGA-HC-7752         TCGA-HC-7818 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-HC-7819         TCGA-HC-7820         TCGA-HC-7821 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-HI-7168         TCGA-HI-7169         TCGA-HI-7170 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-HI-7171 
"17Q GAIN WILD-TYPE" 

Clustering(32) Variable = 18P GAIN MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                  0   1
  18P GAIN MUTATED    12   0
  18P GAIN WILD-TYPE 343   6
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                12                349 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 0                  6 
$`18P GAIN MUTATED`
TCGA-EJ-5495 TCGA-EJ-5527 TCGA-FC-A4JI TCGA-G9-6329 TCGA-G9-6499 TCGA-G9-7521 
       33.11        39.75        13.45        41.62        50.73        30.97 
TCGA-HC-7742 TCGA-HC-8216 TCGA-J9-A52E TCGA-VP-A875 TCGA-XK-AAJT TCGA-YL-A9WY 
        1.48        22.42        10.62        26.47        37.02        28.34 

$`18P GAIN WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 
        1.02         2.04         0.92        44.02        12.00         1.02 
TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 
       23.01         1.02        15.06        24.03         2.04        13.02 
TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 
       15.98        26.99         9.99        32.02        33.01         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
       29.00        27.16        19.56        13.32        29.79        46.52 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       44.88        26.30        45.73        28.93        30.31        27.19 
TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       23.90        38.93        48.13        36.69        48.53        38.53 
TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 
       36.23        60.23        46.55        47.80        52.27        64.50 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5530 
       51.88        68.35        43.07        36.66        38.76        60.23 
TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 
       41.85        47.87        29.06        27.02        49.02        61.15 
TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 
       83.57        21.80         9.70         9.50         9.37        16.77 
TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 
        7.66        17.52         5.75        27.68         6.28         0.30 
TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 
       23.90        38.37        25.87        25.68        20.55        14.53 
TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 
       14.14        18.15        19.59        17.29         3.75        23.05 
TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8474 TCGA-EJ-A46B 
       19.92        64.47        63.98        26.99        10.32         5.33 
TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I 
        4.24        17.49         9.83         3.06         7.53        21.96 
TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J 
       17.62        12.92        13.71        18.41         9.14         2.99 
TCGA-EJ-A65M TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD 
        7.56        28.41        15.42         8.98        17.23        16.24 
TCGA-FC-A8O0 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 
        1.78        87.35        81.04        67.99        66.67        69.37 
TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 
       55.76        18.21        68.68        49.81        46.16        50.70 
TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 
       49.35        47.15        46.52        47.44        45.30        39.39 
TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 
       44.81         3.32        40.18        39.95        38.01        40.31 
TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 
       26.66        31.50        37.97        45.80        25.15        27.29 
TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 
       58.22        56.75        52.87        38.27        38.96        27.91 
TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 
       35.34        28.18        32.68        26.01        21.14         6.08 
TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 
       30.94         3.68        19.76         5.33         2.93         2.01 
TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 
        2.37        14.47        28.54         0.79        28.60         1.97 
TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 
        1.68         2.37         2.93         1.71         0.72         2.10 
TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 
        2.66         1.74         1.68         2.07        24.59        26.04 
TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 
        1.97         1.12         3.22        30.51         1.48        17.85 
TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 
       24.56         1.84        19.36         3.12        23.87         2.17 
TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 
        2.27         1.94        17.95        22.32         1.58        15.88 
TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL 
        1.15        22.36         0.76         1.78         2.01         2.20 
TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX 
        1.61         5.49         2.33         3.48         1.45         1.25 
TCGA-HC-A6HY TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 
        4.41        78.61        88.24        82.92        43.69        20.19 
TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O 
       12.30        21.76        17.03        16.04        16.54        16.14 
TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 
       20.52        14.93        17.19         6.02        13.32        17.36 
TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M 
        9.17         9.17        10.19         6.77        10.39        14.37 
TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52C TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y 
       20.28        13.87         5.85        93.99        56.28        44.68 
TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 
       61.78       115.86        30.02        54.54       151.36        67.59 
TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AZ 
       90.51        49.25       113.33        67.07        58.19        27.62 
TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IB TCGA-KK-A8IF TCGA-KK-A8IL TCGA-M7-A71Y 
       34.95        22.75         2.73        26.43        20.65         5.19 
TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 
        6.87         9.93        13.15        27.02        25.08        15.88 
TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP 
       18.84         3.19        41.00       114.64        47.21        86.14 
TCGA-TP-A8TT TCGA-TP-A8TV TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M 
       11.90         8.19         8.84        25.51        12.95         6.02 
TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 
       15.52        15.81        30.15        32.91        15.09         4.34 
TCGA-VP-A872 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C 
      106.95        84.69        94.65        23.93        75.91        55.56 
TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N 
       60.92        66.97        21.80        48.85        21.53        17.82 
TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DI 
        5.79        37.18        27.81         3.91        38.04        48.03 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW 
        9.04         2.99        25.97        31.96        31.50        31.96 
TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJU TCGA-Y6-A8TL 
       28.54        30.58        29.23        27.09        39.65        25.48 
TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 
       52.96        49.02        38.56        36.95        71.77        62.14 
TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH 
       60.56        16.83        45.50        41.46        45.14        28.77 
TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP 
       47.38        45.86        37.97        26.24       106.75        71.34 
TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK 
       62.79         7.00        14.04        41.39        60.99        62.37 
TCGA-YL-A9WL TCGA-YL-A9WX TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       24.33        49.91         1.64         4.93         1.12         7.86 
TCGA-ZG-A9ND 
        6.02 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              1.48               0.30 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             50.73             151.36 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
            29.655             23.900 
[1] "1.5 - 50.7 (29.7)"  "0.3 - 151.4 (23.9)"
[1] "hr="     "2.6e+07"
D32V2, continuous
                    vv
clus                  T2  T3  T4
  18P GAIN MUTATED     1  11   0
  18P GAIN WILD-TYPE 149 195   5
D32V3, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  T2                1                149
  T3               11                195
  T4                0                  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"
D32V4, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     7   3
  18P GAIN WILD-TYPE 256  41
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      7    3
  18P GAIN WILD-TYPE  256   41
   clus
vv  18P GAIN MUTATED 18P GAIN WILD-TYPE
  0                7                256
  1                3                 41
[1] 2 2
[1] FALSE
D32V5, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     0  12
  18P GAIN WILD-TYPE  13 338
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      0   12
  18P GAIN WILD-TYPE   13  338
                                        clus
vv                                       18P GAIN MUTATED 18P GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                0                 13
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  12                338
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  18P GAIN MUTATED     9   3   0   0
  18P GAIN WILD-TYPE 234  87   5  11
D32V6, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  R0                9                234
  R1                3                 87
  R2                0                  5
  RX                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"
D32V7, continuous
D32V8, continuous
D32V9, continuous
D32V10, continuous
D32V11, continuous
D32V12, continuous
D32V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18P GAIN MUTATED       0                         0     5
  18P GAIN WILD-TYPE     2                         7   141
D32V14, multiclass
                           clus
vv                          18P GAIN MUTATED 18P GAIN WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  7
  WHITE                                    5                141
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(33) Variable = 18Q GAIN MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                  0   1
  18Q GAIN MUTATED     5   0
  18Q GAIN WILD-TYPE 350   6
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 5                356 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 0                  6 
$`18Q GAIN MUTATED`
TCGA-EJ-5527 TCGA-G9-6499 TCGA-HC-8216 TCGA-J9-A52E TCGA-VP-A875 
       39.75        50.73        22.42        10.62        26.47 

$`18Q GAIN WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 
        1.02         2.04         0.92        44.02        12.00         1.02 
TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 
       23.01         1.02        15.06        24.03         2.04        13.02 
TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 
       15.98        26.99         9.99        32.02        33.01         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        27.16        33.11        19.56        13.32        29.79 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        26.30        45.73        28.93        30.31 
TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 
       27.19        23.90        38.93        48.13        36.69        48.53 
TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 
       38.53        36.23        60.23        46.55        47.80        52.27 
TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 
       64.50        51.88        68.35        43.07        36.66        38.76 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 
       60.23        41.85        47.87        29.06        27.02        49.02 
TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 
       61.15        83.57        21.80         9.70         9.50         9.37 
TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 
       16.77         7.66        17.52         5.75        27.68         6.28 
TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 
        0.30        23.90        38.37        25.87        25.68        20.55 
TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 
       14.53        14.14        18.15        19.59        17.29         3.75 
TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8474 
       23.05        19.92        64.47        63.98        26.99        10.32 
TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H 
        5.33         4.24        17.49         9.83         3.06         7.53 
TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G 
       21.96        17.62        12.92        13.71        18.41         9.14 
TCGA-EJ-A65J TCGA-EJ-A65M TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB 
        2.99         7.56        28.41        15.42        13.45         8.98 
TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 
       17.23        16.24         1.78        41.62        87.35        81.04 
TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 
       67.99        66.67        69.37        55.76        18.21        68.68 
TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 
       49.81        46.16        50.70        49.35        47.15        46.52 
TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 
       47.44        45.30        39.39        44.81         3.32        40.18 
TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 
       39.95        38.01        40.31        26.66        31.50        37.97 
TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 
       45.80        25.15        27.29        58.22        56.75        52.87 
TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 
       38.27        38.96        27.91        30.97        35.34        28.18 
TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY 
       32.68        26.01        21.14         6.08        30.94         3.68 
TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 
       19.76         5.33         2.93         2.01         2.37        14.47 
TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 
       28.54         0.79        28.60         1.97         1.68         2.37 
TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 
        2.93         1.71         0.72         2.10         2.66         1.74 
TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 
        1.48         1.68         2.07        24.59        26.04         1.97 
TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 
        1.12         3.22        30.51         1.48        17.85        24.56 
TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 
        1.84        19.36         3.12        23.87         2.17         2.27 
TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 
        1.94        17.95        22.32         1.58        15.88         1.15 
TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN 
       22.36         0.76         1.78         2.01         2.20         1.61 
TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY 
        5.49         2.33         3.48         1.45         1.25         4.41 
TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 
       78.61        88.24        82.92        43.69        20.19        12.30 
TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q 
       21.76        17.03        16.04        16.54        16.14        20.52 
TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 
       14.93        17.19         6.02        13.32        17.36         9.17 
TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N 
        9.17        10.19         6.77        10.39        14.37        20.28 
TCGA-J9-A52B TCGA-J9-A52C TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z 
       13.87         5.85        93.99        56.28        44.68        61.78 
TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 
      115.86        30.02        54.54       151.36        67.59        90.51 
TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AZ TCGA-KK-A7B1 
       49.25       113.33        67.07        58.19        27.62        34.95 
TCGA-KK-A7B2 TCGA-KK-A8IB TCGA-KK-A8IF TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z 
       22.75         2.73        26.43        20.65         5.19         6.87 
TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 
        9.93        13.15        27.02        25.08        15.88        18.84 
TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-TP-A8TT 
        3.19        41.00       114.64        47.21        86.14        11.90 
TCGA-TP-A8TV TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N 
        8.19         8.84        25.51        12.95         6.02        15.52 
TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 
       15.81        30.15        32.91        15.09         4.34       106.95 
TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D 
       84.69        94.65        23.93        75.91        55.56        60.92 
TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI 
       66.97        21.80        48.85        21.53        17.82         5.79 
TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK 
       37.18        27.81         3.91        38.04        48.03         9.04 
TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 
        2.99        25.97        31.96        31.50        31.96        28.54 
TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-Y6-A8TL 
       30.58        29.23        27.09        37.02        39.65        25.48 
TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 
       52.96        49.02        38.56        36.95        71.77        62.14 
TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH 
       60.56        16.83        45.50        41.46        45.14        28.77 
TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP 
       47.38        45.86        37.97        26.24       106.75        71.34 
TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK 
       62.79         7.00        14.04        41.39        60.99        62.37 
TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY 
       24.33        49.91        28.34         1.64         4.93         1.12 
TCGA-ZG-A8QZ TCGA-ZG-A9ND 
        7.86         6.02 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             10.62               0.30 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             50.73             151.36 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
            26.470             23.915 
[1] "10.6 - 50.7 (26.5)" "0.3 - 151.4 (23.9)"
[1] "hr="     "9100000"
D33V2, continuous
                    vv
clus                  T2  T3  T4
  18Q GAIN MUTATED     0   5   0
  18Q GAIN WILD-TYPE 150 201   5
D33V3, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  T2                0                150
  T3                5                201
  T4                0                  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"
D33V4, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     5   0
  18Q GAIN WILD-TYPE 258  44
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      5    0
  18Q GAIN WILD-TYPE  258   44
   clus
vv  18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  0                5                258
  1                0                 44
[1] 2 2
[1] FALSE
D33V5, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     0   5
  18Q GAIN WILD-TYPE  13 345
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      0    5
  18Q GAIN WILD-TYPE   13  345
                                        clus
vv                                       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                0                 13
  PROSTATE ADENOCARCINOMA ACINAR TYPE                   5                345
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  18Q GAIN MUTATED     4   1   0   0
  18Q GAIN WILD-TYPE 239  89   5  11
D33V6, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  R0                4                239
  R1                1                 89
  R2                0                  5
  RX                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"
D33V7, continuous
D33V8, continuous
D33V9, continuous
D33V10, continuous
D33V11, continuous
D33V12, continuous
D33V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18Q GAIN MUTATED       0                         0     2
  18Q GAIN WILD-TYPE     2                         7   144
D33V14, multiclass
[1] "Remove cluster labels:" "18Q GAIN MUTATED"      
clus
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 2                153 
        TCGA-CH-5737         TCGA-CH-5738         TCGA-CH-5739 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CH-5740         TCGA-CH-5741         TCGA-CH-5743 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CH-5744         TCGA-CH-5746         TCGA-CH-5748 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CH-5750         TCGA-CH-5751         TCGA-CH-5752 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CH-5753         TCGA-CH-5754         TCGA-CH-5761 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CH-5762         TCGA-CH-5763         TCGA-CH-5764 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CH-5765         TCGA-CH-5766         TCGA-CH-5767 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CH-5768         TCGA-CH-5769         TCGA-CH-5771 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CH-5772         TCGA-CH-5788         TCGA-CH-5789 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CH-5790         TCGA-CH-5791         TCGA-CH-5792 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CH-5794         TCGA-EJ-5494         TCGA-EJ-5495 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EJ-5496         TCGA-EJ-5497         TCGA-EJ-5498 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EJ-5499         TCGA-EJ-5501         TCGA-EJ-5503 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EJ-5504         TCGA-EJ-5505         TCGA-EJ-5506 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EJ-5507         TCGA-EJ-5508         TCGA-EJ-5509 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EJ-5510         TCGA-EJ-5511         TCGA-EJ-5512 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EJ-5514         TCGA-EJ-5515         TCGA-EJ-5516 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EJ-5517         TCGA-EJ-5518         TCGA-EJ-5519 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EJ-5521         TCGA-EJ-5522         TCGA-EJ-5524 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EJ-5525         TCGA-EJ-5526         TCGA-EJ-5530 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EJ-5531         TCGA-EJ-5532         TCGA-EJ-5542 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EJ-7115         TCGA-EJ-7123         TCGA-EJ-7125 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EJ-7314         TCGA-EJ-7315         TCGA-EJ-7317 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EJ-7321         TCGA-EJ-7327         TCGA-EJ-7328 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EJ-7330         TCGA-EJ-7331         TCGA-EJ-7781 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EJ-7782         TCGA-EJ-7783         TCGA-EJ-7784 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EJ-7785         TCGA-EJ-7786         TCGA-EJ-7788 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EJ-7789         TCGA-EJ-7791         TCGA-EJ-7792 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EJ-7793         TCGA-EJ-7794         TCGA-EJ-7797 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FC-7708         TCGA-FC-7961         TCGA-G9-6329 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G9-6332         TCGA-G9-6333         TCGA-G9-6336 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G9-6338         TCGA-G9-6342         TCGA-G9-6343 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G9-6348         TCGA-G9-6351         TCGA-G9-6353 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G9-6356         TCGA-G9-6361         TCGA-G9-6362 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G9-6363         TCGA-G9-6364         TCGA-G9-6365 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G9-6366         TCGA-G9-6367         TCGA-G9-6369 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G9-6370         TCGA-G9-6371         TCGA-G9-6373 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G9-6377         TCGA-G9-6378         TCGA-G9-6384 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G9-6385         TCGA-G9-6494         TCGA-G9-6496 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-H9-7775         TCGA-HC-7075         TCGA-HC-7077 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-HC-7078         TCGA-HC-7079         TCGA-HC-7080 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-HC-7081         TCGA-HC-7209         TCGA-HC-7210 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-HC-7211         TCGA-HC-7212         TCGA-HC-7213 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-HC-7230         TCGA-HC-7231         TCGA-HC-7232 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-HC-7233         TCGA-HC-7736         TCGA-HC-7737 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-HC-7738         TCGA-HC-7740         TCGA-HC-7742 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-HC-7744         TCGA-HC-7745         TCGA-HC-7747 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-HC-7748         TCGA-HC-7749         TCGA-HC-7750 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-HC-7752         TCGA-HC-7818         TCGA-HC-7819 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-HC-7820         TCGA-HC-7821         TCGA-HI-7168 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-HI-7169         TCGA-HI-7170         TCGA-HI-7171 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 

Clustering(34) Variable = 19P GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                  0   1
  19P GAIN MUTATED     6   0
  19P GAIN WILD-TYPE 349   6
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 6                355 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 0                  6 
$`19P GAIN MUTATED`
TCGA-CH-5751 TCGA-HC-7213 TCGA-VP-A875 TCGA-YL-A8HO TCGA-YL-A8SB TCGA-YL-A9WL 
       35.01         1.97        26.47        71.77        45.50        24.33 

$`19P GAIN WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5753 
        1.97        24.03         1.02        13.02        31.00         1.02 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 
        2.04         0.92        44.02        12.00         1.02        23.01 
TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 
        1.02        15.06        24.03         2.04        13.02        15.98 
TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 
       26.99         9.99        32.02        33.01         2.99        29.00 
TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
       27.16        33.11        19.56        13.32        29.79        46.52 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       44.88        26.30        45.73        28.93        30.31        27.19 
TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       23.90        38.93        48.13        36.69        48.53        38.53 
TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 
       36.23        60.23        46.55        47.80        52.27        64.50 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 
       51.88        68.35        43.07        36.66        38.76        39.75 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 
       60.23        41.85        47.87        29.06        27.02        49.02 
TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 
       61.15        83.57        21.80         9.70         9.50         9.37 
TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 
       16.77         7.66        17.52         5.75        27.68         6.28 
TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 
        0.30        23.90        38.37        25.87        25.68        20.55 
TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 
       14.53        14.14        18.15        19.59        17.29         3.75 
TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8474 
       23.05        19.92        64.47        63.98        26.99        10.32 
TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H 
        5.33         4.24        17.49         9.83         3.06         7.53 
TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G 
       21.96        17.62        12.92        13.71        18.41         9.14 
TCGA-EJ-A65J TCGA-EJ-A65M TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB 
        2.99         7.56        28.41        15.42        13.45         8.98 
TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 
       17.23        16.24         1.78        41.62        87.35        81.04 
TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 
       67.99        66.67        69.37        55.76        18.21        68.68 
TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 
       49.81        46.16        50.70        49.35        47.15        46.52 
TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 
       47.44        45.30        39.39        44.81         3.32        40.18 
TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 
       39.95        38.01        40.31        26.66        31.50        37.97 
TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 
       45.80        25.15        27.29        58.22        56.75        52.87 
TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 
       50.73        38.27        38.96        27.91        30.97        35.34 
TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX 
       28.18        32.68        26.01        21.14         6.08        30.94 
TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 
        3.68        19.76         5.33         2.93         2.01         2.37 
TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7230 TCGA-HC-7231 
       14.47        28.54         0.79        28.60         1.68         2.37 
TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 
        2.93         1.71         0.72         2.10         2.66         1.74 
TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 
        1.48         1.68         2.07        24.59        26.04         1.97 
TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 
        1.12         3.22        30.51         1.48        17.85        24.56 
TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 
        1.84        19.36        22.42         3.12        23.87         2.17 
TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 
        2.27         1.94        17.95        22.32         1.58        15.88 
TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL 
        1.15        22.36         0.76         1.78         2.01         2.20 
TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX 
        1.61         5.49         2.33         3.48         1.45         1.25 
TCGA-HC-A6HY TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 
        4.41        78.61        88.24        82.92        43.69        20.19 
TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O 
       12.30        21.76        17.03        16.04        16.54        16.14 
TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 
       20.52        14.93        17.19         6.02        13.32        17.36 
TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M 
        9.17         9.17        10.19         6.77        10.39        14.37 
TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-KK-A59V TCGA-KK-A59X 
       20.28        13.87         5.85        10.62        93.99        56.28 
TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 
       44.68        61.78       115.86        30.02        54.54       151.36 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 
       67.59        90.51        49.25       113.33        67.07        58.19 
TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IB TCGA-KK-A8IF TCGA-KK-A8IL 
       27.62        34.95        22.75         2.73        26.43        20.65 
TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 
        5.19         6.87         9.93        13.15        27.02        25.08 
TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO 
       15.88        18.84         3.19        41.00       114.64        47.21 
TCGA-QU-A6IP TCGA-TP-A8TT TCGA-TP-A8TV TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L 
       86.14        11.90         8.19         8.84        25.51        12.95 
TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R 
        6.02        15.52        15.81        30.15        32.91        15.09 
TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B 
        4.34       106.95        84.69        94.65        23.93        75.91 
TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K 
       55.56        60.92        66.97        21.80        48.85        21.53 
TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83G 
       17.82         5.79        37.18        27.81         3.91        38.04 
TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV 
       48.03         9.04         2.99        25.97        31.96        31.50 
TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT 
       31.96        28.54        30.58        29.23        27.09        37.02 
TCGA-XK-AAJU TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM 
       39.65        25.48        52.96        49.02        38.56        36.95 
TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH 
       62.14        60.56        16.83        41.46        45.14        28.77 
TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP 
       47.38        45.86        37.97        26.24       106.75        71.34 
TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK 
       62.79         7.00        14.04        41.39        60.99        62.37 
TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       49.91        28.34         1.64         4.93         1.12         7.86 
TCGA-ZG-A9ND 
        6.02 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              1.97               0.30 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             71.77             151.36 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             30.74              23.90 
[1] "2.0 - 71.8 (30.7)"  "0.3 - 151.4 (23.9)"
[1] "hr="     "9200000"
D34V2, continuous
                    vv
clus                  T2  T3  T4
  19P GAIN MUTATED     0   5   1
  19P GAIN WILD-TYPE 150 201   4
D34V3, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  T2                0                150
  T3                5                201
  T4                1                  4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V4, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     5   1
  19P GAIN WILD-TYPE 258  43
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      5    1
  19P GAIN WILD-TYPE  258   43
   clus
vv  19P GAIN MUTATED 19P GAIN WILD-TYPE
  0                5                258
  1                1                 43
[1] 2 2
[1] FALSE
D34V5, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     0   6
  19P GAIN WILD-TYPE  13 344
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      0    6
  19P GAIN WILD-TYPE   13  344
                                        clus
vv                                       19P GAIN MUTATED 19P GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                0                 13
  PROSTATE ADENOCARCINOMA ACINAR TYPE                   6                344
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  19P GAIN MUTATED     3   3   0   0
  19P GAIN WILD-TYPE 240  87   5  11
D34V6, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  R0                3                240
  R1                3                 87
  R2                0                  5
  RX                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"
D34V7, continuous
D34V8, continuous
D34V9, continuous
D34V10, continuous
D34V11, continuous
D34V12, continuous
D34V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19P GAIN MUTATED       0                         0     2
  19P GAIN WILD-TYPE     2                         7   144
D34V14, multiclass
[1] "Remove cluster labels:" "19P GAIN MUTATED"      
clus
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 2                153 
        TCGA-CH-5737         TCGA-CH-5738         TCGA-CH-5739 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CH-5740         TCGA-CH-5741         TCGA-CH-5743 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CH-5744         TCGA-CH-5746         TCGA-CH-5748 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CH-5750         TCGA-CH-5752         TCGA-CH-5753 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CH-5754         TCGA-CH-5761         TCGA-CH-5762 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CH-5763         TCGA-CH-5764         TCGA-CH-5765 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CH-5766         TCGA-CH-5767         TCGA-CH-5768 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CH-5769         TCGA-CH-5771         TCGA-CH-5772 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CH-5788         TCGA-CH-5789         TCGA-CH-5790 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CH-5791         TCGA-CH-5792         TCGA-CH-5794 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EJ-5494         TCGA-EJ-5495         TCGA-EJ-5496 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EJ-5497         TCGA-EJ-5498         TCGA-EJ-5499 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EJ-5501         TCGA-EJ-5503         TCGA-EJ-5504 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EJ-5505         TCGA-EJ-5506         TCGA-EJ-5507 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EJ-5508         TCGA-EJ-5509         TCGA-EJ-5510 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EJ-5511         TCGA-EJ-5512         TCGA-EJ-5514 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EJ-5515         TCGA-EJ-5516         TCGA-EJ-5517 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EJ-5518         TCGA-EJ-5519         TCGA-EJ-5521 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EJ-5522         TCGA-EJ-5524         TCGA-EJ-5525 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EJ-5526         TCGA-EJ-5527         TCGA-EJ-5530 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EJ-5531         TCGA-EJ-5532         TCGA-EJ-5542 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EJ-7115         TCGA-EJ-7123         TCGA-EJ-7125 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EJ-7314         TCGA-EJ-7315         TCGA-EJ-7317 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EJ-7321         TCGA-EJ-7327         TCGA-EJ-7328 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EJ-7330         TCGA-EJ-7331         TCGA-EJ-7781 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EJ-7782         TCGA-EJ-7783         TCGA-EJ-7784 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EJ-7785         TCGA-EJ-7786         TCGA-EJ-7788 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EJ-7789         TCGA-EJ-7791         TCGA-EJ-7792 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EJ-7793         TCGA-EJ-7794         TCGA-EJ-7797 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FC-7708         TCGA-FC-7961         TCGA-G9-6329 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G9-6332         TCGA-G9-6333         TCGA-G9-6336 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G9-6338         TCGA-G9-6342         TCGA-G9-6343 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G9-6348         TCGA-G9-6351         TCGA-G9-6353 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G9-6356         TCGA-G9-6361         TCGA-G9-6362 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G9-6363         TCGA-G9-6364         TCGA-G9-6365 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G9-6366         TCGA-G9-6367         TCGA-G9-6369 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G9-6370         TCGA-G9-6371         TCGA-G9-6373 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G9-6377         TCGA-G9-6378         TCGA-G9-6384 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G9-6385         TCGA-G9-6494         TCGA-G9-6496 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G9-6499         TCGA-H9-7775         TCGA-HC-7075 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-HC-7077         TCGA-HC-7078         TCGA-HC-7079 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-HC-7080         TCGA-HC-7081         TCGA-HC-7209 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-HC-7210         TCGA-HC-7211         TCGA-HC-7212 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-HC-7230         TCGA-HC-7231         TCGA-HC-7232 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-HC-7233         TCGA-HC-7736         TCGA-HC-7737 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-HC-7738         TCGA-HC-7740         TCGA-HC-7742 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-HC-7744         TCGA-HC-7745         TCGA-HC-7747 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-HC-7748         TCGA-HC-7749         TCGA-HC-7750 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-HC-7752         TCGA-HC-7818         TCGA-HC-7819 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-HC-7820         TCGA-HC-7821         TCGA-HI-7168 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-HI-7169         TCGA-HI-7170         TCGA-HI-7171 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 

Clustering(35) Variable = 19Q GAIN MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                  0   1
  19Q GAIN MUTATED     6   0
  19Q GAIN WILD-TYPE 349   6
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 6                355 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 0                  6 
$`19Q GAIN MUTATED`
TCGA-CH-5751 TCGA-HC-7213 TCGA-HI-7168 TCGA-VP-A875 TCGA-YL-A8HO TCGA-YL-A8SB 
       35.01         1.97        78.61        26.47        71.77        45.50 

$`19Q GAIN WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5753 
        1.97        24.03         1.02        13.02        31.00         1.02 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 
        2.04         0.92        44.02        12.00         1.02        23.01 
TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 
        1.02        15.06        24.03         2.04        13.02        15.98 
TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 
       26.99         9.99        32.02        33.01         2.99        29.00 
TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
       27.16        33.11        19.56        13.32        29.79        46.52 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       44.88        26.30        45.73        28.93        30.31        27.19 
TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       23.90        38.93        48.13        36.69        48.53        38.53 
TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 
       36.23        60.23        46.55        47.80        52.27        64.50 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 
       51.88        68.35        43.07        36.66        38.76        39.75 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 
       60.23        41.85        47.87        29.06        27.02        49.02 
TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 
       61.15        83.57        21.80         9.70         9.50         9.37 
TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 
       16.77         7.66        17.52         5.75        27.68         6.28 
TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 
        0.30        23.90        38.37        25.87        25.68        20.55 
TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 
       14.53        14.14        18.15        19.59        17.29         3.75 
TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8474 
       23.05        19.92        64.47        63.98        26.99        10.32 
TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H 
        5.33         4.24        17.49         9.83         3.06         7.53 
TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G 
       21.96        17.62        12.92        13.71        18.41         9.14 
TCGA-EJ-A65J TCGA-EJ-A65M TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB 
        2.99         7.56        28.41        15.42        13.45         8.98 
TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 
       17.23        16.24         1.78        41.62        87.35        81.04 
TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 
       67.99        66.67        69.37        55.76        18.21        68.68 
TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 
       49.81        46.16        50.70        49.35        47.15        46.52 
TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 
       47.44        45.30        39.39        44.81         3.32        40.18 
TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 
       39.95        38.01        40.31        26.66        31.50        37.97 
TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 
       45.80        25.15        27.29        58.22        56.75        52.87 
TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 
       50.73        38.27        38.96        27.91        30.97        35.34 
TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX 
       28.18        32.68        26.01        21.14         6.08        30.94 
TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 
        3.68        19.76         5.33         2.93         2.01         2.37 
TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7230 TCGA-HC-7231 
       14.47        28.54         0.79        28.60         1.68         2.37 
TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 
        2.93         1.71         0.72         2.10         2.66         1.74 
TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 
        1.48         1.68         2.07        24.59        26.04         1.97 
TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 
        1.12         3.22        30.51         1.48        17.85        24.56 
TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 
        1.84        19.36        22.42         3.12        23.87         2.17 
TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 
        2.27         1.94        17.95        22.32         1.58        15.88 
TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL 
        1.15        22.36         0.76         1.78         2.01         2.20 
TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX 
        1.61         5.49         2.33         3.48         1.45         1.25 
TCGA-HC-A6HY TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 
        4.41        88.24        82.92        43.69        20.19        12.30 
TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q 
       21.76        17.03        16.04        16.54        16.14        20.52 
TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 
       14.93        17.19         6.02        13.32        17.36         9.17 
TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N 
        9.17        10.19         6.77        10.39        14.37        20.28 
TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y 
       13.87         5.85        10.62        93.99        56.28        44.68 
TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 
       61.78       115.86        30.02        54.54       151.36        67.59 
TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AZ 
       90.51        49.25       113.33        67.07        58.19        27.62 
TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IB TCGA-KK-A8IF TCGA-KK-A8IL TCGA-M7-A71Y 
       34.95        22.75         2.73        26.43        20.65         5.19 
TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 
        6.87         9.93        13.15        27.02        25.08        15.88 
TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP 
       18.84         3.19        41.00       114.64        47.21        86.14 
TCGA-TP-A8TT TCGA-TP-A8TV TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M 
       11.90         8.19         8.84        25.51        12.95         6.02 
TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 
       15.52        15.81        30.15        32.91        15.09         4.34 
TCGA-VP-A872 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C 
      106.95        84.69        94.65        23.93        75.91        55.56 
TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N 
       60.92        66.97        21.80        48.85        21.53        17.82 
TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DI 
        5.79        37.18        27.81         3.91        38.04        48.03 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW 
        9.04         2.99        25.97        31.96        31.50        31.96 
TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU 
       28.54        30.58        29.23        27.09        37.02        39.65 
TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8S8 
       25.48        52.96        49.02        38.56        36.95        62.14 
TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI 
       60.56        16.83        41.46        45.14        28.77        47.38 
TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ 
       45.86        37.97        26.24       106.75        71.34        62.79 
TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL 
        7.00        14.04        41.39        60.99        62.37        24.33 
TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       49.91        28.34         1.64         4.93         1.12         7.86 
TCGA-ZG-A9ND 
        6.02 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              1.97               0.30 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             78.61             151.36 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            40.255             23.900 
[1] "2.0 - 78.6 (40.3)"  "0.3 - 151.4 (23.9)"
[1] "hr="     "2.6e+07"
D35V2, continuous
                    vv
clus                  T2  T3  T4
  19Q GAIN MUTATED     0   5   1
  19Q GAIN WILD-TYPE 150 201   4
D35V3, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  T2                0                150
  T3                5                201
  T4                1                  4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V4, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     5   1
  19Q GAIN WILD-TYPE 258  43
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      5    1
  19Q GAIN WILD-TYPE  258   43
   clus
vv  19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  0                5                258
  1                1                 43
[1] 2 2
[1] FALSE
D35V5, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     0   6
  19Q GAIN WILD-TYPE  13 344
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      0    6
  19Q GAIN WILD-TYPE   13  344
                                        clus
vv                                       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                0                 13
  PROSTATE ADENOCARCINOMA ACINAR TYPE                   6                344
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  19Q GAIN MUTATED     3   3   0   0
  19Q GAIN WILD-TYPE 240  87   5  11
D35V6, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  R0                3                240
  R1                3                 87
  R2                0                  5
  RX                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"
D35V7, continuous
D35V8, continuous
D35V9, continuous
D35V10, continuous
D35V11, continuous
D35V12, continuous
D35V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19Q GAIN MUTATED       0                         0     3
  19Q GAIN WILD-TYPE     2                         7   143
D35V14, multiclass
                           clus
vv                          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  7
  WHITE                                    3                143
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(36) Variable = 20P GAIN MUTATION ANALYSIS
D36V1, survival
                    sevent
clus2                  0   1
  20P GAIN MUTATED    13   0
  20P GAIN WILD-TYPE 342   6
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                13                348 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 0                  6 
$`20P GAIN MUTATED`
TCGA-EJ-A65M TCGA-G9-6499 TCGA-HI-7168 TCGA-J9-A52E TCGA-KK-A6E8 TCGA-KK-A7AZ 
        7.56        50.73        78.61        10.62        58.19        27.62 
TCGA-KK-A8IF TCGA-VP-A875 TCGA-VP-A87D TCGA-XK-AAIV TCGA-YL-A8HM TCGA-YL-A9WH 
       26.43        26.47        60.92        31.50        36.95        14.04 
TCGA-YL-A9WI 
       41.39 

$`20P GAIN WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 
        1.02         2.04         0.92        44.02        12.00         1.02 
TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 
       23.01         1.02        15.06        24.03         2.04        13.02 
TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 
       15.98        26.99         9.99        32.02        33.01         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        27.16        33.11        19.56        13.32        29.79 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        26.30        45.73        28.93        30.31 
TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 
       27.19        23.90        38.93        48.13        36.69        48.53 
TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 
       38.53        36.23        60.23        46.55        47.80        52.27 
TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 
       64.50        51.88        68.35        43.07        36.66        38.76 
TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 
       39.75        60.23        41.85        47.87        29.06        27.02 
TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 
       49.02        61.15        83.57        21.80         9.70         9.50 
TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 
        9.37        16.77         7.66        17.52         5.75        27.68 
TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 
        6.28         0.30        23.90        38.37        25.87        25.68 
TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 
       20.55        14.53        14.14        18.15        19.59        17.29 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 
        3.75        23.05        19.92        64.47        63.98        26.99 
TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G 
       10.32         5.33         4.24        17.49         9.83         3.06 
TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F 
        7.53        21.96        17.62        12.92        13.71        18.41 
TCGA-EJ-A65G TCGA-EJ-A65J TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB 
        9.14         2.99        28.41        15.42        13.45         8.98 
TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 
       17.23        16.24         1.78        41.62        87.35        81.04 
TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 
       67.99        66.67        69.37        55.76        18.21        68.68 
TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 
       49.81        46.16        50.70        49.35        47.15        46.52 
TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 
       47.44        45.30        39.39        44.81         3.32        40.18 
TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 
       39.95        38.01        40.31        26.66        31.50        37.97 
TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 
       45.80        25.15        27.29        58.22        56.75        52.87 
TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 
       38.27        38.96        27.91        30.97        35.34        28.18 
TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY 
       32.68        26.01        21.14         6.08        30.94         3.68 
TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 
       19.76         5.33         2.93         2.01         2.37        14.47 
TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 
       28.54         0.79        28.60         1.97         1.68         2.37 
TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 
        2.93         1.71         0.72         2.10         2.66         1.74 
TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 
        1.48         1.68         2.07        24.59        26.04         1.97 
TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 
        1.12         3.22        30.51         1.48        17.85        24.56 
TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 
        1.84        19.36        22.42         3.12        23.87         2.17 
TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 
        2.27         1.94        17.95        22.32         1.58        15.88 
TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL 
        1.15        22.36         0.76         1.78         2.01         2.20 
TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX 
        1.61         5.49         2.33         3.48         1.45         1.25 
TCGA-HC-A6HY TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 
        4.41        88.24        82.92        43.69        20.19        12.30 
TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q 
       21.76        17.03        16.04        16.54        16.14        20.52 
TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 
       14.93        17.19         6.02        13.32        17.36         9.17 
TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N 
        9.17        10.19         6.77        10.39        14.37        20.28 
TCGA-J9-A52B TCGA-J9-A52C TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z 
       13.87         5.85        93.99        56.28        44.68        61.78 
TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 
      115.86        30.02        54.54       151.36        67.59        90.51 
TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IB 
       49.25       113.33        67.07        34.95        22.75         2.73 
TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 
       20.65         5.19         6.87         9.93        13.15        27.02 
TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN 
       25.08        15.88        18.84         3.19        41.00       114.64 
TCGA-QU-A6IO TCGA-QU-A6IP TCGA-TP-A8TT TCGA-TP-A8TV TCGA-VN-A88I TCGA-VN-A88K 
       47.21        86.14        11.90         8.19         8.84        25.51 
TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q 
       12.95         6.02        15.52        15.81        30.15        32.91 
TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 
       15.09         4.34       106.95        84.69        94.65        23.93 
TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K 
       75.91        55.56        66.97        21.80        48.85        21.53 
TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83G 
       17.82         5.79        37.18        27.81         3.91        38.04 
TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIW 
       48.03         9.04         2.99        25.97        31.96        31.96 
TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU 
       28.54        30.58        29.23        27.09        37.02        39.65 
TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HO TCGA-YL-A8S8 
       25.48        52.96        49.02        38.56        71.77        62.14 
TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH 
       60.56        16.83        45.50        41.46        45.14        28.77 
TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP 
       47.38        45.86        37.97        26.24       106.75        71.34 
TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX 
       62.79         7.00        60.99        62.37        24.33        49.91 
TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9ND 
       28.34         1.64         4.93         1.12         7.86         6.02 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              7.56               0.30 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             78.61             151.36 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             31.50              23.46 
[1] "7.6 - 78.6 (31.5)"  "0.3 - 151.4 (23.5)"
[1] "hr="     "2.6e+07"
D36V2, continuous
                    vv
clus                  T2  T3  T4
  20P GAIN MUTATED     2  11   0
  20P GAIN WILD-TYPE 148 195   5
D36V3, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  T2                2                148
  T3               11                195
  T4                0                  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"
D36V4, binary
                    cls
clus                   0   1
  20P GAIN MUTATED     9   4
  20P GAIN WILD-TYPE 254  40
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      9    4
  20P GAIN WILD-TYPE  254   40
   clus
vv  20P GAIN MUTATED 20P GAIN WILD-TYPE
  0                9                254
  1                4                 40
[1] 2 2
[1] FALSE
D36V5, binary
                    cls
clus                   0   1
  20P GAIN MUTATED     0  13
  20P GAIN WILD-TYPE  13 337
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      0   13
  20P GAIN WILD-TYPE   13  337
                                        clus
vv                                       20P GAIN MUTATED 20P GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                0                 13
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  13                337
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  20P GAIN MUTATED     8   3   0   1
  20P GAIN WILD-TYPE 235  87   5  10
D36V6, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  R0                8                235
  R1                3                 87
  R2                0                  5
  RX                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"
D36V7, continuous
D36V8, continuous
D36V9, continuous
D36V10, continuous
D36V11, continuous
D36V12, continuous
D36V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20P GAIN MUTATED       0                         0     2
  20P GAIN WILD-TYPE     2                         7   144
D36V14, multiclass
[1] "Remove cluster labels:" "20P GAIN MUTATED"      
clus
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 2                153 
        TCGA-CH-5737         TCGA-CH-5738         TCGA-CH-5739 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CH-5740         TCGA-CH-5741         TCGA-CH-5743 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CH-5744         TCGA-CH-5746         TCGA-CH-5748 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CH-5750         TCGA-CH-5751         TCGA-CH-5752 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CH-5753         TCGA-CH-5754         TCGA-CH-5761 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CH-5762         TCGA-CH-5763         TCGA-CH-5764 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CH-5765         TCGA-CH-5766         TCGA-CH-5767 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CH-5768         TCGA-CH-5769         TCGA-CH-5771 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CH-5772         TCGA-CH-5788         TCGA-CH-5789 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CH-5790         TCGA-CH-5791         TCGA-CH-5792 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CH-5794         TCGA-EJ-5494         TCGA-EJ-5495 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EJ-5496         TCGA-EJ-5497         TCGA-EJ-5498 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EJ-5499         TCGA-EJ-5501         TCGA-EJ-5503 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EJ-5504         TCGA-EJ-5505         TCGA-EJ-5506 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EJ-5507         TCGA-EJ-5508         TCGA-EJ-5509 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EJ-5510         TCGA-EJ-5511         TCGA-EJ-5512 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EJ-5514         TCGA-EJ-5515         TCGA-EJ-5516 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EJ-5517         TCGA-EJ-5518         TCGA-EJ-5519 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EJ-5521         TCGA-EJ-5522         TCGA-EJ-5524 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EJ-5525         TCGA-EJ-5526         TCGA-EJ-5527 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EJ-5530         TCGA-EJ-5531         TCGA-EJ-5532 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EJ-5542         TCGA-EJ-7115         TCGA-EJ-7123 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EJ-7125         TCGA-EJ-7314         TCGA-EJ-7315 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EJ-7317         TCGA-EJ-7321         TCGA-EJ-7327 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EJ-7328         TCGA-EJ-7330         TCGA-EJ-7331 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EJ-7781         TCGA-EJ-7782         TCGA-EJ-7783 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EJ-7784         TCGA-EJ-7785         TCGA-EJ-7786 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EJ-7788         TCGA-EJ-7789         TCGA-EJ-7791 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EJ-7792         TCGA-EJ-7793         TCGA-EJ-7794 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EJ-7797         TCGA-FC-7708         TCGA-FC-7961 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-G9-6329         TCGA-G9-6332         TCGA-G9-6333 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-G9-6336         TCGA-G9-6338         TCGA-G9-6342 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-G9-6343         TCGA-G9-6348         TCGA-G9-6351 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-G9-6353         TCGA-G9-6356         TCGA-G9-6361 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-G9-6362         TCGA-G9-6363         TCGA-G9-6364 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-G9-6365         TCGA-G9-6366         TCGA-G9-6367 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-G9-6369         TCGA-G9-6370         TCGA-G9-6371 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-G9-6373         TCGA-G9-6377         TCGA-G9-6378 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-G9-6384         TCGA-G9-6385         TCGA-G9-6494 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-G9-6496         TCGA-H9-7775         TCGA-HC-7075 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-HC-7077         TCGA-HC-7078         TCGA-HC-7079 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-HC-7080         TCGA-HC-7081         TCGA-HC-7209 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-HC-7210         TCGA-HC-7211         TCGA-HC-7212 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-HC-7213         TCGA-HC-7230         TCGA-HC-7231 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-HC-7232         TCGA-HC-7233         TCGA-HC-7736 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-HC-7737         TCGA-HC-7738         TCGA-HC-7740 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-HC-7742         TCGA-HC-7744         TCGA-HC-7745 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-HC-7747         TCGA-HC-7748         TCGA-HC-7749 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-HC-7750         TCGA-HC-7752         TCGA-HC-7818 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-HC-7819         TCGA-HC-7820         TCGA-HC-7821 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-HI-7169         TCGA-HI-7170         TCGA-HI-7171 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 

Clustering(37) Variable = 20Q GAIN MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                  0   1
  20Q GAIN MUTATED    16   0
  20Q GAIN WILD-TYPE 339   6
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                16                345 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 0                  6 
$`20Q GAIN MUTATED`
TCGA-CH-5762 TCGA-EJ-5518 TCGA-EJ-7314 TCGA-EJ-A65M TCGA-G9-6499 TCGA-HI-7168 
       44.02        52.27         9.70         7.56        50.73        78.61 
TCGA-J9-A52E TCGA-KK-A6E8 TCGA-KK-A8IF TCGA-VP-A875 TCGA-VP-A87D TCGA-XK-AAIV 
       10.62        58.19        26.43        26.47        60.92        31.50 
TCGA-YL-A8HM TCGA-YL-A8S8 TCGA-YL-A9WH TCGA-YL-A9WI 
       36.95        62.14        14.04        41.39 

$`20Q GAIN WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 
        1.02         2.04         0.92        12.00         1.02        23.01 
TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 
        1.02        15.06        24.03         2.04        13.02        15.98 
TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 
       26.99         9.99        32.02        33.01         2.99        29.00 
TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
       27.16        33.11        19.56        13.32        29.79        46.52 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       44.88        26.30        45.73        28.93        30.31        27.19 
TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       23.90        38.93        48.13        36.69        48.53        38.53 
TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5519 TCGA-EJ-5521 
       36.23        60.23        46.55        47.80        64.50        51.88 
TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 
       68.35        43.07        36.66        38.76        39.75        60.23 
TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 
       41.85        47.87        29.06        27.02        49.02        61.15 
TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 
       83.57        21.80         9.50         9.37        16.77         7.66 
TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 
       17.52         5.75        27.68         6.28         0.30        23.90 
TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 
       38.37        25.87        25.68        20.55        14.53        14.14 
TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 
       18.15        19.59        17.29         3.75        23.05        19.92 
TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D 
       64.47        63.98        26.99        10.32         5.33         4.24 
TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B 
       17.49         9.83         3.06         7.53        21.96        17.62 
TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-FC-7708 
       12.92        13.71        18.41         9.14         2.99        28.41 
TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 
       15.42        13.45         8.98        17.23        16.24         1.78 
TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 
       41.62        87.35        81.04        67.99        66.67        69.37 
TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 
       55.76        18.21        68.68        49.81        46.16        50.70 
TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 
       49.35        47.15        46.52        47.44        45.30        39.39 
TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 
       44.81         3.32        40.18        39.95        38.01        40.31 
TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 
       26.66        31.50        37.97        45.80        25.15        27.29 
TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 
       58.22        56.75        52.87        38.27        38.96        27.91 
TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 
       30.97        35.34        28.18        32.68        26.01        21.14 
TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 
        6.08        30.94         3.68        19.76         5.33         2.93 
TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 
        2.01         2.37        14.47        28.54         0.79        28.60 
TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 
        1.97         1.68         2.37         2.93         1.71         0.72 
TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 
        2.10         2.66         1.74         1.48         1.68         2.07 
TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 
       24.59        26.04         1.97         1.12         3.22        30.51 
TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 
        1.48        17.85        24.56         1.84        19.36        22.42 
TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 
        3.12        23.87         2.17         2.27         1.94        17.95 
TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV 
       22.32         1.58        15.88         1.15        22.36         0.76 
TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP 
        1.78         2.01         2.20         1.61         5.49         2.33 
TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HI-7169 TCGA-HI-7170 
        3.48         1.45         1.25         4.41        88.24        82.92 
TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M 
       43.69        20.19        12.30        21.76        17.03        16.04 
TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T 
       16.54        16.14        20.52        14.93        17.19         6.02 
TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K 
       13.32        17.36         9.17         9.17        10.19         6.77 
TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52C TCGA-KK-A59V 
       10.39        14.37        20.28        13.87         5.85        93.99 
TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 
       56.28        44.68        61.78       115.86        30.02        54.54 
TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 
      151.36        67.59        90.51        49.25       113.33        67.07 
TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IB TCGA-KK-A8IL TCGA-M7-A71Y 
       27.62        34.95        22.75         2.73        20.65         5.19 
TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 
        6.87         9.93        13.15        27.02        25.08        15.88 
TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP 
       18.84         3.19        41.00       114.64        47.21        86.14 
TCGA-TP-A8TT TCGA-TP-A8TV TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M 
       11.90         8.19         8.84        25.51        12.95         6.02 
TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 
       15.52        15.81        30.15        32.91        15.09         4.34 
TCGA-VP-A872 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C 
      106.95        84.69        94.65        23.93        75.91        55.56 
TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI 
       66.97        21.80        48.85        21.53        17.82         5.79 
TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK 
       37.18        27.81         3.91        38.04        48.03         9.04 
TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA 
        2.99        25.97        31.96        31.96        28.54        30.58 
TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-Y6-A8TL TCGA-YL-A8HJ 
       29.23        27.09        37.02        39.65        25.48        52.96 
TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HO TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB 
       49.02        38.56        71.77        60.56        16.83        45.50 
TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK 
       41.46        45.14        28.77        47.38        45.86        37.97 
TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WJ 
       26.24       106.75        71.34        62.79         7.00        60.99 
TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX 
       62.37        24.33        49.91        28.34         1.64         4.93 
TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9ND 
        1.12         7.86         6.02 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              7.56               0.30 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             78.61             151.36 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             39.17              23.05 
[1] "7.6 - 78.6 (39.2)"  "0.3 - 151.4 (23.1)"
[1] "hr="     "2.7e+07"
D37V2, continuous
                    vv
clus                  T2  T3  T4
  20Q GAIN MUTATED     2  13   1
  20Q GAIN WILD-TYPE 148 193   4
D37V3, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T2                2                148
  T3               13                193
  T4                1                  4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V4, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED    12   4
  20Q GAIN WILD-TYPE 251  40
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     12    4
  20Q GAIN WILD-TYPE  251   40
   clus
vv  20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  0               12                251
  1                4                 40
[1] 2 2
[1] FALSE
D37V5, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED     0  16
  20Q GAIN WILD-TYPE  13 334
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      0   16
  20Q GAIN WILD-TYPE   13  334
                                        clus
vv                                       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                0                 13
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  16                334
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  20Q GAIN MUTATED     8   6   0   1
  20Q GAIN WILD-TYPE 235  84   5  10
D37V6, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  R0                8                235
  R1                6                 84
  R2                0                  5
  RX                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"
D37V7, continuous
D37V8, continuous
D37V9, continuous
D37V10, continuous
D37V11, continuous
D37V12, continuous
D37V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20Q GAIN MUTATED       0                         0     5
  20Q GAIN WILD-TYPE     2                         7   141
D37V14, multiclass
                           clus
vv                          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  7
  WHITE                                    5                141
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(38) Variable = 21Q GAIN MUTATION ANALYSIS
D38V1, survival
                    sevent
clus2                  0   1
  21Q GAIN MUTATED    13   0
  21Q GAIN WILD-TYPE 342   6
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                13                348 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 0                  6 
$`21Q GAIN MUTATED`
TCGA-EJ-7784 TCGA-G9-6499 TCGA-HI-7168 TCGA-J9-A52E TCGA-KK-A59Z TCGA-VP-A872 
       25.68        50.73        78.61        10.62        61.78       106.95 
TCGA-VP-A875 TCGA-VP-A87H TCGA-XK-AAIV TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A9WH 
       26.47        21.80        31.50        71.77        62.14        14.04 
TCGA-YL-A9WI 
       41.39 

$`21Q GAIN WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 
        1.02         2.04         0.92        44.02        12.00         1.02 
TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 
       23.01         1.02        15.06        24.03         2.04        13.02 
TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 
       15.98        26.99         9.99        32.02        33.01         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        27.16        33.11        19.56        13.32        29.79 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        26.30        45.73        28.93        30.31 
TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 
       27.19        23.90        38.93        48.13        36.69        48.53 
TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 
       38.53        36.23        60.23        46.55        47.80        52.27 
TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 
       64.50        51.88        68.35        43.07        36.66        38.76 
TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 
       39.75        60.23        41.85        47.87        29.06        27.02 
TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 
       49.02        61.15        83.57        21.80         9.70         9.50 
TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 
        9.37        16.77         7.66        17.52         5.75        27.68 
TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7785 
        6.28         0.30        23.90        38.37        25.87        20.55 
TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 
       14.53        14.14        18.15        19.59        17.29         3.75 
TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8474 
       23.05        19.92        64.47        63.98        26.99        10.32 
TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H 
        5.33         4.24        17.49         9.83         3.06         7.53 
TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G 
       21.96        17.62        12.92        13.71        18.41         9.14 
TCGA-EJ-A65J TCGA-EJ-A65M TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB 
        2.99         7.56        28.41        15.42        13.45         8.98 
TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 
       17.23        16.24         1.78        41.62        87.35        81.04 
TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 
       67.99        66.67        69.37        55.76        18.21        68.68 
TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 
       49.81        46.16        50.70        49.35        47.15        46.52 
TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 
       47.44        45.30        39.39        44.81         3.32        40.18 
TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 
       39.95        38.01        40.31        26.66        31.50        37.97 
TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 
       45.80        25.15        27.29        58.22        56.75        52.87 
TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 
       38.27        38.96        27.91        30.97        35.34        28.18 
TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY 
       32.68        26.01        21.14         6.08        30.94         3.68 
TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 
       19.76         5.33         2.93         2.01         2.37        14.47 
TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 
       28.54         0.79        28.60         1.97         1.68         2.37 
TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 
        2.93         1.71         0.72         2.10         2.66         1.74 
TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 
        1.48         1.68         2.07        24.59        26.04         1.97 
TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 
        1.12         3.22        30.51         1.48        17.85        24.56 
TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 
        1.84        19.36        22.42         3.12        23.87         2.17 
TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 
        2.27         1.94        17.95        22.32         1.58        15.88 
TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL 
        1.15        22.36         0.76         1.78         2.01         2.20 
TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX 
        1.61         5.49         2.33         3.48         1.45         1.25 
TCGA-HC-A6HY TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 
        4.41        88.24        82.92        43.69        20.19        12.30 
TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q 
       21.76        17.03        16.04        16.54        16.14        20.52 
TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 
       14.93        17.19         6.02        13.32        17.36         9.17 
TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N 
        9.17        10.19         6.77        10.39        14.37        20.28 
TCGA-J9-A52B TCGA-J9-A52C TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A6DY 
       13.87         5.85        93.99        56.28        44.68       115.86 
TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 
       30.02        54.54       151.36        67.59        90.51        49.25 
TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 
      113.33        67.07        58.19        27.62        34.95        22.75 
TCGA-KK-A8IB TCGA-KK-A8IF TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 
        2.73        26.43        20.65         5.19         6.87         9.93 
TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL 
       13.15        27.02        25.08        15.88        18.84         3.19 
TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-TP-A8TT TCGA-TP-A8TV 
       41.00       114.64        47.21        86.14        11.90         8.19 
TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O 
        8.84        25.51        12.95         6.02        15.52        15.81 
TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A876 TCGA-VP-A878 
       30.15        32.91        15.09         4.34        84.69        94.65 
TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87J 
       23.93        75.91        55.56        60.92        66.97        48.85 
TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR 
       21.53        17.82         5.79        37.18        27.81         3.91 
TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR 
       38.04        48.03         9.04         2.99        25.97        31.96 
TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT 
       31.96        28.54        30.58        29.23        27.09        37.02 
TCGA-XK-AAJU TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM 
       39.65        25.48        52.96        49.02        38.56        36.95 
TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH 
       60.56        16.83        45.50        41.46        45.14        28.77 
TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP 
       47.38        45.86        37.97        26.24       106.75        71.34 
TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX 
       62.79         7.00        60.99        62.37        24.33        49.91 
TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9ND 
       28.34         1.64         4.93         1.12         7.86         6.02 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             10.62               0.30 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            106.95             151.36 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             41.39              23.46 
[1] "10.6 - 107.0 (41.4)" "0.3 - 151.4 (23.5)" 
[1] "hr="     "7.5e+07"
D38V2, continuous
                    vv
clus                  T2  T3  T4
  21Q GAIN MUTATED     2  11   0
  21Q GAIN WILD-TYPE 148 195   5
D38V3, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  T2                2                148
  T3               11                195
  T4                0                  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"
D38V4, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    10   3
  21Q GAIN WILD-TYPE 253  41
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     10    3
  21Q GAIN WILD-TYPE  253   41
   clus
vv  21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  0               10                253
  1                3                 41
[1] 2 2
[1] FALSE
D38V5, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     1  12
  21Q GAIN WILD-TYPE  12 338
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      1   12
  21Q GAIN WILD-TYPE   12  338
                                        clus
vv                                       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                1                 12
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  12                338
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  21Q GAIN MUTATED     7   5   1   0
  21Q GAIN WILD-TYPE 236  85   4  11
D38V6, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  R0                7                236
  R1                5                 85
  R2                1                  4
  RX                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"
D38V7, continuous
D38V8, continuous
D38V9, continuous
D38V10, continuous
D38V11, continuous
D38V12, continuous
D38V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  21Q GAIN MUTATED       0                         0     3
  21Q GAIN WILD-TYPE     2                         7   143
D38V14, multiclass
                           clus
vv                          21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  7
  WHITE                                    3                143
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(39) Variable = XQ GAIN MUTATION ANALYSIS
D39V1, survival
                   sevent
clus2                 0   1
  XQ GAIN MUTATED     4   0
  XQ GAIN WILD-TYPE 351   6
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                4               357 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                0                 6 
$`XQ GAIN MUTATED`
TCGA-HC-A4ZV TCGA-VP-A87H TCGA-XK-AAJA TCGA-YL-A8S8 
        0.76        21.80        30.58        62.14 

$`XQ GAIN WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 
        1.02         2.04         0.92        44.02        12.00         1.02 
TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 
       23.01         1.02        15.06        24.03         2.04        13.02 
TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 
       15.98        26.99         9.99        32.02        33.01         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        27.16        33.11        19.56        13.32        29.79 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        26.30        45.73        28.93        30.31 
TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 
       27.19        23.90        38.93        48.13        36.69        48.53 
TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 
       38.53        36.23        60.23        46.55        47.80        52.27 
TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 
       64.50        51.88        68.35        43.07        36.66        38.76 
TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 
       39.75        60.23        41.85        47.87        29.06        27.02 
TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 
       49.02        61.15        83.57        21.80         9.70         9.50 
TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 
        9.37        16.77         7.66        17.52         5.75        27.68 
TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 
        6.28         0.30        23.90        38.37        25.87        25.68 
TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 
       20.55        14.53        14.14        18.15        19.59        17.29 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 
        3.75        23.05        19.92        64.47        63.98        26.99 
TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G 
       10.32         5.33         4.24        17.49         9.83         3.06 
TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F 
        7.53        21.96        17.62        12.92        13.71        18.41 
TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI 
        9.14         2.99         7.56        28.41        15.42        13.45 
TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 
        8.98        17.23        16.24         1.78        41.62        87.35 
TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 
       81.04        67.99        66.67        69.37        55.76        18.21 
TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 
       68.68        49.81        46.16        50.70        49.35        47.15 
TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 
       46.52        47.44        45.30        39.39        44.81         3.32 
TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 
       40.18        39.95        38.01        40.31        26.66        31.50 
TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 
       37.97        45.80        25.15        27.29        58.22        56.75 
TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 
       52.87        50.73        38.27        38.96        27.91        30.97 
TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 
       35.34        28.18        32.68        26.01        21.14         6.08 
TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 
       30.94         3.68        19.76         5.33         2.93         2.01 
TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 
        2.37        14.47        28.54         0.79        28.60         1.97 
TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 
        1.68         2.37         2.93         1.71         0.72         2.10 
TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 
        2.66         1.74         1.48         1.68         2.07        24.59 
TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 
       26.04         1.97         1.12         3.22        30.51         1.48 
TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 
       17.85        24.56         1.84        19.36        22.42         3.12 
TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 
       23.87         2.17         2.27         1.94        17.95        22.32 
TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A631 TCGA-HC-A632 
        1.58        15.88         1.15        22.36         1.78         2.01 
TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS 
        2.20         1.61         5.49         2.33         3.48         1.45 
TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
        1.25         4.41        78.61        88.24        82.92        43.69 
TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N 
       20.19        12.30        21.76        17.03        16.04        16.54 
TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 
       16.14        20.52        14.93        17.19         6.02        13.32 
TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L 
       17.36         9.17         9.17        10.19         6.77        10.39 
TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-KK-A59V 
       14.37        20.28        13.87         5.85        10.62        93.99 
TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 
       56.28        44.68        61.78       115.86        30.02        54.54 
TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 
      151.36        67.59        90.51        49.25       113.33        67.07 
TCGA-KK-A6E8 TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IB TCGA-KK-A8IF 
       58.19        27.62        34.95        22.75         2.73        26.43 
TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 
       20.65         5.19         6.87         9.93        13.15        27.02 
TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN 
       25.08        15.88        18.84         3.19        41.00       114.64 
TCGA-QU-A6IO TCGA-QU-A6IP TCGA-TP-A8TT TCGA-TP-A8TV TCGA-VN-A88I TCGA-VN-A88K 
       47.21        86.14        11.90         8.19         8.84        25.51 
TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q 
       12.95         6.02        15.52        15.81        30.15        32.91 
TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 
       15.09         4.34       106.95        26.47        84.69        94.65 
TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87J 
       23.93        75.91        55.56        60.92        66.97        48.85 
TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR 
       21.53        17.82         5.79        37.18        27.81         3.91 
TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR 
       38.04        48.03         9.04         2.99        25.97        31.96 
TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT 
       31.50        31.96        28.54        29.23        27.09        37.02 
TCGA-XK-AAJU TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM 
       39.65        25.48        52.96        49.02        38.56        36.95 
TCGA-YL-A8HO TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF 
       71.77        60.56        16.83        45.50        41.46        45.14 
TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO 
       28.77        47.38        45.86        37.97        26.24       106.75 
TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ 
       71.34        62.79         7.00        14.04        41.39        60.99 
TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX 
       62.37        24.33        49.91        28.34         1.64         4.93 
TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9ND 
        1.12         7.86         6.02 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             0.76              0.30 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            62.14            151.36 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            26.19             23.93 
[1] "0.8 - 62.1 (26.2)"  "0.3 - 151.4 (23.9)"
[1] "hr="     "9100000"
D39V2, continuous
                   vv
clus                 T2  T3  T4
  XQ GAIN MUTATED     0   4   0
  XQ GAIN WILD-TYPE 150 202   5
D39V3, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  T2               0               150
  T3               4               202
  T4               0                 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"
D39V4, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     4   0
  XQ GAIN WILD-TYPE 259  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      4    0
  XQ GAIN WILD-TYPE  259   44
   clus
vv  XQ GAIN MUTATED XQ GAIN WILD-TYPE
  0               4               259
  1               0                44
[1] 2 2
[1] FALSE
D39V5, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     0   4
  XQ GAIN WILD-TYPE  13 346
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      0    4
  XQ GAIN WILD-TYPE   13  346
                                        clus
vv                                       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE               0                13
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  4               346
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  XQ GAIN MUTATED     1   2   1   0
  XQ GAIN WILD-TYPE 242  88   4  11
D39V6, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  R0               1               242
  R1               2                88
  R2               1                 4
  RX               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"
D39V7, continuous
D39V8, continuous
D39V9, continuous
D39V10, continuous
D39V11, continuous
D39V12, continuous
D39V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XQ GAIN MUTATED       0                         0     0
  XQ GAIN WILD-TYPE     2                         7   146
D39V14, multiclass

Clustering(40) Variable = 1P LOSS MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                 0   1
  1P LOSS MUTATED    13   0
  1P LOSS WILD-TYPE 342   6
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               13               348 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                0                 6 
$`1P LOSS MUTATED`
TCGA-EJ-7784 TCGA-G9-6361 TCGA-HC-7213 TCGA-HI-7168 TCGA-KK-A59Z TCGA-KK-A6E0 
       25.68        46.52         1.97        78.61        61.78        30.02 
TCGA-KK-A6E6 TCGA-M7-A725 TCGA-VP-AA1N TCGA-YL-A8SJ TCGA-YL-A8SQ TCGA-YL-A9WH 
      113.33        18.84        17.82        45.86        62.79        14.04 
TCGA-YL-A9WL 
       24.33 

$`1P LOSS WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 
        1.02         2.04         0.92        44.02        12.00         1.02 
TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 
       23.01         1.02        15.06        24.03         2.04        13.02 
TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 
       15.98        26.99         9.99        32.02        33.01         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        27.16        33.11        19.56        13.32        29.79 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        26.30        45.73        28.93        30.31 
TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 
       27.19        23.90        38.93        48.13        36.69        48.53 
TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 
       38.53        36.23        60.23        46.55        47.80        52.27 
TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 
       64.50        51.88        68.35        43.07        36.66        38.76 
TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 
       39.75        60.23        41.85        47.87        29.06        27.02 
TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 
       49.02        61.15        83.57        21.80         9.70         9.50 
TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 
        9.37        16.77         7.66        17.52         5.75        27.68 
TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7785 
        6.28         0.30        23.90        38.37        25.87        20.55 
TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 
       14.53        14.14        18.15        19.59        17.29         3.75 
TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8474 
       23.05        19.92        64.47        63.98        26.99        10.32 
TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H 
        5.33         4.24        17.49         9.83         3.06         7.53 
TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G 
       21.96        17.62        12.92        13.71        18.41         9.14 
TCGA-EJ-A65J TCGA-EJ-A65M TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB 
        2.99         7.56        28.41        15.42        13.45         8.98 
TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 
       17.23        16.24         1.78        41.62        87.35        81.04 
TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 
       67.99        66.67        69.37        55.76        18.21        68.68 
TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6362 
       49.81        46.16        50.70        49.35        47.15        47.44 
TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 
       45.30        39.39        44.81         3.32        40.18        39.95 
TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 
       38.01        40.31        26.66        31.50        37.97        45.80 
TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 
       25.15        27.29        58.22        56.75        52.87        50.73 
TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 
       38.27        38.96        27.91        30.97        35.34        28.18 
TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY 
       32.68        26.01        21.14         6.08        30.94         3.68 
TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 
       19.76         5.33         2.93         2.01         2.37        14.47 
TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 
       28.54         0.79        28.60         1.68         2.37         2.93 
TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 
        1.71         0.72         2.10         2.66         1.74         1.48 
TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 
        1.68         2.07        24.59        26.04         1.97         1.12 
TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 
        3.22        30.51         1.48        17.85        24.56         1.84 
TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 
       19.36        22.42         3.12        23.87         2.17         2.27 
TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 
        1.94        17.95        22.32         1.58        15.88         1.15 
TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN 
       22.36         0.76         1.78         2.01         2.20         1.61 
TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY 
        5.49         2.33         3.48         1.45         1.25         4.41 
TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K 
       88.24        82.92        43.69        20.19        12.30        21.76 
TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R 
       17.03        16.04        16.54        16.14        20.52        14.93 
TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I 
       17.19         6.02        13.32        17.36         9.17         9.17 
TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B 
       10.19         6.77        10.39        14.37        20.28        13.87 
TCGA-J9-A52C TCGA-J9-A52E TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A6DY 
        5.85        10.62        93.99        56.28        44.68       115.86 
TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E7 
       54.54       151.36        67.59        90.51        49.25        67.07 
TCGA-KK-A6E8 TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IB TCGA-KK-A8IF 
       58.19        27.62        34.95        22.75         2.73        26.43 
TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 
       20.65         5.19         6.87         9.93        13.15        27.02 
TCGA-M7-A723 TCGA-M7-A724 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO 
       25.08        15.88         3.19        41.00       114.64        47.21 
TCGA-QU-A6IP TCGA-TP-A8TT TCGA-TP-A8TV TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L 
       86.14        11.90         8.19         8.84        25.51        12.95 
TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R 
        6.02        15.52        15.81        30.15        32.91        15.09 
TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 
        4.34       106.95        26.47        84.69        94.65        23.93 
TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J 
       75.91        55.56        60.92        66.97        21.80        48.85 
TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83G 
       21.53         5.79        37.18        27.81         3.91        38.04 
TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV 
       48.03         9.04         2.99        25.97        31.96        31.50 
TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT 
       31.96        28.54        30.58        29.23        27.09        37.02 
TCGA-XK-AAJU TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM 
       39.65        25.48        52.96        49.02        38.56        36.95 
TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC 
       71.77        62.14        60.56        16.83        45.50        41.46 
TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO 
       45.14        28.77        47.38        37.97        26.24       106.75 
TCGA-YL-A8SP TCGA-YL-A8SR TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WX 
       71.34         7.00        41.39        60.99        62.37        49.91 
TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9ND 
       28.34         1.64         4.93         1.12         7.86         6.02 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             1.97              0.30 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           113.33            151.36 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           30.020            23.885 
[1] "2.0 - 113.3 (30.0)" "0.3 - 151.4 (23.9)"
[1] "hr="     "2.7e+07"
D40V2, continuous
                   vv
clus                 T2  T3  T4
  1P LOSS MUTATED     2  11   0
  1P LOSS WILD-TYPE 148 195   5
D40V3, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  T2               2               148
  T3              11               195
  T4               0                 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"
D40V4, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    12   1
  1P LOSS WILD-TYPE 251  43
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     12    1
  1P LOSS WILD-TYPE  251   43
   clus
vv  1P LOSS MUTATED 1P LOSS WILD-TYPE
  0              12               251
  1               1                43
[1] 2 2
[1] FALSE
D40V5, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     0  13
  1P LOSS WILD-TYPE  13 337
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      0   13
  1P LOSS WILD-TYPE   13  337
                                        clus
vv                                       1P LOSS MUTATED 1P LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE               0                13
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 13               337
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  1P LOSS MUTATED     8   5   0   0
  1P LOSS WILD-TYPE 235  85   5  11
D40V6, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  R0               8               235
  R1               5                85
  R2               0                 5
  RX               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"
D40V7, continuous
D40V8, continuous
D40V9, continuous
D40V10, continuous
D40V11, continuous
D40V12, continuous
D40V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1P LOSS MUTATED       0                         0     4
  1P LOSS WILD-TYPE     2                         7   142
D40V14, multiclass
                           clus
vv                          1P LOSS MUTATED 1P LOSS WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 7
  WHITE                                   4               142
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(41) Variable = 2P LOSS MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                 0   1
  2P LOSS MUTATED     9   0
  2P LOSS WILD-TYPE 346   6
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                9               352 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                0                 6 
$`2P LOSS MUTATED`
TCGA-HC-7213 TCGA-HC-7749 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-VP-A875 TCGA-XK-AAJT 
        1.97         1.97        90.51        49.25        26.47        37.02 
TCGA-YL-A8HO TCGA-YL-A8SJ TCGA-YL-A9WK 
       71.77        45.86        62.37 

$`2P LOSS WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 
        1.02         2.04         0.92        44.02        12.00         1.02 
TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 
       23.01         1.02        15.06        24.03         2.04        13.02 
TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 
       15.98        26.99         9.99        32.02        33.01         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        27.16        33.11        19.56        13.32        29.79 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        26.30        45.73        28.93        30.31 
TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 
       27.19        23.90        38.93        48.13        36.69        48.53 
TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 
       38.53        36.23        60.23        46.55        47.80        52.27 
TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 
       64.50        51.88        68.35        43.07        36.66        38.76 
TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 
       39.75        60.23        41.85        47.87        29.06        27.02 
TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 
       49.02        61.15        83.57        21.80         9.70         9.50 
TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 
        9.37        16.77         7.66        17.52         5.75        27.68 
TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 
        6.28         0.30        23.90        38.37        25.87        25.68 
TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 
       20.55        14.53        14.14        18.15        19.59        17.29 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 
        3.75        23.05        19.92        64.47        63.98        26.99 
TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G 
       10.32         5.33         4.24        17.49         9.83         3.06 
TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F 
        7.53        21.96        17.62        12.92        13.71        18.41 
TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI 
        9.14         2.99         7.56        28.41        15.42        13.45 
TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 
        8.98        17.23        16.24         1.78        41.62        87.35 
TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 
       81.04        67.99        66.67        69.37        55.76        18.21 
TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 
       68.68        49.81        46.16        50.70        49.35        47.15 
TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 
       46.52        47.44        45.30        39.39        44.81         3.32 
TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 
       40.18        39.95        38.01        40.31        26.66        31.50 
TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 
       37.97        45.80        25.15        27.29        58.22        56.75 
TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 
       52.87        50.73        38.27        38.96        27.91        30.97 
TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 
       35.34        28.18        32.68        26.01        21.14         6.08 
TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 
       30.94         3.68        19.76         5.33         2.93         2.01 
TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7230 
        2.37        14.47        28.54         0.79        28.60         1.68 
TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 
        2.37         2.93         1.71         0.72         2.10         2.66 
TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 
        1.74         1.48         1.68         2.07        24.59        26.04 
TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 
        1.12         3.22        30.51         1.48        17.85        24.56 
TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 
        1.84        19.36        22.42         3.12        23.87         2.17 
TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 
        2.27         1.94        17.95        22.32         1.58        15.88 
TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL 
        1.15        22.36         0.76         1.78         2.01         2.20 
TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX 
        1.61         5.49         2.33         3.48         1.45         1.25 
TCGA-HC-A6HY TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 
        4.41        78.61        88.24        82.92        43.69        20.19 
TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O 
       12.30        21.76        17.03        16.04        16.54        16.14 
TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 
       20.52        14.93        17.19         6.02        13.32        17.36 
TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M 
        9.17         9.17        10.19         6.77        10.39        14.37 
TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-KK-A59V TCGA-KK-A59X 
       20.28        13.87         5.85        10.62        93.99        56.28 
TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 
       44.68        61.78       115.86        30.02        54.54       151.36 
TCGA-KK-A6E3 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AZ TCGA-KK-A7B1 
       67.59       113.33        67.07        58.19        27.62        34.95 
TCGA-KK-A7B2 TCGA-KK-A8IB TCGA-KK-A8IF TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z 
       22.75         2.73        26.43        20.65         5.19         6.87 
TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 
        9.93        13.15        27.02        25.08        15.88        18.84 
TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-TP-A8TT 
        3.19        41.00       114.64        47.21        86.14        11.90 
TCGA-TP-A8TV TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N 
        8.19         8.84        25.51        12.95         6.02        15.52 
TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 
       15.81        30.15        32.91        15.09         4.34       106.95 
TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D 
       84.69        94.65        23.93        75.91        55.56        60.92 
TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI 
       66.97        21.80        48.85        21.53        17.82         5.79 
TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK 
       37.18        27.81         3.91        38.04        48.03         9.04 
TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 
        2.99        25.97        31.96        31.50        31.96        28.54 
TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJU TCGA-Y6-A8TL TCGA-YL-A8HJ 
       30.58        29.23        27.09        39.65        25.48        52.96 
TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA 
       49.02        38.56        36.95        62.14        60.56        16.83 
TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SK 
       45.50        41.46        45.14        28.77        47.38        37.97 
TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH 
       26.24       106.75        71.34        62.79         7.00        14.04 
TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW 
       41.39        60.99        24.33        49.91        28.34         1.64 
TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9ND 
        4.93         1.12         7.86         6.02 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             1.97              0.30 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            90.51            151.36 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
           45.860            23.885 
[1] "2.0 - 90.5 (45.9)"  "0.3 - 151.4 (23.9)"
[1] "hr="     "2.6e+07"
D41V2, continuous
                   vv
clus                 T2  T3  T4
  2P LOSS MUTATED     1   8   0
  2P LOSS WILD-TYPE 149 198   5
D41V3, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  T2               1               149
  T3               8               198
  T4               0                 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"
D41V4, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     9   0
  2P LOSS WILD-TYPE 254  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      9    0
  2P LOSS WILD-TYPE  254   44
   clus
vv  2P LOSS MUTATED 2P LOSS WILD-TYPE
  0               9               254
  1               0                44
[1] 2 2
[1] FALSE
D41V5, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     0   9
  2P LOSS WILD-TYPE  13 341
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      0    9
  2P LOSS WILD-TYPE   13  341
                                        clus
vv                                       2P LOSS MUTATED 2P LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE               0                13
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  9               341
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  2P LOSS MUTATED     6   3   0   0
  2P LOSS WILD-TYPE 237  87   5  11
D41V6, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  R0               6               237
  R1               3                87
  R2               0                 5
  RX               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"
D41V7, continuous
D41V8, continuous
D41V9, continuous
D41V10, continuous
D41V11, continuous
D41V12, continuous
D41V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2P LOSS MUTATED       0                         0     2
  2P LOSS WILD-TYPE     2                         7   144
D41V14, multiclass
[1] "Remove cluster labels:" "2P LOSS MUTATED"       
clus
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                2               153 
       TCGA-CH-5737        TCGA-CH-5738        TCGA-CH-5739        TCGA-CH-5740 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CH-5741        TCGA-CH-5743        TCGA-CH-5744        TCGA-CH-5746 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CH-5748        TCGA-CH-5750        TCGA-CH-5751        TCGA-CH-5752 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CH-5753        TCGA-CH-5754        TCGA-CH-5761        TCGA-CH-5762 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CH-5763        TCGA-CH-5764        TCGA-CH-5765        TCGA-CH-5766 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CH-5767        TCGA-CH-5768        TCGA-CH-5769        TCGA-CH-5771 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CH-5772        TCGA-CH-5788        TCGA-CH-5789        TCGA-CH-5790 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CH-5791        TCGA-CH-5792        TCGA-CH-5794        TCGA-EJ-5494 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EJ-5495        TCGA-EJ-5496        TCGA-EJ-5497        TCGA-EJ-5498 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EJ-5499        TCGA-EJ-5501        TCGA-EJ-5503        TCGA-EJ-5504 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EJ-5505        TCGA-EJ-5506        TCGA-EJ-5507        TCGA-EJ-5508 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EJ-5509        TCGA-EJ-5510        TCGA-EJ-5511        TCGA-EJ-5512 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EJ-5514        TCGA-EJ-5515        TCGA-EJ-5516        TCGA-EJ-5517 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EJ-5518        TCGA-EJ-5519        TCGA-EJ-5521        TCGA-EJ-5522 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EJ-5524        TCGA-EJ-5525        TCGA-EJ-5526        TCGA-EJ-5527 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EJ-5530        TCGA-EJ-5531        TCGA-EJ-5532        TCGA-EJ-5542 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EJ-7115        TCGA-EJ-7123        TCGA-EJ-7125        TCGA-EJ-7314 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EJ-7315        TCGA-EJ-7317        TCGA-EJ-7321        TCGA-EJ-7327 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EJ-7328        TCGA-EJ-7330        TCGA-EJ-7331        TCGA-EJ-7781 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EJ-7782        TCGA-EJ-7783        TCGA-EJ-7784        TCGA-EJ-7785 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EJ-7786        TCGA-EJ-7788        TCGA-EJ-7789        TCGA-EJ-7791 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EJ-7792        TCGA-EJ-7793        TCGA-EJ-7794        TCGA-EJ-7797 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FC-7708        TCGA-FC-7961        TCGA-G9-6329        TCGA-G9-6332 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G9-6333        TCGA-G9-6336        TCGA-G9-6338        TCGA-G9-6342 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G9-6343        TCGA-G9-6348        TCGA-G9-6351        TCGA-G9-6353 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G9-6356        TCGA-G9-6361        TCGA-G9-6362        TCGA-G9-6363 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G9-6364        TCGA-G9-6365        TCGA-G9-6366        TCGA-G9-6367 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G9-6369        TCGA-G9-6370        TCGA-G9-6371        TCGA-G9-6373 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G9-6377        TCGA-G9-6378        TCGA-G9-6384        TCGA-G9-6385 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G9-6494        TCGA-G9-6496        TCGA-G9-6499        TCGA-H9-7775 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-HC-7075        TCGA-HC-7077        TCGA-HC-7078        TCGA-HC-7079 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-HC-7080        TCGA-HC-7081        TCGA-HC-7209        TCGA-HC-7210 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-HC-7211        TCGA-HC-7212        TCGA-HC-7230        TCGA-HC-7231 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-HC-7232        TCGA-HC-7233        TCGA-HC-7736        TCGA-HC-7737 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-HC-7738        TCGA-HC-7740        TCGA-HC-7742        TCGA-HC-7744 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-HC-7745        TCGA-HC-7747        TCGA-HC-7748        TCGA-HC-7750 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-HC-7752        TCGA-HC-7818        TCGA-HC-7819        TCGA-HC-7820 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-HC-7821        TCGA-HI-7168        TCGA-HI-7169        TCGA-HI-7170 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-HI-7171 
"2P LOSS WILD-TYPE" 

Clustering(42) Variable = 2Q LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                 0   1
  2Q LOSS MUTATED    10   0
  2Q LOSS WILD-TYPE 345   6
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               10               351 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                0                 6 
$`2Q LOSS MUTATED`
TCGA-HC-7213 TCGA-HC-7749 TCGA-HC-8266 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-VP-A875 
        1.97         1.97         1.15        90.51        49.25        26.47 
TCGA-XK-AAJT TCGA-YL-A8HO TCGA-YL-A8SJ TCGA-YL-A9WK 
       37.02        71.77        45.86        62.37 

$`2Q LOSS WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 
        1.02         2.04         0.92        44.02        12.00         1.02 
TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 
       23.01         1.02        15.06        24.03         2.04        13.02 
TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 
       15.98        26.99         9.99        32.02        33.01         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        27.16        33.11        19.56        13.32        29.79 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        26.30        45.73        28.93        30.31 
TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 
       27.19        23.90        38.93        48.13        36.69        48.53 
TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 
       38.53        36.23        60.23        46.55        47.80        52.27 
TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 
       64.50        51.88        68.35        43.07        36.66        38.76 
TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 
       39.75        60.23        41.85        47.87        29.06        27.02 
TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 
       49.02        61.15        83.57        21.80         9.70         9.50 
TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 
        9.37        16.77         7.66        17.52         5.75        27.68 
TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 
        6.28         0.30        23.90        38.37        25.87        25.68 
TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 
       20.55        14.53        14.14        18.15        19.59        17.29 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 
        3.75        23.05        19.92        64.47        63.98        26.99 
TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G 
       10.32         5.33         4.24        17.49         9.83         3.06 
TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F 
        7.53        21.96        17.62        12.92        13.71        18.41 
TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI 
        9.14         2.99         7.56        28.41        15.42        13.45 
TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 
        8.98        17.23        16.24         1.78        41.62        87.35 
TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 
       81.04        67.99        66.67        69.37        55.76        18.21 
TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 
       68.68        49.81        46.16        50.70        49.35        47.15 
TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 
       46.52        47.44        45.30        39.39        44.81         3.32 
TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 
       40.18        39.95        38.01        40.31        26.66        31.50 
TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 
       37.97        45.80        25.15        27.29        58.22        56.75 
TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 
       52.87        50.73        38.27        38.96        27.91        30.97 
TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 
       35.34        28.18        32.68        26.01        21.14         6.08 
TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 
       30.94         3.68        19.76         5.33         2.93         2.01 
TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7230 
        2.37        14.47        28.54         0.79        28.60         1.68 
TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 
        2.37         2.93         1.71         0.72         2.10         2.66 
TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 
        1.74         1.48         1.68         2.07        24.59        26.04 
TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 
        1.12         3.22        30.51         1.48        17.85        24.56 
TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 
        1.84        19.36        22.42         3.12        23.87         2.17 
TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 
        2.27         1.94        17.95        22.32         1.58        15.88 
TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN 
       22.36         0.76         1.78         2.01         2.20         1.61 
TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY 
        5.49         2.33         3.48         1.45         1.25         4.41 
TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 
       78.61        88.24        82.92        43.69        20.19        12.30 
TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q 
       21.76        17.03        16.04        16.54        16.14        20.52 
TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 
       14.93        17.19         6.02        13.32        17.36         9.17 
TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N 
        9.17        10.19         6.77        10.39        14.37        20.28 
TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y 
       13.87         5.85        10.62        93.99        56.28        44.68 
TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 
       61.78       115.86        30.02        54.54       151.36        67.59 
TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 
      113.33        67.07        58.19        27.62        34.95        22.75 
TCGA-KK-A8IB TCGA-KK-A8IF TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 
        2.73        26.43        20.65         5.19         6.87         9.93 
TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL 
       13.15        27.02        25.08        15.88        18.84         3.19 
TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-TP-A8TT TCGA-TP-A8TV 
       41.00       114.64        47.21        86.14        11.90         8.19 
TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O 
        8.84        25.51        12.95         6.02        15.52        15.81 
TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A876 
       30.15        32.91        15.09         4.34       106.95        84.69 
TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E 
       94.65        23.93        75.91        55.56        60.92        66.97 
TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ 
       21.80        48.85        21.53        17.82         5.79        37.18 
TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ 
       27.81         3.91        38.04        48.03         9.04         2.99 
TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA 
       25.97        31.96        31.50        31.96        28.54        30.58 
TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJU TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK 
       29.23        27.09        39.65        25.48        52.96        49.02 
TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB 
       38.56        36.95        62.14        60.56        16.83        45.50 
TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SK TCGA-YL-A8SL 
       41.46        45.14        28.77        47.38        37.97        26.24 
TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI 
      106.75        71.34        62.79         7.00        14.04        41.39 
TCGA-YL-A9WJ TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX 
       60.99        24.33        49.91        28.34         1.64         4.93 
TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9ND 
        1.12         7.86         6.02 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             1.15              0.30 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            90.51            151.36 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            41.44             23.90 
[1] "1.1 - 90.5 (41.4)"  "0.3 - 151.4 (23.9)"
[1] "hr="     "2.6e+07"
D42V2, continuous
                   vv
clus                 T2  T3  T4
  2Q LOSS MUTATED     1   9   0
  2Q LOSS WILD-TYPE 149 197   5
D42V3, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  T2               1               149
  T3               9               197
  T4               0                 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"
D42V4, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    10   0
  2Q LOSS WILD-TYPE 253  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     10    0
  2Q LOSS WILD-TYPE  253   44
   clus
vv  2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  0              10               253
  1               0                44
[1] 2 2
[1] FALSE
D42V5, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     0  10
  2Q LOSS WILD-TYPE  13 340
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      0   10
  2Q LOSS WILD-TYPE   13  340
                                        clus
vv                                       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE               0                13
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 10               340
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  2Q LOSS MUTATED     6   4   0   0
  2Q LOSS WILD-TYPE 237  86   5  11
D42V6, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  R0               6               237
  R1               4                86
  R2               0                 5
  RX               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"
D42V7, continuous
D42V8, continuous
D42V9, continuous
D42V10, continuous
D42V11, continuous
D42V12, continuous
D42V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2Q LOSS MUTATED       0                         0     2
  2Q LOSS WILD-TYPE     2                         7   144
D42V14, multiclass
[1] "Remove cluster labels:" "2Q LOSS MUTATED"       
clus
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                2               153 
       TCGA-CH-5737        TCGA-CH-5738        TCGA-CH-5739        TCGA-CH-5740 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CH-5741        TCGA-CH-5743        TCGA-CH-5744        TCGA-CH-5746 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CH-5748        TCGA-CH-5750        TCGA-CH-5751        TCGA-CH-5752 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CH-5753        TCGA-CH-5754        TCGA-CH-5761        TCGA-CH-5762 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CH-5763        TCGA-CH-5764        TCGA-CH-5765        TCGA-CH-5766 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CH-5767        TCGA-CH-5768        TCGA-CH-5769        TCGA-CH-5771 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CH-5772        TCGA-CH-5788        TCGA-CH-5789        TCGA-CH-5790 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CH-5791        TCGA-CH-5792        TCGA-CH-5794        TCGA-EJ-5494 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EJ-5495        TCGA-EJ-5496        TCGA-EJ-5497        TCGA-EJ-5498 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EJ-5499        TCGA-EJ-5501        TCGA-EJ-5503        TCGA-EJ-5504 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EJ-5505        TCGA-EJ-5506        TCGA-EJ-5507        TCGA-EJ-5508 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EJ-5509        TCGA-EJ-5510        TCGA-EJ-5511        TCGA-EJ-5512 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EJ-5514        TCGA-EJ-5515        TCGA-EJ-5516        TCGA-EJ-5517 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EJ-5518        TCGA-EJ-5519        TCGA-EJ-5521        TCGA-EJ-5522 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EJ-5524        TCGA-EJ-5525        TCGA-EJ-5526        TCGA-EJ-5527 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EJ-5530        TCGA-EJ-5531        TCGA-EJ-5532        TCGA-EJ-5542 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EJ-7115        TCGA-EJ-7123        TCGA-EJ-7125        TCGA-EJ-7314 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EJ-7315        TCGA-EJ-7317        TCGA-EJ-7321        TCGA-EJ-7327 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EJ-7328        TCGA-EJ-7330        TCGA-EJ-7331        TCGA-EJ-7781 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EJ-7782        TCGA-EJ-7783        TCGA-EJ-7784        TCGA-EJ-7785 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EJ-7786        TCGA-EJ-7788        TCGA-EJ-7789        TCGA-EJ-7791 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EJ-7792        TCGA-EJ-7793        TCGA-EJ-7794        TCGA-EJ-7797 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-FC-7708        TCGA-FC-7961        TCGA-G9-6329        TCGA-G9-6332 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G9-6333        TCGA-G9-6336        TCGA-G9-6338        TCGA-G9-6342 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G9-6343        TCGA-G9-6348        TCGA-G9-6351        TCGA-G9-6353 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G9-6356        TCGA-G9-6361        TCGA-G9-6362        TCGA-G9-6363 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G9-6364        TCGA-G9-6365        TCGA-G9-6366        TCGA-G9-6367 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G9-6369        TCGA-G9-6370        TCGA-G9-6371        TCGA-G9-6373 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G9-6377        TCGA-G9-6378        TCGA-G9-6384        TCGA-G9-6385 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G9-6494        TCGA-G9-6496        TCGA-G9-6499        TCGA-H9-7775 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-HC-7075        TCGA-HC-7077        TCGA-HC-7078        TCGA-HC-7079 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-HC-7080        TCGA-HC-7081        TCGA-HC-7209        TCGA-HC-7210 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-HC-7211        TCGA-HC-7212        TCGA-HC-7230        TCGA-HC-7231 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-HC-7232        TCGA-HC-7233        TCGA-HC-7736        TCGA-HC-7737 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-HC-7738        TCGA-HC-7740        TCGA-HC-7742        TCGA-HC-7744 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-HC-7745        TCGA-HC-7747        TCGA-HC-7748        TCGA-HC-7750 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-HC-7752        TCGA-HC-7818        TCGA-HC-7819        TCGA-HC-7820 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-HC-7821        TCGA-HI-7168        TCGA-HI-7169        TCGA-HI-7170 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-HI-7171 
"2Q LOSS WILD-TYPE" 

Clustering(43) Variable = 3P LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                 0   1
  3P LOSS MUTATED     6   0
  3P LOSS WILD-TYPE 349   6
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                6               355 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                0                 6 
$`3P LOSS MUTATED`
TCGA-CH-5753 TCGA-G9-7523 TCGA-KK-A6E1 TCGA-KK-A6E6 TCGA-VP-A876 TCGA-YL-A8SQ 
        1.02        28.18        54.54       113.33        84.69        62.79 

$`3P LOSS WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 
        2.04         0.92        44.02        12.00         1.02        23.01 
TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 
        1.02        15.06        24.03         2.04        13.02        15.98 
TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 
       26.99         9.99        32.02        33.01         2.99        29.00 
TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
       27.16        33.11        19.56        13.32        29.79        46.52 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       44.88        26.30        45.73        28.93        30.31        27.19 
TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       23.90        38.93        48.13        36.69        48.53        38.53 
TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 
       36.23        60.23        46.55        47.80        52.27        64.50 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 
       51.88        68.35        43.07        36.66        38.76        39.75 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 
       60.23        41.85        47.87        29.06        27.02        49.02 
TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 
       61.15        83.57        21.80         9.70         9.50         9.37 
TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 
       16.77         7.66        17.52         5.75        27.68         6.28 
TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 
        0.30        23.90        38.37        25.87        25.68        20.55 
TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 
       14.53        14.14        18.15        19.59        17.29         3.75 
TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8474 
       23.05        19.92        64.47        63.98        26.99        10.32 
TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H 
        5.33         4.24        17.49         9.83         3.06         7.53 
TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G 
       21.96        17.62        12.92        13.71        18.41         9.14 
TCGA-EJ-A65J TCGA-EJ-A65M TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB 
        2.99         7.56        28.41        15.42        13.45         8.98 
TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 
       17.23        16.24         1.78        41.62        87.35        81.04 
TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 
       67.99        66.67        69.37        55.76        18.21        68.68 
TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 
       49.81        46.16        50.70        49.35        47.15        46.52 
TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 
       47.44        45.30        39.39        44.81         3.32        40.18 
TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 
       39.95        38.01        40.31        26.66        31.50        37.97 
TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 
       45.80        25.15        27.29        58.22        56.75        52.87 
TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 
       50.73        38.27        38.96        27.91        30.97        35.34 
TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY 
       32.68        26.01        21.14         6.08        30.94         3.68 
TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 
       19.76         5.33         2.93         2.01         2.37        14.47 
TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 
       28.54         0.79        28.60         1.97         1.68         2.37 
TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 
        2.93         1.71         0.72         2.10         2.66         1.74 
TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 
        1.48         1.68         2.07        24.59        26.04         1.97 
TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 
        1.12         3.22        30.51         1.48        17.85        24.56 
TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 
        1.84        19.36        22.42         3.12        23.87         2.17 
TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 
        2.27         1.94        17.95        22.32         1.58        15.88 
TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL 
        1.15        22.36         0.76         1.78         2.01         2.20 
TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX 
        1.61         5.49         2.33         3.48         1.45         1.25 
TCGA-HC-A6HY TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 
        4.41        78.61        88.24        82.92        43.69        20.19 
TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O 
       12.30        21.76        17.03        16.04        16.54        16.14 
TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 
       20.52        14.93        17.19         6.02        13.32        17.36 
TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M 
        9.17         9.17        10.19         6.77        10.39        14.37 
TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-KK-A59V TCGA-KK-A59X 
       20.28        13.87         5.85        10.62        93.99        56.28 
TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E2 TCGA-KK-A6E3 
       44.68        61.78       115.86        30.02       151.36        67.59 
TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AZ TCGA-KK-A7B1 
       90.51        49.25        67.07        58.19        27.62        34.95 
TCGA-KK-A7B2 TCGA-KK-A8IB TCGA-KK-A8IF TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z 
       22.75         2.73        26.43        20.65         5.19         6.87 
TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 
        9.93        13.15        27.02        25.08        15.88        18.84 
TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-TP-A8TT 
        3.19        41.00       114.64        47.21        86.14        11.90 
TCGA-TP-A8TV TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N 
        8.19         8.84        25.51        12.95         6.02        15.52 
TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 
       15.81        30.15        32.91        15.09         4.34       106.95 
TCGA-VP-A875 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D 
       26.47        94.65        23.93        75.91        55.56        60.92 
TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI 
       66.97        21.80        48.85        21.53        17.82         5.79 
TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK 
       37.18        27.81         3.91        38.04        48.03         9.04 
TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 
        2.99        25.97        31.96        31.50        31.96        28.54 
TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-Y6-A8TL 
       30.58        29.23        27.09        37.02        39.65        25.48 
TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 
       52.96        49.02        38.56        36.95        71.77        62.14 
TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH 
       60.56        16.83        45.50        41.46        45.14        28.77 
TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP 
       47.38        45.86        37.97        26.24       106.75        71.34 
TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL 
        7.00        14.04        41.39        60.99        62.37        24.33 
TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       49.91        28.34         1.64         4.93         1.12         7.86 
TCGA-ZG-A9ND 
        6.02 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             1.02              0.30 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           113.33            151.36 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           58.665            23.900 
[1] "1.0 - 113.3 (58.7)" "0.3 - 151.4 (23.9)"
[1] "hr="     "2.6e+07"
D43V2, continuous
                   vv
clus                 T2  T3  T4
  3P LOSS MUTATED     1   5   0
  3P LOSS WILD-TYPE 149 201   5
D43V3, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  T2               1               149
  T3               5               201
  T4               0                 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"
D43V4, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     4   2
  3P LOSS WILD-TYPE 259  42
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      4    2
  3P LOSS WILD-TYPE  259   42
   clus
vv  3P LOSS MUTATED 3P LOSS WILD-TYPE
  0               4               259
  1               2                42
[1] 2 2
[1] FALSE
D43V5, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     0   6
  3P LOSS WILD-TYPE  13 344
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      0    6
  3P LOSS WILD-TYPE   13  344
                                        clus
vv                                       3P LOSS MUTATED 3P LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE               0                13
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  6               344
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  3P LOSS MUTATED     3   2   0   1
  3P LOSS WILD-TYPE 240  88   5  10
D43V6, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  R0               3               240
  R1               2                88
  R2               0                 5
  RX               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"
D43V7, continuous
D43V8, continuous
D43V9, continuous
D43V10, continuous
D43V11, continuous
D43V12, continuous
D43V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3P LOSS MUTATED       0                         0     1
  3P LOSS WILD-TYPE     2                         7   145
D43V14, multiclass
[1] "Remove cluster labels:" "3P LOSS MUTATED"       
clus
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                1               154 
       TCGA-CH-5737        TCGA-CH-5738        TCGA-CH-5739        TCGA-CH-5740 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CH-5741        TCGA-CH-5743        TCGA-CH-5744        TCGA-CH-5746 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CH-5748        TCGA-CH-5750        TCGA-CH-5751        TCGA-CH-5752 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CH-5754        TCGA-CH-5761        TCGA-CH-5762        TCGA-CH-5763 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CH-5764        TCGA-CH-5765        TCGA-CH-5766        TCGA-CH-5767 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CH-5768        TCGA-CH-5769        TCGA-CH-5771        TCGA-CH-5772 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CH-5788        TCGA-CH-5789        TCGA-CH-5790        TCGA-CH-5791 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-CH-5792        TCGA-CH-5794        TCGA-EJ-5494        TCGA-EJ-5495 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EJ-5496        TCGA-EJ-5497        TCGA-EJ-5498        TCGA-EJ-5499 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EJ-5501        TCGA-EJ-5503        TCGA-EJ-5504        TCGA-EJ-5505 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EJ-5506        TCGA-EJ-5507        TCGA-EJ-5508        TCGA-EJ-5509 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EJ-5510        TCGA-EJ-5511        TCGA-EJ-5512        TCGA-EJ-5514 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EJ-5515        TCGA-EJ-5516        TCGA-EJ-5517        TCGA-EJ-5518 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EJ-5519        TCGA-EJ-5521        TCGA-EJ-5522        TCGA-EJ-5524 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EJ-5525        TCGA-EJ-5526        TCGA-EJ-5527        TCGA-EJ-5530 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EJ-5531        TCGA-EJ-5532        TCGA-EJ-5542        TCGA-EJ-7115 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EJ-7123        TCGA-EJ-7125        TCGA-EJ-7314        TCGA-EJ-7315 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EJ-7317        TCGA-EJ-7321        TCGA-EJ-7327        TCGA-EJ-7328 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EJ-7330        TCGA-EJ-7331        TCGA-EJ-7781        TCGA-EJ-7782 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EJ-7783        TCGA-EJ-7784        TCGA-EJ-7785        TCGA-EJ-7786 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EJ-7788        TCGA-EJ-7789        TCGA-EJ-7791        TCGA-EJ-7792 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EJ-7793        TCGA-EJ-7794        TCGA-EJ-7797        TCGA-FC-7708 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FC-7961        TCGA-G9-6329        TCGA-G9-6332        TCGA-G9-6333 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-G9-6336        TCGA-G9-6338        TCGA-G9-6342        TCGA-G9-6343 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-G9-6348        TCGA-G9-6351        TCGA-G9-6353        TCGA-G9-6356 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-G9-6361        TCGA-G9-6362        TCGA-G9-6363        TCGA-G9-6364 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-G9-6365        TCGA-G9-6366        TCGA-G9-6367        TCGA-G9-6369 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-G9-6370        TCGA-G9-6371        TCGA-G9-6373        TCGA-G9-6377 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-G9-6378        TCGA-G9-6384        TCGA-G9-6385        TCGA-G9-6494 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-G9-6496        TCGA-G9-6499        TCGA-H9-7775        TCGA-HC-7075 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-HC-7077        TCGA-HC-7078        TCGA-HC-7079        TCGA-HC-7080 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-HC-7081        TCGA-HC-7209        TCGA-HC-7210        TCGA-HC-7211 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-HC-7212        TCGA-HC-7213        TCGA-HC-7230        TCGA-HC-7231 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-HC-7232        TCGA-HC-7233        TCGA-HC-7736        TCGA-HC-7737 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-HC-7738        TCGA-HC-7740        TCGA-HC-7742        TCGA-HC-7744 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-HC-7745        TCGA-HC-7747        TCGA-HC-7748        TCGA-HC-7749 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-HC-7750        TCGA-HC-7752        TCGA-HC-7818        TCGA-HC-7819 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-HC-7820        TCGA-HC-7821        TCGA-HI-7168        TCGA-HI-7169 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-HI-7170        TCGA-HI-7171 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 

Clustering(44) Variable = 3Q LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                 0   1
  3Q LOSS MUTATED     4   0
  3Q LOSS WILD-TYPE 351   6
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                4               357 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                0                 6 
$`3Q LOSS MUTATED`
TCGA-G9-7523 TCGA-KK-A6E6 TCGA-VP-A876 TCGA-YL-A8SQ 
       28.18       113.33        84.69        62.79 

$`3Q LOSS WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 
        1.02         2.04         0.92        44.02        12.00         1.02 
TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 
       23.01         1.02        15.06        24.03         2.04        13.02 
TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 
       15.98        26.99         9.99        32.02        33.01         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        27.16        33.11        19.56        13.32        29.79 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        26.30        45.73        28.93        30.31 
TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 
       27.19        23.90        38.93        48.13        36.69        48.53 
TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 
       38.53        36.23        60.23        46.55        47.80        52.27 
TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 
       64.50        51.88        68.35        43.07        36.66        38.76 
TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 
       39.75        60.23        41.85        47.87        29.06        27.02 
TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 
       49.02        61.15        83.57        21.80         9.70         9.50 
TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 
        9.37        16.77         7.66        17.52         5.75        27.68 
TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 
        6.28         0.30        23.90        38.37        25.87        25.68 
TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 
       20.55        14.53        14.14        18.15        19.59        17.29 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 
        3.75        23.05        19.92        64.47        63.98        26.99 
TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G 
       10.32         5.33         4.24        17.49         9.83         3.06 
TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F 
        7.53        21.96        17.62        12.92        13.71        18.41 
TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI 
        9.14         2.99         7.56        28.41        15.42        13.45 
TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 
        8.98        17.23        16.24         1.78        41.62        87.35 
TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 
       81.04        67.99        66.67        69.37        55.76        18.21 
TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 
       68.68        49.81        46.16        50.70        49.35        47.15 
TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 
       46.52        47.44        45.30        39.39        44.81         3.32 
TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 
       40.18        39.95        38.01        40.31        26.66        31.50 
TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 
       37.97        45.80        25.15        27.29        58.22        56.75 
TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 
       52.87        50.73        38.27        38.96        27.91        30.97 
TCGA-G9-7522 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX 
       35.34        32.68        26.01        21.14         6.08        30.94 
TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 
        3.68        19.76         5.33         2.93         2.01         2.37 
TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 
       14.47        28.54         0.79        28.60         1.97         1.68 
TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 
        2.37         2.93         1.71         0.72         2.10         2.66 
TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 
        1.74         1.48         1.68         2.07        24.59        26.04 
TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 
        1.97         1.12         3.22        30.51         1.48        17.85 
TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 
       24.56         1.84        19.36        22.42         3.12        23.87 
TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 
        2.17         2.27         1.94        17.95        22.32         1.58 
TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 
       15.88         1.15        22.36         0.76         1.78         2.01 
TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS 
        2.20         1.61         5.49         2.33         3.48         1.45 
TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
        1.25         4.41        78.61        88.24        82.92        43.69 
TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N 
       20.19        12.30        21.76        17.03        16.04        16.54 
TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 
       16.14        20.52        14.93        17.19         6.02        13.32 
TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L 
       17.36         9.17         9.17        10.19         6.77        10.39 
TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-KK-A59V 
       14.37        20.28        13.87         5.85        10.62        93.99 
TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 
       56.28        44.68        61.78       115.86        30.02        54.54 
TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E7 TCGA-KK-A6E8 
      151.36        67.59        90.51        49.25        67.07        58.19 
TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IB TCGA-KK-A8IF TCGA-KK-A8IL 
       27.62        34.95        22.75         2.73        26.43        20.65 
TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 
        5.19         6.87         9.93        13.15        27.02        25.08 
TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO 
       15.88        18.84         3.19        41.00       114.64        47.21 
TCGA-QU-A6IP TCGA-TP-A8TT TCGA-TP-A8TV TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L 
       86.14        11.90         8.19         8.84        25.51        12.95 
TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R 
        6.02        15.52        15.81        30.15        32.91        15.09 
TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B 
        4.34       106.95        26.47        94.65        23.93        75.91 
TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K 
       55.56        60.92        66.97        21.80        48.85        21.53 
TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83G 
       17.82         5.79        37.18        27.81         3.91        38.04 
TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV 
       48.03         9.04         2.99        25.97        31.96        31.50 
TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT 
       31.96        28.54        30.58        29.23        27.09        37.02 
TCGA-XK-AAJU TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM 
       39.65        25.48        52.96        49.02        38.56        36.95 
TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC 
       71.77        62.14        60.56        16.83        45.50        41.46 
TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL 
       45.14        28.77        47.38        45.86        37.97        26.24 
TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ 
      106.75        71.34         7.00        14.04        41.39        60.99 
TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX 
       62.37        24.33        49.91        28.34         1.64         4.93 
TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9ND 
        1.12         7.86         6.02 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            28.18              0.30 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
           113.33            151.36 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            73.74             23.90 
[1] "28.2 - 113.3 (73.7)" "0.3 - 151.4 (23.9)" 
[1] "hr="     "2.6e+07"
D44V2, continuous
                   vv
clus                 T2  T3  T4
  3Q LOSS MUTATED     1   3   0
  3Q LOSS WILD-TYPE 149 203   5
D44V3, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  T2               1               149
  T3               3               203
  T4               0                 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"
D44V4, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     4   0
  3Q LOSS WILD-TYPE 259  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      4    0
  3Q LOSS WILD-TYPE  259   44
   clus
vv  3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  0               4               259
  1               0                44
[1] 2 2
[1] FALSE
D44V5, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     0   4
  3Q LOSS WILD-TYPE  13 346
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      0    4
  3Q LOSS WILD-TYPE   13  346
                                        clus
vv                                       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE               0                13
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  4               346
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  3Q LOSS MUTATED     2   2   0   0
  3Q LOSS WILD-TYPE 241  88   5  11
D44V6, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  R0               2               241
  R1               2                88
  R2               0                 5
  RX               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"
D44V7, continuous
D44V8, continuous
D44V9, continuous
D44V10, continuous
D44V11, continuous
D44V12, continuous
D44V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3Q LOSS MUTATED       0                         0     0
  3Q LOSS WILD-TYPE     2                         7   146
D44V14, multiclass

Clustering(45) Variable = 4P LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                 0   1
  4P LOSS MUTATED    14   0
  4P LOSS WILD-TYPE 341   6
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               14               347 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                0                 6 
$`4P LOSS MUTATED`
TCGA-CH-5751 TCGA-CH-5753 TCGA-CH-5754 TCGA-EJ-A65B TCGA-FC-7961 TCGA-HC-A48F 
       35.01         1.02         2.04        17.62        15.42        22.36 
TCGA-J9-A52B TCGA-KK-A59Z TCGA-KK-A6E1 TCGA-KK-A6E7 TCGA-XK-AAJT TCGA-YL-A8HK 
       13.87        61.78        54.54        67.07        37.02        49.02 
TCGA-YL-A8SL TCGA-YL-A9WH 
       26.24        14.04 

$`4P LOSS WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5761 
        1.97        24.03         1.02        13.02        31.00         0.92 
TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 
       44.02        12.00         1.02        23.01         1.02        15.06 
TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 
       24.03         2.04        13.02        15.98        26.99         9.99 
TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 
       32.02        33.01         2.99        29.00        27.16        33.11 
TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 
       19.56        13.32        29.79        46.52        44.88        26.30 
TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 
       45.73        28.93        30.31        27.19        23.90        38.93 
TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 
       48.13        36.69        48.53        38.53        36.23        60.23 
TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 
       46.55        47.80        52.27        64.50        51.88        68.35 
TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 
       43.07        36.66        38.76        39.75        60.23        41.85 
TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 
       47.87        29.06        27.02        49.02        61.15        83.57 
TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 
       21.80         9.70         9.50         9.37        16.77         7.66 
TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 
       17.52         5.75        27.68         6.28         0.30        23.90 
TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 
       38.37        25.87        25.68        20.55        14.53        14.14 
TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 
       18.15        19.59        17.29         3.75        23.05        19.92 
TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D 
       64.47        63.98        26.99        10.32         5.33         4.24 
TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65D 
       17.49         9.83         3.06         7.53        21.96        12.92 
TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-FC-7708 
       13.71        18.41         9.14         2.99         7.56        28.41 
TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 
       13.45         8.98        17.23        16.24         1.78        41.62 
TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 
       87.35        81.04        67.99        66.67        69.37        55.76 
TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 
       18.21        68.68        49.81        46.16        50.70        49.35 
TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 
       47.15        46.52        47.44        45.30        39.39        44.81 
TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 
        3.32        40.18        39.95        38.01        40.31        26.66 
TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 
       31.50        37.97        45.80        25.15        27.29        58.22 
TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 
       56.75        52.87        50.73        38.27        38.96        27.91 
TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 
       30.97        35.34        28.18        32.68        26.01        21.14 
TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 
        6.08        30.94         3.68        19.76         5.33         2.93 
TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 
        2.01         2.37        14.47        28.54         0.79        28.60 
TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 
        1.97         1.68         2.37         2.93         1.71         0.72 
TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 
        2.10         2.66         1.74         1.48         1.68         2.07 
TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 
       24.59        26.04         1.97         1.12         3.22        30.51 
TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 
        1.48        17.85        24.56         1.84        19.36        22.42 
TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 
        3.12        23.87         2.17         2.27         1.94        17.95 
TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A4ZV TCGA-HC-A631 
       22.32         1.58        15.88         1.15         0.76         1.78 
TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ 
        2.01         2.20         1.61         5.49         2.33         3.48 
TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 
        1.45         1.25         4.41        78.61        88.24        82.92 
TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M 
       43.69        20.19        12.30        21.76        17.03        16.04 
TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T 
       16.54        16.14        20.52        14.93        17.19         6.02 
TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K 
       13.32        17.36         9.17         9.17        10.19         6.77 
TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52C TCGA-J9-A52E TCGA-KK-A59V 
       10.39        14.37        20.28         5.85        10.62        93.99 
TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E2 TCGA-KK-A6E3 
       56.28        44.68       115.86        30.02       151.36        67.59 
TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E8 TCGA-KK-A7AZ TCGA-KK-A7B1 
       90.51        49.25       113.33        58.19        27.62        34.95 
TCGA-KK-A7B2 TCGA-KK-A8IB TCGA-KK-A8IF TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z 
       22.75         2.73        26.43        20.65         5.19         6.87 
TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 
        9.93        13.15        27.02        25.08        15.88        18.84 
TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-TP-A8TT 
        3.19        41.00       114.64        47.21        86.14        11.90 
TCGA-TP-A8TV TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N 
        8.19         8.84        25.51        12.95         6.02        15.52 
TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 
       15.81        30.15        32.91        15.09         4.34       106.95 
TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C 
       26.47        84.69        94.65        23.93        75.91        55.56 
TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N 
       60.92        66.97        21.80        48.85        21.53        17.82 
TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DI 
        5.79        37.18        27.81         3.91        38.04        48.03 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW 
        9.04         2.99        25.97        31.96        31.50        31.96 
TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJU TCGA-Y6-A8TL 
       28.54        30.58        29.23        27.09        39.65        25.48 
TCGA-YL-A8HJ TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 
       52.96        38.56        36.95        71.77        62.14        60.56 
TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI 
       16.83        45.50        41.46        45.14        28.77        47.38 
TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR 
       45.86        37.97       106.75        71.34        62.79         7.00 
TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY 
       41.39        60.99        62.37        24.33        49.91        28.34 
TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9ND 
        1.64         4.93         1.12         7.86         6.02 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             1.02              0.30 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            67.07            151.36 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            24.30             23.93 
[1] "1.0 - 67.1 (24.3)"  "0.3 - 151.4 (23.9)"
[1] "hr="     "2.6e+07"
D45V2, continuous
                   vv
clus                 T2  T3  T4
  4P LOSS MUTATED     2  11   1
  4P LOSS WILD-TYPE 148 195   4
D45V3, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  T2               2               148
  T3              11               195
  T4               1                 4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V4, binary
                   cls
clus                  0   1
  4P LOSS MUTATED     6   8
  4P LOSS WILD-TYPE 257  36
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      6    8
  4P LOSS WILD-TYPE  257   36
   clus
vv  4P LOSS MUTATED 4P LOSS WILD-TYPE
  0               6               257
  1               8                36
[1] 2 2
[1] FALSE
D45V5, binary
                   cls
clus                  0   1
  4P LOSS MUTATED     1  13
  4P LOSS WILD-TYPE  12 337
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      1   13
  4P LOSS WILD-TYPE   12  337
                                        clus
vv                                       4P LOSS MUTATED 4P LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE               1                12
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 13               337
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  4P LOSS MUTATED     3   9   0   1
  4P LOSS WILD-TYPE 240  81   5  10
D45V6, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  R0               3               240
  R1               9                81
  R2               0                 5
  RX               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"
D45V7, continuous
D45V8, continuous
D45V9, continuous
D45V10, continuous
D45V11, continuous
D45V12, continuous
D45V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4P LOSS MUTATED       0                         0     4
  4P LOSS WILD-TYPE     2                         7   142
D45V14, multiclass
                           clus
vv                          4P LOSS MUTATED 4P LOSS WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 7
  WHITE                                   4               142
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(46) Variable = 4Q LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                 0   1
  4Q LOSS MUTATED    10   0
  4Q LOSS WILD-TYPE 345   6
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               10               351 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                0                 6 
$`4Q LOSS MUTATED`
TCGA-CH-5751 TCGA-EJ-A65B TCGA-FC-7961 TCGA-G9-6499 TCGA-HC-A48F TCGA-J9-A52B 
       35.01        17.62        15.42        50.73        22.36        13.87 
TCGA-KK-A59Z TCGA-YL-A8HK TCGA-YL-A8SL TCGA-YL-A9WH 
       61.78        49.02        26.24        14.04 

$`4Q LOSS WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5753 
        1.97        24.03         1.02        13.02        31.00         1.02 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 
        2.04         0.92        44.02        12.00         1.02        23.01 
TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 
        1.02        15.06        24.03         2.04        13.02        15.98 
TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 
       26.99         9.99        32.02        33.01         2.99        29.00 
TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
       27.16        33.11        19.56        13.32        29.79        46.52 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       44.88        26.30        45.73        28.93        30.31        27.19 
TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       23.90        38.93        48.13        36.69        48.53        38.53 
TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 
       36.23        60.23        46.55        47.80        52.27        64.50 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 
       51.88        68.35        43.07        36.66        38.76        39.75 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 
       60.23        41.85        47.87        29.06        27.02        49.02 
TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 
       61.15        83.57        21.80         9.70         9.50         9.37 
TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 
       16.77         7.66        17.52         5.75        27.68         6.28 
TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 
        0.30        23.90        38.37        25.87        25.68        20.55 
TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 
       14.53        14.14        18.15        19.59        17.29         3.75 
TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8474 
       23.05        19.92        64.47        63.98        26.99        10.32 
TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H 
        5.33         4.24        17.49         9.83         3.06         7.53 
TCGA-EJ-A46I TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J 
       21.96        12.92        13.71        18.41         9.14         2.99 
TCGA-EJ-A65M TCGA-FC-7708 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD 
        7.56        28.41        13.45         8.98        17.23        16.24 
TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 
        1.78        41.62        87.35        81.04        67.99        66.67 
TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 
       69.37        55.76        18.21        68.68        49.81        46.16 
TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 
       50.70        49.35        47.15        46.52        47.44        45.30 
TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 
       39.39        44.81         3.32        40.18        39.95        38.01 
TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 
       40.31        26.66        31.50        37.97        45.80        25.15 
TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-7509 TCGA-G9-7510 
       27.29        58.22        56.75        52.87        38.27        38.96 
TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 
       27.91        30.97        35.34        28.18        32.68        26.01 
TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 
       21.14         6.08        30.94         3.68        19.76         5.33 
TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 
        2.93         2.01         2.37        14.47        28.54         0.79 
TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 
       28.60         1.97         1.68         2.37         2.93         1.71 
TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 
        0.72         2.10         2.66         1.74         1.48         1.68 
TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 
        2.07        24.59        26.04         1.97         1.12         3.22 
TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 
       30.51         1.48        17.85        24.56         1.84        19.36 
TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 
       22.42         3.12        23.87         2.17         2.27         1.94 
TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A4ZV 
       17.95        22.32         1.58        15.88         1.15         0.76 
TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP 
        1.78         2.01         2.20         1.61         5.49         2.33 
TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HI-7168 TCGA-HI-7169 
        3.48         1.45         1.25         4.41        78.61        88.24 
TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L 
       82.92        43.69        20.19        12.30        21.76        17.03 
TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S 
       16.04        16.54        16.14        20.52        14.93        17.19 
TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J 
        6.02        13.32        17.36         9.17         9.17        10.19 
TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52C TCGA-J9-A52E 
        6.77        10.39        14.37        20.28         5.85        10.62 
TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 
       93.99        56.28        44.68       115.86        30.02        54.54 
TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 
      151.36        67.59        90.51        49.25       113.33        67.07 
TCGA-KK-A6E8 TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IB TCGA-KK-A8IF 
       58.19        27.62        34.95        22.75         2.73        26.43 
TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 
       20.65         5.19         6.87         9.93        13.15        27.02 
TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN 
       25.08        15.88        18.84         3.19        41.00       114.64 
TCGA-QU-A6IO TCGA-QU-A6IP TCGA-TP-A8TT TCGA-TP-A8TV TCGA-VN-A88I TCGA-VN-A88K 
       47.21        86.14        11.90         8.19         8.84        25.51 
TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q 
       12.95         6.02        15.52        15.81        30.15        32.91 
TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 
       15.09         4.34       106.95        26.47        84.69        94.65 
TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H 
       23.93        75.91        55.56        60.92        66.97        21.80 
TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS 
       48.85        21.53        17.82         5.79        37.18        27.81 
TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX 
        3.91        38.04        48.03         9.04         2.99        25.97 
TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP 
       31.96        31.50        31.96        28.54        30.58        29.23 
TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HL 
       27.09        37.02        39.65        25.48        52.96        38.56 
TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB 
       36.95        71.77        62.14        60.56        16.83        45.50 
TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK 
       41.46        45.14        28.77        47.38        45.86        37.97 
TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WI TCGA-YL-A9WJ 
      106.75        71.34        62.79         7.00        41.39        60.99 
TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX 
       62.37        24.33        49.91        28.34         1.64         4.93 
TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9ND 
        1.12         7.86         6.02 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            13.87              0.30 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            61.78            151.36 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            24.30             23.93 
[1] "13.9 - 61.8 (24.3)" "0.3 - 151.4 (23.9)"
[1] "hr="     "2.5e+07"
D46V2, continuous
                   vv
clus                 T2  T3  T4
  4Q LOSS MUTATED     2   7   1
  4Q LOSS WILD-TYPE 148 199   4
D46V3, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  T2               2               148
  T3               7               199
  T4               1                 4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V4, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED     6   4
  4Q LOSS WILD-TYPE 257  40
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      6    4
  4Q LOSS WILD-TYPE  257   40
   clus
vv  4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  0               6               257
  1               4                40
[1] 2 2
[1] FALSE
D46V5, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED     1   9
  4Q LOSS WILD-TYPE  12 341
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      1    9
  4Q LOSS WILD-TYPE   12  341
                                        clus
vv                                       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE               1                12
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  9               341
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  4Q LOSS MUTATED     3   6   0   0
  4Q LOSS WILD-TYPE 240  84   5  11
D46V6, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  R0               3               240
  R1               6                84
  R2               0                 5
  RX               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"
D46V7, continuous
D46V8, continuous
D46V9, continuous
D46V10, continuous
D46V11, continuous
D46V12, continuous
D46V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4Q LOSS MUTATED       0                         0     3
  4Q LOSS WILD-TYPE     2                         7   143
D46V14, multiclass
                           clus
vv                          4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 7
  WHITE                                   3               143
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(47) Variable = 5P LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                 0   1
  5P LOSS MUTATED     7   0
  5P LOSS WILD-TYPE 348   6
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                7               354 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                0                 6 
$`5P LOSS MUTATED`
TCGA-CH-5751 TCGA-CH-5766 TCGA-HI-7168 TCGA-J9-A52B TCGA-VP-AA1N TCGA-YL-A9WL 
       35.01         1.02        78.61        13.87        17.82        24.33 
TCGA-ZG-A9ND 
        6.02 

$`5P LOSS WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5753 
        1.97        24.03         1.02        13.02        31.00         1.02 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 
        2.04         0.92        44.02        12.00         1.02        23.01 
TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 
       15.06        24.03         2.04        13.02        15.98        26.99 
TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 
        9.99        32.02        33.01         2.99        29.00        27.16 
TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 
       33.11        19.56        13.32        29.79        46.52        44.88 
TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 
       26.30        45.73        28.93        30.31        27.19        23.90 
TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 
       38.93        48.13        36.69        48.53        38.53        36.23 
TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 
       60.23        46.55        47.80        52.27        64.50        51.88 
TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 
       68.35        43.07        36.66        38.76        39.75        60.23 
TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 
       41.85        47.87        29.06        27.02        49.02        61.15 
TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 
       83.57        21.80         9.70         9.50         9.37        16.77 
TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 
        7.66        17.52         5.75        27.68         6.28         0.30 
TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 
       23.90        38.37        25.87        25.68        20.55        14.53 
TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 
       14.14        18.15        19.59        17.29         3.75        23.05 
TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8474 TCGA-EJ-A46B 
       19.92        64.47        63.98        26.99        10.32         5.33 
TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I 
        4.24        17.49         9.83         3.06         7.53        21.96 
TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J 
       17.62        12.92        13.71        18.41         9.14         2.99 
TCGA-EJ-A65M TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V 
        7.56        28.41        15.42        13.45         8.98        17.23 
TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 
       16.24         1.78        41.62        87.35        81.04        67.99 
TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 
       66.67        69.37        55.76        18.21        68.68        49.81 
TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 
       46.16        50.70        49.35        47.15        46.52        47.44 
TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 
       45.30        39.39        44.81         3.32        40.18        39.95 
TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 
       38.01        40.31        26.66        31.50        37.97        45.80 
TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 
       25.15        27.29        58.22        56.75        52.87        50.73 
TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 
       38.27        38.96        27.91        30.97        35.34        28.18 
TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY 
       32.68        26.01        21.14         6.08        30.94         3.68 
TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 
       19.76         5.33         2.93         2.01         2.37        14.47 
TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 
       28.54         0.79        28.60         1.97         1.68         2.37 
TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 
        2.93         1.71         0.72         2.10         2.66         1.74 
TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 
        1.48         1.68         2.07        24.59        26.04         1.97 
TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 
        1.12         3.22        30.51         1.48        17.85        24.56 
TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 
        1.84        19.36        22.42         3.12        23.87         2.17 
TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 
        2.27         1.94        17.95        22.32         1.58        15.88 
TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL 
        1.15        22.36         0.76         1.78         2.01         2.20 
TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX 
        1.61         5.49         2.33         3.48         1.45         1.25 
TCGA-HC-A6HY TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 
        4.41        88.24        82.92        43.69        20.19        12.30 
TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q 
       21.76        17.03        16.04        16.54        16.14        20.52 
TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 
       14.93        17.19         6.02        13.32        17.36         9.17 
TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N 
        9.17        10.19         6.77        10.39        14.37        20.28 
TCGA-J9-A52C TCGA-J9-A52E TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z 
        5.85        10.62        93.99        56.28        44.68        61.78 
TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 
      115.86        30.02        54.54       151.36        67.59        90.51 
TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AZ TCGA-KK-A7B1 
       49.25       113.33        67.07        58.19        27.62        34.95 
TCGA-KK-A7B2 TCGA-KK-A8IB TCGA-KK-A8IF TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z 
       22.75         2.73        26.43        20.65         5.19         6.87 
TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 
        9.93        13.15        27.02        25.08        15.88        18.84 
TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-TP-A8TT 
        3.19        41.00       114.64        47.21        86.14        11.90 
TCGA-TP-A8TV TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N 
        8.19         8.84        25.51        12.95         6.02        15.52 
TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 
       15.81        30.15        32.91        15.09         4.34       106.95 
TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C 
       26.47        84.69        94.65        23.93        75.91        55.56 
TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI 
       60.92        66.97        21.80        48.85        21.53         5.79 
TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK 
       37.18        27.81         3.91        38.04        48.03         9.04 
TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 
        2.99        25.97        31.96        31.50        31.96        28.54 
TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-Y6-A8TL 
       30.58        29.23        27.09        37.02        39.65        25.48 
TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 
       52.96        49.02        38.56        36.95        71.77        62.14 
TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH 
       60.56        16.83        45.50        41.46        45.14        28.77 
TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP 
       47.38        45.86        37.97        26.24       106.75        71.34 
TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK 
       62.79         7.00        14.04        41.39        60.99        62.37 
TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       49.91        28.34         1.64         4.93         1.12         7.86 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             1.02              0.30 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            78.61            151.36 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            17.82             23.98 
[1] "1.0 - 78.6 (17.8)"  "0.3 - 151.4 (24.0)"
[1] "hr="     "9100000"
D47V2, continuous
                   vv
clus                 T2  T3  T4
  5P LOSS MUTATED     0   6   1
  5P LOSS WILD-TYPE 150 200   4
D47V3, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  T2               0               150
  T3               6               200
  T4               1                 4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V4, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     5   2
  5P LOSS WILD-TYPE 258  42
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      5    2
  5P LOSS WILD-TYPE  258   42
   clus
vv  5P LOSS MUTATED 5P LOSS WILD-TYPE
  0               5               258
  1               2                42
[1] 2 2
[1] FALSE
D47V5, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     0   7
  5P LOSS WILD-TYPE  13 343
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      0    7
  5P LOSS WILD-TYPE   13  343
                                        clus
vv                                       5P LOSS MUTATED 5P LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE               0                13
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  7               343
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  5P LOSS MUTATED     4   3   0   0
  5P LOSS WILD-TYPE 239  87   5  11
D47V6, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  R0               4               239
  R1               3                87
  R2               0                 5
  RX               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"
D47V7, continuous
D47V8, continuous
D47V9, continuous
D47V10, continuous
D47V11, continuous
D47V12, continuous
D47V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5P LOSS MUTATED       0                         0     3
  5P LOSS WILD-TYPE     2                         7   143
D47V14, multiclass
                           clus
vv                          5P LOSS MUTATED 5P LOSS WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 7
  WHITE                                   3               143
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(48) Variable = 5Q LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                 0   1
  5Q LOSS MUTATED    12   0
  5Q LOSS WILD-TYPE 343   6
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               12               349 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                0                 6 
$`5Q LOSS MUTATED`
TCGA-CH-5751 TCGA-CH-5761 TCGA-EJ-5507 TCGA-FC-A4JI TCGA-HC-8266 TCGA-HC-A48F 
       35.01         0.92        23.90        13.45         1.15        22.36 
TCGA-HI-7168 TCGA-J9-A52B TCGA-KK-A8IF TCGA-VP-AA1N TCGA-YL-A9WI TCGA-YL-A9WL 
       78.61        13.87        26.43        17.82        41.39        24.33 

$`5Q LOSS WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5753 
        1.97        24.03         1.02        13.02        31.00         1.02 
TCGA-CH-5754 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 
        2.04        44.02        12.00         1.02        23.01         1.02 
TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 
       15.06        24.03         2.04        13.02        15.98        26.99 
TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 
        9.99        32.02        33.01         2.99        29.00        27.16 
TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 
       33.11        19.56        13.32        29.79        46.52        44.88 
TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5508 
       26.30        45.73        28.93        30.31        27.19        38.93 
TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 
       48.13        36.69        48.53        38.53        36.23        60.23 
TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 
       46.55        47.80        52.27        64.50        51.88        68.35 
TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 
       43.07        36.66        38.76        39.75        60.23        41.85 
TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 
       47.87        29.06        27.02        49.02        61.15        83.57 
TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 
       21.80         9.70         9.50         9.37        16.77         7.66 
TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 
       17.52         5.75        27.68         6.28         0.30        23.90 
TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 
       38.37        25.87        25.68        20.55        14.53        14.14 
TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 
       18.15        19.59        17.29         3.75        23.05        19.92 
TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D 
       64.47        63.98        26.99        10.32         5.33         4.24 
TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B 
       17.49         9.83         3.06         7.53        21.96        17.62 
TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M 
       12.92        13.71        18.41         9.14         2.99         7.56 
TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 
       28.41        15.42         8.98        17.23        16.24         1.78 
TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 
       41.62        87.35        81.04        67.99        66.67        69.37 
TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 
       55.76        18.21        68.68        49.81        46.16        50.70 
TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 
       49.35        47.15        46.52        47.44        45.30        39.39 
TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 
       44.81         3.32        40.18        39.95        38.01        40.31 
TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 
       26.66        31.50        37.97        45.80        25.15        27.29 
TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 
       58.22        56.75        52.87        50.73        38.27        38.96 
TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 
       27.91        30.97        35.34        28.18        32.68        26.01 
TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 
       21.14         6.08        30.94         3.68        19.76         5.33 
TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 
        2.93         2.01         2.37        14.47        28.54         0.79 
TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 
       28.60         1.97         1.68         2.37         2.93         1.71 
TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 
        0.72         2.10         2.66         1.74         1.48         1.68 
TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 
        2.07        24.59        26.04         1.97         1.12         3.22 
TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 
       30.51         1.48        17.85        24.56         1.84        19.36 
TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 
       22.42         3.12        23.87         2.17         2.27         1.94 
TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-A4ZV TCGA-HC-A631 
       17.95        22.32         1.58        15.88         0.76         1.78 
TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ 
        2.01         2.20         1.61         5.49         2.33         3.48 
TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
        1.45         1.25         4.41        88.24        82.92        43.69 
TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N 
       20.19        12.30        21.76        17.03        16.04        16.54 
TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 
       16.14        20.52        14.93        17.19         6.02        13.32 
TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L 
       17.36         9.17         9.17        10.19         6.77        10.39 
TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52C TCGA-J9-A52E TCGA-KK-A59V TCGA-KK-A59X 
       14.37        20.28         5.85        10.62        93.99        56.28 
TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 
       44.68        61.78       115.86        30.02        54.54       151.36 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 
       67.59        90.51        49.25       113.33        67.07        58.19 
TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IB TCGA-KK-A8IL TCGA-M7-A71Y 
       27.62        34.95        22.75         2.73        20.65         5.19 
TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 
        6.87         9.93        13.15        27.02        25.08        15.88 
TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP 
       18.84         3.19        41.00       114.64        47.21        86.14 
TCGA-TP-A8TT TCGA-TP-A8TV TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M 
       11.90         8.19         8.84        25.51        12.95         6.02 
TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 
       15.52        15.81        30.15        32.91        15.09         4.34 
TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B 
      106.95        26.47        84.69        94.65        23.93        75.91 
TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K 
       55.56        60.92        66.97        21.80        48.85        21.53 
TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DI 
        5.79        37.18        27.81         3.91        38.04        48.03 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW 
        9.04         2.99        25.97        31.96        31.50        31.96 
TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU 
       28.54        30.58        29.23        27.09        37.02        39.65 
TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO 
       25.48        52.96        49.02        38.56        36.95        71.77 
TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF 
       62.14        60.56        16.83        45.50        41.46        45.14 
TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO 
       28.77        47.38        45.86        37.97        26.24       106.75 
TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WJ TCGA-YL-A9WK 
       71.34        62.79         7.00        14.04        60.99        62.37 
TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       49.91        28.34         1.64         4.93         1.12         7.86 
TCGA-ZG-A9ND 
        6.02 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             0.92              0.30 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            78.61            151.36 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            23.13             24.03 
[1] "0.9 - 78.6 (23.1)"  "0.3 - 151.4 (24.0)"
[1] "hr="     "9300000"
D48V2, continuous
                   vv
clus                 T2  T3  T4
  5Q LOSS MUTATED     1  10   1
  5Q LOSS WILD-TYPE 149 196   4
D48V3, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  T2               1               149
  T3              10               196
  T4               1                 4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V4, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED     7   4
  5Q LOSS WILD-TYPE 256  40
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      7    4
  5Q LOSS WILD-TYPE  256   40
   clus
vv  5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  0               7               256
  1               4                40
[1] 2 2
[1] FALSE
D48V5, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED     0  12
  5Q LOSS WILD-TYPE  13 338
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      0   12
  5Q LOSS WILD-TYPE   13  338
                                        clus
vv                                       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE               0                13
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 12               338
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  5Q LOSS MUTATED     7   5   0   0
  5Q LOSS WILD-TYPE 236  85   5  11
D48V6, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  R0               7               236
  R1               5                85
  R2               0                 5
  RX               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"
D48V7, continuous
D48V8, continuous
D48V9, continuous
D48V10, continuous
D48V11, continuous
D48V12, continuous
D48V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5Q LOSS MUTATED       0                         0     4
  5Q LOSS WILD-TYPE     2                         7   142
D48V14, multiclass
                           clus
vv                          5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 7
  WHITE                                   4               142
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(49) Variable = 6P LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                 0   1
  6P LOSS MUTATED    15   0
  6P LOSS WILD-TYPE 340   6
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               15               346 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                0                 6 
$`6P LOSS MUTATED`
TCGA-EJ-5507 TCGA-EJ-5511 TCGA-EJ-5518 TCGA-EJ-7784 TCGA-HC-7213 TCGA-HC-7821 
       23.90        48.53        52.27        25.68         1.97         1.84 
TCGA-HC-A48F TCGA-HC-A632 TCGA-J9-A52B TCGA-VP-AA1N TCGA-YL-A8HO TCGA-YL-A8SQ 
       22.36         2.01        13.87        17.82        71.77        62.79 
TCGA-YL-A9WH TCGA-YL-A9WI TCGA-ZG-A8QW 
       14.04        41.39         1.64 

$`6P LOSS WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 
        1.02         2.04         0.92        44.02        12.00         1.02 
TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 
       23.01         1.02        15.06        24.03         2.04        13.02 
TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 
       15.98        26.99         9.99        32.02        33.01         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        27.16        33.11        19.56        13.32        29.79 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        26.30        45.73        28.93        30.31 
TCGA-EJ-5506 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5512 TCGA-EJ-5514 
       27.19        38.93        48.13        36.69        38.53        36.23 
TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 
       60.23        46.55        47.80        64.50        51.88        68.35 
TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 
       43.07        36.66        38.76        39.75        60.23        41.85 
TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 
       47.87        29.06        27.02        49.02        61.15        83.57 
TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 
       21.80         9.70         9.50         9.37        16.77         7.66 
TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 
       17.52         5.75        27.68         6.28         0.30        23.90 
TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 
       38.37        25.87        20.55        14.53        14.14        18.15 
TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 
       19.59        17.29         3.75        23.05        19.92        64.47 
TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E 
       63.98        26.99        10.32         5.33         4.24        17.49 
TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D 
        9.83         3.06         7.53        21.96        17.62        12.92 
TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-FC-7708 
       13.71        18.41         9.14         2.99         7.56        28.41 
TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 
       15.42        13.45         8.98        17.23        16.24         1.78 
TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 
       41.62        87.35        81.04        67.99        66.67        69.37 
TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 
       55.76        18.21        68.68        49.81        46.16        50.70 
TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 
       49.35        47.15        46.52        47.44        45.30        39.39 
TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 
       44.81         3.32        40.18        39.95        38.01        40.31 
TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 
       26.66        31.50        37.97        45.80        25.15        27.29 
TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 
       58.22        56.75        52.87        50.73        38.27        38.96 
TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 
       27.91        30.97        35.34        28.18        32.68        26.01 
TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 
       21.14         6.08        30.94         3.68        19.76         5.33 
TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 
        2.93         2.01         2.37        14.47        28.54         0.79 
TCGA-HC-7212 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 
       28.60         1.68         2.37         2.93         1.71         0.72 
TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 
        2.10         2.66         1.74         1.48         1.68         2.07 
TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 
       24.59        26.04         1.97         1.12         3.22        30.51 
TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 
        1.48        17.85        24.56        19.36        22.42         3.12 
TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 
       23.87         2.17         2.27         1.94        17.95        22.32 
TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A6AL 
        1.58        15.88         1.15         0.76         1.78         2.20 
TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX 
        1.61         5.49         2.33         3.48         1.45         1.25 
TCGA-HC-A6HY TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 
        4.41        78.61        88.24        82.92        43.69        20.19 
TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O 
       12.30        21.76        17.03        16.04        16.54        16.14 
TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 
       20.52        14.93        17.19         6.02        13.32        17.36 
TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M 
        9.17         9.17        10.19         6.77        10.39        14.37 
TCGA-J4-A83N TCGA-J9-A52C TCGA-J9-A52E TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y 
       20.28         5.85        10.62        93.99        56.28        44.68 
TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 
       61.78       115.86        30.02        54.54       151.36        67.59 
TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AZ 
       90.51        49.25       113.33        67.07        58.19        27.62 
TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IB TCGA-KK-A8IF TCGA-KK-A8IL TCGA-M7-A71Y 
       34.95        22.75         2.73        26.43        20.65         5.19 
TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 
        6.87         9.93        13.15        27.02        25.08        15.88 
TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP 
       18.84         3.19        41.00       114.64        47.21        86.14 
TCGA-TP-A8TT TCGA-TP-A8TV TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M 
       11.90         8.19         8.84        25.51        12.95         6.02 
TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 
       15.52        15.81        30.15        32.91        15.09         4.34 
TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B 
      106.95        26.47        84.69        94.65        23.93        75.91 
TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K 
       55.56        60.92        66.97        21.80        48.85        21.53 
TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DI 
        5.79        37.18        27.81         3.91        38.04        48.03 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW 
        9.04         2.99        25.97        31.96        31.50        31.96 
TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU 
       28.54        30.58        29.23        27.09        37.02        39.65 
TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8S8 
       25.48        52.96        49.02        38.56        36.95        62.14 
TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH 
       60.56        16.83        45.50        41.46        45.14        28.77 
TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP 
       47.38        45.86        37.97        26.24       106.75        71.34 
TCGA-YL-A8SR TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY 
        7.00        60.99        62.37        24.33        49.91        28.34 
TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9ND 
        4.93         1.12         7.86         6.02 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             1.64              0.30 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            71.77            151.36 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            22.36             24.03 
[1] "1.6 - 71.8 (22.4)"  "0.3 - 151.4 (24.0)"
[1] "hr="     "2.6e+07"
D49V2, continuous
                   vv
clus                 T2  T3  T4
  6P LOSS MUTATED     2  12   1
  6P LOSS WILD-TYPE 148 194   4
D49V3, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  T2               2               148
  T3              12               194
  T4               1                 4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V4, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     9   6
  6P LOSS WILD-TYPE 254  38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      9    6
  6P LOSS WILD-TYPE  254   38
   clus
vv  6P LOSS MUTATED 6P LOSS WILD-TYPE
  0               9               254
  1               6                38
[1] 2 2
[1] FALSE
D49V5, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     0  15
  6P LOSS WILD-TYPE  13 335
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      0   15
  6P LOSS WILD-TYPE   13  335
                                        clus
vv                                       6P LOSS MUTATED 6P LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE               0                13
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 15               335
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  6P LOSS MUTATED     7   7   0   0
  6P LOSS WILD-TYPE 236  83   5  11
D49V6, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  R0               7               236
  R1               7                83
  R2               0                 5
  RX               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"
D49V7, continuous
D49V8, continuous
D49V9, continuous
D49V10, continuous
D49V11, continuous
D49V12, continuous
D49V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6P LOSS MUTATED       0                         1     5
  6P LOSS WILD-TYPE     2                         6   141
D49V14, multiclass
                           clus
vv                          6P LOSS MUTATED 6P LOSS WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               1                 6
  WHITE                                   5               141
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(50) Variable = 6Q LOSS MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                 0   1
  6Q LOSS MUTATED    28   1
  6Q LOSS WILD-TYPE 327   5
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               29               332 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                1                 5 
$`6Q LOSS MUTATED`
TCGA-CH-5753 TCGA-EJ-5507 TCGA-EJ-5511 TCGA-EJ-5518 TCGA-EJ-7782 TCGA-EJ-7784 
        1.02        23.90        48.53        52.27        38.37        25.68 
TCGA-EJ-7786 TCGA-FC-7961 TCGA-G9-A9S0 TCGA-HC-7078 TCGA-HC-7213 TCGA-HC-7821 
       14.53        15.42        26.01         5.33         1.97         1.84 
TCGA-HC-A48F TCGA-HC-A632 TCGA-J9-A52B TCGA-J9-A52E TCGA-KK-A6E1 TCGA-VN-A88O 
       22.36         2.01        13.87        10.62        54.54        15.81 
TCGA-VP-AA1N TCGA-X4-A8KQ TCGA-XJ-A9DI TCGA-XK-AAIV TCGA-YL-A8HO TCGA-YL-A8SQ 
       17.82        37.18        48.03        31.50        71.77        62.79 
TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WK TCGA-ZG-A8QW TCGA-ZG-A9ND 
       14.04        41.39        62.37         1.64         6.02 

$`6Q LOSS WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 
        2.04         0.92        44.02        12.00         1.02        23.01 
TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 
        1.02        15.06        24.03         2.04        13.02        15.98 
TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 
       26.99         9.99        32.02        33.01         2.99        29.00 
TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
       27.16        33.11        19.56        13.32        29.79        46.52 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       44.88        26.30        45.73        28.93        30.31        27.19 
TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 
       38.93        48.13        36.69        38.53        36.23        60.23 
TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 
       46.55        47.80        64.50        51.88        68.35        43.07 
TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 
       36.66        38.76        39.75        60.23        41.85        47.87 
TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 
       29.06        27.02        49.02        61.15        83.57        21.80 
TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 
        9.70         9.50         9.37        16.77         7.66        17.52 
TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7783 
        5.75        27.68         6.28         0.30        23.90        25.87 
TCGA-EJ-7785 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 
       20.55        14.14        18.15        19.59        17.29         3.75 
TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8474 
       23.05        19.92        64.47        63.98        26.99        10.32 
TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H 
        5.33         4.24        17.49         9.83         3.06         7.53 
TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G 
       21.96        17.62        12.92        13.71        18.41         9.14 
TCGA-EJ-A65J TCGA-EJ-A65M TCGA-FC-7708 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V 
        2.99         7.56        28.41        13.45         8.98        17.23 
TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 
       16.24         1.78        41.62        87.35        81.04        67.99 
TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 
       66.67        69.37        55.76        18.21        68.68        49.81 
TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 
       46.16        50.70        49.35        47.15        46.52        47.44 
TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 
       45.30        39.39        44.81         3.32        40.18        39.95 
TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 
       38.01        40.31        26.66        31.50        37.97        45.80 
TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 
       25.15        27.29        58.22        56.75        52.87        50.73 
TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 
       38.27        38.96        27.91        30.97        35.34        28.18 
TCGA-G9-7525 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 
       32.68        21.14         6.08        30.94         3.68        19.76 
TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 
        2.93         2.01         2.37        14.47        28.54         0.79 
TCGA-HC-7212 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 
       28.60         1.68         2.37         2.93         1.71         0.72 
TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 
        2.10         2.66         1.74         1.48         1.68         2.07 
TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 
       24.59        26.04         1.97         1.12         3.22        30.51 
TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 
        1.48        17.85        24.56        19.36        22.42         3.12 
TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 
       23.87         2.17         2.27         1.94        17.95        22.32 
TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A6AL 
        1.58        15.88         1.15         0.76         1.78         2.20 
TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX 
        1.61         5.49         2.33         3.48         1.45         1.25 
TCGA-HC-A6HY TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 
        4.41        78.61        88.24        82.92        43.69        20.19 
TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O 
       12.30        21.76        17.03        16.04        16.54        16.14 
TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 
       20.52        14.93        17.19         6.02        13.32        17.36 
TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M 
        9.17         9.17        10.19         6.77        10.39        14.37 
TCGA-J4-A83N TCGA-J9-A52C TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z 
       20.28         5.85        93.99        56.28        44.68        61.78 
TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 
      115.86        30.02       151.36        67.59        90.51        49.25 
TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 
      113.33        67.07        58.19        27.62        34.95        22.75 
TCGA-KK-A8IB TCGA-KK-A8IF TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 
        2.73        26.43        20.65         5.19         6.87         9.93 
TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL 
       13.15        27.02        25.08        15.88        18.84         3.19 
TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-TP-A8TT TCGA-TP-A8TV 
       41.00       114.64        47.21        86.14        11.90         8.19 
TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88P 
        8.84        25.51        12.95         6.02        15.52        30.15 
TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 
       32.91        15.09         4.34       106.95        26.47        84.69 
TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E 
       94.65        23.93        75.91        55.56        60.92        66.97 
TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KS TCGA-XA-A8JR 
       21.80        48.85        21.53         5.79        27.81         3.91 
TCGA-XJ-A83G TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIW 
       38.04         9.04         2.99        25.97        31.96        31.96 
TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU 
       28.54        30.58        29.23        27.09        37.02        39.65 
TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8S8 
       25.48        52.96        49.02        38.56        36.95        62.14 
TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH 
       60.56        16.83        45.50        41.46        45.14        28.77 
TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP 
       47.38        45.86        37.97        26.24       106.75        71.34 
TCGA-YL-A8SR TCGA-YL-A9WJ TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QX 
        7.00        60.99        24.33        49.91        28.34         4.93 
TCGA-ZG-A8QY TCGA-ZG-A8QZ 
        1.12         7.86 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             1.02              0.30 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            71.77            151.36 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            22.36             24.03 
[1] "1.0 - 71.8 (22.4)"  "0.3 - 151.4 (24.0)"
[1] "hr=" "2.4"
D50V2, continuous
                   vv
clus                 T2  T3  T4
  6Q LOSS MUTATED     5  23   1
  6Q LOSS WILD-TYPE 145 183   4
D50V3, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T2               5               145
  T3              23               183
  T4               1                 4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V4, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    19  10
  6Q LOSS WILD-TYPE 244  34
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     19   10
  6Q LOSS WILD-TYPE  244   34
   clus
vv  6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  0              19               244
  1              10                34
[1] 2 2
[1] FALSE
D50V5, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED     1  28
  6Q LOSS WILD-TYPE  12 322
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      1   28
  6Q LOSS WILD-TYPE   12  322
                                        clus
vv                                       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE               1                12
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 28               322
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  6Q LOSS MUTATED    14  11   0   2
  6Q LOSS WILD-TYPE 229  79   5   9
D50V6, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  R0              14               229
  R1              11                79
  R2               0                 5
  RX               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"
D50V7, continuous
D50V8, continuous
D50V9, continuous
D50V10, continuous
D50V11, continuous
D50V12, continuous
D50V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6Q LOSS MUTATED       0                         2     9
  6Q LOSS WILD-TYPE     2                         5   137
D50V14, multiclass
                           clus
vv                          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               2                 5
  WHITE                                   9               137
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(51) Variable = 8P LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                 0   1
  8P LOSS MUTATED   117   2
  8P LOSS WILD-TYPE 238   4
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              119               242 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                2                 4 
$`8P LOSS MUTATED`
TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 TCGA-CH-5739 TCGA-CH-5744 
       22.06        33.96         3.68        25.35        22.06         1.97 
TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 
        1.02         2.04         1.02        23.01         1.02        15.06 
TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5790 TCGA-CH-5791 TCGA-EJ-5499 TCGA-EJ-5501 
       13.02        26.99        32.02        33.01        46.52        44.88 
TCGA-EJ-5507 TCGA-EJ-5511 TCGA-EJ-5518 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5532 
       23.90        48.53        52.27        39.75        60.23        47.87 
TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7314 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7330 
       29.06        27.02         9.70         7.66        17.52         6.28 
TCGA-EJ-7781 TCGA-EJ-7783 TCGA-EJ-7788 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8474 
       23.90        25.87        14.14        63.98        26.99        10.32 
TCGA-EJ-A65D TCGA-EJ-A65E TCGA-FC-7708 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6339 
       12.92        13.71        28.41        87.35        81.04        69.37 
TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6354 TCGA-G9-6361 TCGA-G9-6364 TCGA-G9-6369 
       55.76        18.21        49.35        46.52        39.39        39.95 
TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6384 TCGA-G9-6494 TCGA-G9-6496 
       40.31        26.66        31.50        25.15        58.22        56.75 
TCGA-G9-7509 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-HC-7213 TCGA-HC-7231 
       38.27        26.01        21.14         6.08         1.97         2.37 
TCGA-HC-7744 TCGA-HC-7819 TCGA-HC-7821 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 
        1.68        17.85         1.84        22.42         3.12        23.87 
TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-A48F TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN 
       22.32         1.58        22.36         2.01         2.20         1.61 
TCGA-HC-A6AQ TCGA-HI-7168 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-A67M TCGA-J4-A67N 
        3.48        78.61        82.92        43.69        16.04        16.54 
TCGA-J4-A67S TCGA-J4-A83I TCGA-J4-A83N TCGA-J9-A52E TCGA-KK-A59Y TCGA-KK-A6E1 
       17.19         9.17        20.28        10.62        44.68        54.54 
TCGA-KK-A6E5 TCGA-KK-A7AZ TCGA-KK-A8IF TCGA-M7-A71Z TCGA-M7-A725 TCGA-QU-A6IO 
       49.25        27.62        26.43         6.87        18.84        47.21 
TCGA-TP-A8TV TCGA-VN-A88K TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88R TCGA-VP-A875 
        8.19        25.51        15.81        30.15        15.09        26.47 
TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87J TCGA-VP-A87K TCGA-XJ-A83G TCGA-XJ-A9DQ 
       75.91        55.56        48.85        21.53        38.04         2.99 
TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAJ3 TCGA-XK-AAJP TCGA-XK-AAJR TCGA-YL-A8HK 
       31.96        31.50        28.54        29.23        27.09        49.02 
TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SJ TCGA-YL-A8SL TCGA-YL-A8SP TCGA-YL-A8SR 
       41.46        45.14        45.86        26.24        71.34         7.00 
TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WL TCGA-YL-A9WX TCGA-ZG-A9ND 
       14.04        41.39        24.33        49.91         6.02 

$`8P LOSS WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5740 TCGA-CH-5741 
       20.42        43.79         2.99         6.97         1.02        12.99 
TCGA-CH-5743 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
       13.97        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5772 
        0.92        44.02        12.00        24.03         2.04        15.98 
TCGA-CH-5789 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 
        9.99         2.99        29.00        27.16        33.11        19.56 
TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       13.32        29.79        26.30        45.73        28.93        30.31 
TCGA-EJ-5506 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5512 TCGA-EJ-5514 
       27.19        38.93        48.13        36.69        38.53        36.23 
TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 
       60.23        46.55        47.80        64.50        51.88        68.35 
TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5531 TCGA-EJ-7123 TCGA-EJ-7125 
       43.07        36.66        38.76        41.85        49.02        61.15 
TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7327 
       83.57        21.80         9.50         9.37        16.77         5.75 
TCGA-EJ-7328 TCGA-EJ-7331 TCGA-EJ-7782 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 
       27.68         0.30        38.37        25.68        20.55        14.53 
TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 
       18.15        19.59        17.29         3.75        23.05        19.92 
TCGA-EJ-8468 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G 
       64.47         5.33         4.24        17.49         9.83         3.06 
TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J 
        7.53        21.96        17.62        18.41         9.14         2.99 
TCGA-EJ-A65M TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD 
        7.56        15.42        13.45         8.98        17.23        16.24 
TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6347 TCGA-G9-6348 
        1.78        41.62        67.99        66.67        68.68        49.81 
TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6356 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6365 
       46.16        50.70        47.15        47.44        45.30        44.81 
TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6370 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6385 
        3.32        40.18        38.01        37.97        45.80        27.29 
TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 
       52.87        50.73        38.96        27.91        30.97        35.34 
TCGA-G9-7523 TCGA-G9-7525 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 
       28.18        32.68        30.94         3.68        19.76         5.33 
TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 
        2.93         2.01         2.37        14.47        28.54         0.79 
TCGA-HC-7212 TCGA-HC-7230 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 
       28.60         1.68         2.93         1.71         0.72         2.10 
TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 
        2.66         1.74         1.48         2.07        24.59        26.04 
TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7820 
        1.97         1.12         3.22        30.51         1.48        24.56 
TCGA-HC-8213 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8265 
       19.36         2.17         2.27         1.94        17.95        15.88 
TCGA-HC-8266 TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AS 
        1.15         0.76         1.78         5.49         2.33         1.45 
TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HI-7169 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K 
        1.25         4.41        88.24        20.19        12.30        21.76 
TCGA-J4-A67L TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67T TCGA-J4-A6G1 
       17.03        16.14        20.52        14.93         6.02        13.32 
TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M 
       17.36         9.17        10.19         6.77        10.39        14.37 
TCGA-J9-A52B TCGA-J9-A52C TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Z TCGA-KK-A6DY 
       13.87         5.85        93.99        56.28        61.78       115.86 
TCGA-KK-A6E0 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E6 TCGA-KK-A6E7 
       30.02       151.36        67.59        90.51       113.33        67.07 
TCGA-KK-A6E8 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IB TCGA-KK-A8IL TCGA-M7-A71Y 
       58.19        34.95        22.75         2.73        20.65         5.19 
TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-QU-A6IL 
        9.93        13.15        27.02        25.08        15.88         3.19 
TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IP TCGA-TP-A8TT TCGA-VN-A88I TCGA-VN-A88L 
       41.00       114.64        86.14        11.90         8.84        12.95 
TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88Q TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A876 
        6.02        15.52        32.91         4.34       106.95        84.69 
TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-AA1N 
       94.65        23.93        60.92        66.97        21.80        17.82 
TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A9DI TCGA-XJ-A9DK 
        5.79        37.18        27.81         3.91        48.03         9.04 
TCGA-XJ-A9DX TCGA-XK-AAIW TCGA-XK-AAJA TCGA-XK-AAJT TCGA-XK-AAJU TCGA-Y6-A8TL 
       25.97        31.96        30.58        37.02        39.65        25.48 
TCGA-YL-A8HJ TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 
       52.96        38.56        36.95        71.77        62.14        60.56 
TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SK TCGA-YL-A8SO 
       16.83        45.50        28.77        47.38        37.97       106.75 
TCGA-YL-A8SQ TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX 
       62.79        60.99        62.37        28.34         1.64         4.93 
TCGA-ZG-A8QY TCGA-ZG-A8QZ 
        1.12         7.86 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             1.02              0.30 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            87.35            151.36 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            25.87             21.80 
[1] "1.0 - 87.3 (25.9)"  "0.3 - 151.4 (21.8)"
[1] "hr=" "1"  
D51V2, continuous
                   vv
clus                 T2  T3  T4
  8P LOSS MUTATED    35  84   2
  8P LOSS WILD-TYPE 115 122   3
D51V3, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  T2              35               115
  T3              84               122
  T4               2                 3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V4, binary
                   cls
clus                  0   1
  8P LOSS MUTATED    88  19
  8P LOSS WILD-TYPE 175  25
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     88   19
  8P LOSS WILD-TYPE  175   25
   clus
vv  8P LOSS MUTATED 8P LOSS WILD-TYPE
  0              88               175
  1              19                25
[1] 2 2
[1] FALSE
D51V5, binary
                   cls
clus                  0   1
  8P LOSS MUTATED     4 117
  8P LOSS WILD-TYPE   9 233
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      4  117
  8P LOSS WILD-TYPE    9  233
                                        clus
vv                                       8P LOSS MUTATED 8P LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE               4                 9
  PROSTATE ADENOCARCINOMA ACINAR TYPE                117               233
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  8P LOSS MUTATED    83  28   2   4
  8P LOSS WILD-TYPE 160  62   3   7
D51V6, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  R0              83               160
  R1              28                62
  R2               2                 3
  RX               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"
D51V7, continuous
D51V8, continuous
D51V9, continuous
D51V10, continuous
D51V11, continuous
D51V12, continuous
D51V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8P LOSS MUTATED       2                         3    47
  8P LOSS WILD-TYPE     0                         4    99
D51V14, multiclass
                           clus
vv                          8P LOSS MUTATED 8P LOSS WILD-TYPE
  ASIAN                                   2                 0
  BLACK OR AFRICAN AMERICAN               3                 4
  WHITE                                  47                99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(52) Variable = 8Q LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                 0   1
  8Q LOSS MUTATED    17   2
  8Q LOSS WILD-TYPE 338   4
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               19               342 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                2                 4 
$`8Q LOSS MUTATED`
TCGA-CH-5739 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5764 TCGA-EJ-5507 TCGA-EJ-5527 
       22.06         1.02         2.04         1.02        23.90        39.75 
TCGA-G9-6494 TCGA-G9-7509 TCGA-G9-A9S0 TCGA-HC-7744 TCGA-HI-7168 TCGA-HI-7171 
       58.22        38.27        26.01         1.68        78.61        43.69 
TCGA-J9-A52E TCGA-KK-A59Y TCGA-KK-A8IF TCGA-TP-A8TV TCGA-YL-A8SF TCGA-YL-A9WH 
       10.62        44.68        26.43         8.19        45.14        14.04 
TCGA-YL-A9WI 
       41.39 

$`8Q LOSS WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 
        2.99         6.97         1.02        12.99        13.97         1.97 
TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5761 
       24.03         1.02        13.02        35.01        31.00         0.92 
TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 
       44.02        12.00        23.01         1.02        15.06        24.03 
TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 
        2.04        13.02        15.98        26.99         9.99        32.02 
TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 
       33.01         2.99        29.00        27.16        33.11        19.56 
TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 
       13.32        29.79        46.52        44.88        26.30        45.73 
TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 
       28.93        30.31        27.19        38.93        48.13        36.69 
TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 
       48.53        38.53        36.23        60.23        46.55        47.80 
TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 
       52.27        64.50        51.88        68.35        43.07        36.66 
TCGA-EJ-5526 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 
       38.76        60.23        41.85        47.87        29.06        27.02 
TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 
       49.02        61.15        83.57        21.80         9.70         9.50 
TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 
        9.37        16.77         7.66        17.52         5.75        27.68 
TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 
        6.28         0.30        23.90        38.37        25.87        25.68 
TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 
       20.55        14.53        14.14        18.15        19.59        17.29 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 
        3.75        23.05        19.92        64.47        63.98        26.99 
TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G 
       10.32         5.33         4.24        17.49         9.83         3.06 
TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F 
        7.53        21.96        17.62        12.92        13.71        18.41 
TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI 
        9.14         2.99         7.56        28.41        15.42        13.45 
TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 
        8.98        17.23        16.24         1.78        41.62        87.35 
TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 
       81.04        67.99        66.67        69.37        55.76        18.21 
TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 
       68.68        49.81        46.16        50.70        49.35        47.15 
TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 
       46.52        47.44        45.30        39.39        44.81         3.32 
TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 
       40.18        39.95        38.01        40.31        26.66        31.50 
TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6496 TCGA-G9-6498 
       37.97        45.80        25.15        27.29        56.75        52.87 
TCGA-G9-6499 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 
       50.73        38.96        27.91        30.97        35.34        28.18 
TCGA-G9-7525 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 
       32.68        21.14         6.08        30.94         3.68        19.76 
TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 
        5.33         2.93         2.01         2.37        14.47        28.54 
TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 
        0.79        28.60         1.97         1.68         2.37         2.93 
TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 
        1.71         0.72         2.10         2.66         1.74         1.48 
TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 
        2.07        24.59        26.04         1.97         1.12         3.22 
TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 
       30.51         1.48        17.85        24.56         1.84        19.36 
TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 
       22.42         3.12        23.87         2.17         2.27         1.94 
TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F 
       17.95        22.32         1.58        15.88         1.15        22.36 
TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO 
        0.76         1.78         2.01         2.20         1.61         5.49 
TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HI-7169 
        2.33         3.48         1.45         1.25         4.41        88.24 
TCGA-HI-7170 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M 
       82.92        20.19        12.30        21.76        17.03        16.04 
TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T 
       16.54        16.14        20.52        14.93        17.19         6.02 
TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K 
       13.32        17.36         9.17         9.17        10.19         6.77 
TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52C TCGA-KK-A59V 
       10.39        14.37        20.28        13.87         5.85        93.99 
TCGA-KK-A59X TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 
       56.28        61.78       115.86        30.02        54.54       151.36 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 
       67.59        90.51        49.25       113.33        67.07        58.19 
TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IB TCGA-KK-A8IL TCGA-M7-A71Y 
       27.62        34.95        22.75         2.73        20.65         5.19 
TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 
        6.87         9.93        13.15        27.02        25.08        15.88 
TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP 
       18.84         3.19        41.00       114.64        47.21        86.14 
TCGA-TP-A8TT TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N 
       11.90         8.84        25.51        12.95         6.02        15.52 
TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 
       15.81        30.15        32.91        15.09         4.34       106.95 
TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C 
       26.47        84.69        94.65        23.93        75.91        55.56 
TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N 
       60.92        66.97        21.80        48.85        21.53        17.82 
TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DI 
        5.79        37.18        27.81         3.91        38.04        48.03 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW 
        9.04         2.99        25.97        31.96        31.50        31.96 
TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU 
       28.54        30.58        29.23        27.09        37.02        39.65 
TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO 
       25.48        52.96        49.02        38.56        36.95        71.77 
TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SH 
       62.14        60.56        16.83        45.50        41.46        28.77 
TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP 
       47.38        45.86        37.97        26.24       106.75        71.34 
TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX 
       62.79         7.00        60.99        62.37        24.33        49.91 
TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9ND 
       28.34         1.64         4.93         1.12         7.86         6.02 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             1.02              0.30 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            78.61            151.36 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
           26.010            23.915 
[1] "1.0 - 78.6 (26.0)"  "0.3 - 151.4 (23.9)"
[1] "hr=" "9.1"
D52V2, continuous
                   vv
clus                 T2  T3  T4
  8Q LOSS MUTATED     2  16   1
  8Q LOSS WILD-TYPE 148 190   4
D52V3, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  T2               2               148
  T3              16               190
  T4               1                 4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V4, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    11   7
  8Q LOSS WILD-TYPE 252  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     11    7
  8Q LOSS WILD-TYPE  252   37
   clus
vv  8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  0              11               252
  1               7                37
[1] 2 2
[1] FALSE
D52V5, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     0  19
  8Q LOSS WILD-TYPE  13 331
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      0   19
  8Q LOSS WILD-TYPE   13  331
                                        clus
vv                                       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE               0                13
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 19               331
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  8Q LOSS MUTATED     9   9   0   1
  8Q LOSS WILD-TYPE 234  81   5  10
D52V6, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  R0               9               234
  R1               9                81
  R2               0                 5
  RX               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"
D52V7, continuous
D52V8, continuous
D52V9, continuous
D52V10, continuous
D52V11, continuous
D52V12, continuous
D52V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8Q LOSS MUTATED       0                         0    10
  8Q LOSS WILD-TYPE     2                         7   136
D52V14, multiclass
                           clus
vv                          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 7
  WHITE                                  10               136
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(53) Variable = 9P LOSS MUTATION ANALYSIS
D53V1, survival
                   sevent
clus2                 0   1
  9P LOSS MUTATED    15   0
  9P LOSS WILD-TYPE 340   6
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               15               346 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                0                 6 
$`9P LOSS MUTATED`
TCGA-CH-5751 TCGA-EJ-5507 TCGA-EJ-5521 TCGA-EJ-7781 TCGA-FC-7961 TCGA-G9-7521 
       35.01        23.90        51.88        23.90        15.42        30.97 
TCGA-HC-8216 TCGA-HC-A631 TCGA-HI-7168 TCGA-J4-A67L TCGA-J9-A52E TCGA-KK-A6DY 
       22.42         1.78        78.61        17.03        10.62       115.86 
TCGA-KK-A8IB TCGA-VP-A87D TCGA-YL-A9WY 
        2.73        60.92        28.34 

$`9P LOSS WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5753 
        1.97        24.03         1.02        13.02        31.00         1.02 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 
        2.04         0.92        44.02        12.00         1.02        23.01 
TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 
        1.02        15.06        24.03         2.04        13.02        15.98 
TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 
       26.99         9.99        32.02        33.01         2.99        29.00 
TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
       27.16        33.11        19.56        13.32        29.79        46.52 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       44.88        26.30        45.73        28.93        30.31        27.19 
TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 
       38.93        48.13        36.69        48.53        38.53        36.23 
TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5522 
       60.23        46.55        47.80        52.27        64.50        68.35 
TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 
       43.07        36.66        38.76        39.75        60.23        41.85 
TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 
       47.87        29.06        27.02        49.02        61.15        83.57 
TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 
       21.80         9.70         9.50         9.37        16.77         7.66 
TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7782 
       17.52         5.75        27.68         6.28         0.30        38.37 
TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 
       25.87        25.68        20.55        14.53        14.14        18.15 
TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 
       19.59        17.29         3.75        23.05        19.92        64.47 
TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E 
       63.98        26.99        10.32         5.33         4.24        17.49 
TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D 
        9.83         3.06         7.53        21.96        17.62        12.92 
TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-FC-7708 
       13.71        18.41         9.14         2.99         7.56        28.41 
TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 
       13.45         8.98        17.23        16.24         1.78        41.62 
TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 
       87.35        81.04        67.99        66.67        69.37        55.76 
TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 
       18.21        68.68        49.81        46.16        50.70        49.35 
TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 
       47.15        46.52        47.44        45.30        39.39        44.81 
TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 
        3.32        40.18        39.95        38.01        40.31        26.66 
TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 
       31.50        37.97        45.80        25.15        27.29        58.22 
TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 
       56.75        52.87        50.73        38.27        38.96        27.91 
TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 
       35.34        28.18        32.68        26.01        21.14         6.08 
TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 
       30.94         3.68        19.76         5.33         2.93         2.01 
TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 
        2.37        14.47        28.54         0.79        28.60         1.97 
TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 
        1.68         2.37         2.93         1.71         0.72         2.10 
TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 
        2.66         1.74         1.48         1.68         2.07        24.59 
TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 
       26.04         1.97         1.12         3.22        30.51         1.48 
TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8256 TCGA-HC-8257 
       17.85        24.56         1.84        19.36         3.12        23.87 
TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 
        2.17         2.27         1.94        17.95        22.32         1.58 
TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A632 TCGA-HC-A6AL 
       15.88         1.15        22.36         0.76         2.01         2.20 
TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX 
        1.61         5.49         2.33         3.48         1.45         1.25 
TCGA-HC-A6HY TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 
        4.41        88.24        82.92        43.69        20.19        12.30 
TCGA-J4-A67K TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R 
       21.76        16.04        16.54        16.14        20.52        14.93 
TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I 
       17.19         6.02        13.32        17.36         9.17         9.17 
TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B 
       10.19         6.77        10.39        14.37        20.28        13.87 
TCGA-J9-A52C TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6E0 
        5.85        93.99        56.28        44.68        61.78        30.02 
TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 
       54.54       151.36        67.59        90.51        49.25       113.33 
TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IF 
       67.07        58.19        27.62        34.95        22.75        26.43 
TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 
       20.65         5.19         6.87         9.93        13.15        27.02 
TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN 
       25.08        15.88        18.84         3.19        41.00       114.64 
TCGA-QU-A6IO TCGA-QU-A6IP TCGA-TP-A8TT TCGA-TP-A8TV TCGA-VN-A88I TCGA-VN-A88K 
       47.21        86.14        11.90         8.19         8.84        25.51 
TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q 
       12.95         6.02        15.52        15.81        30.15        32.91 
TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 
       15.09         4.34       106.95        26.47        84.69        94.65 
TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J 
       23.93        75.91        55.56        66.97        21.80        48.85 
TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR 
       21.53        17.82         5.79        37.18        27.81         3.91 
TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR 
       38.04        48.03         9.04         2.99        25.97        31.96 
TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR 
       31.50        31.96        28.54        30.58        29.23        27.09 
TCGA-XK-AAJT TCGA-XK-AAJU TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL 
       37.02        39.65        25.48        52.96        49.02        38.56 
TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB 
       36.95        71.77        62.14        60.56        16.83        45.50 
TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK 
       41.46        45.14        28.77        47.38        45.86        37.97 
TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH 
       26.24       106.75        71.34        62.79         7.00        14.04 
TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-ZG-A8QW 
       41.39        60.99        62.37        24.33        49.91         1.64 
TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9ND 
        4.93         1.12         7.86         6.02 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             1.78              0.30 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           115.86            151.36 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            23.90             23.98 
[1] "1.8 - 115.9 (23.9)" "0.3 - 151.4 (24.0)"
[1] "hr="     "2.6e+07"
D53V2, continuous
                   vv
clus                 T2  T3  T4
  9P LOSS MUTATED     3  11   1
  9P LOSS WILD-TYPE 147 195   4
D53V3, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  T2               3               147
  T3              11               195
  T4               1                 4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V4, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    10   5
  9P LOSS WILD-TYPE 253  39
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     10    5
  9P LOSS WILD-TYPE  253   39
   clus
vv  9P LOSS MUTATED 9P LOSS WILD-TYPE
  0              10               253
  1               5                39
[1] 2 2
[1] FALSE
D53V5, binary
                   cls
clus                  0   1
  9P LOSS MUTATED     0  15
  9P LOSS WILD-TYPE  13 335
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      0   15
  9P LOSS WILD-TYPE   13  335
                                        clus
vv                                       9P LOSS MUTATED 9P LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE               0                13
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 15               335
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  9P LOSS MUTATED     9   5   0   0
  9P LOSS WILD-TYPE 234  85   5  11
D53V6, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  R0               9               234
  R1               5                85
  R2               0                 5
  RX               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"
D53V7, continuous
D53V8, continuous
D53V9, continuous
D53V10, continuous
D53V11, continuous
D53V12, continuous
D53V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9P LOSS MUTATED       0                         0     6
  9P LOSS WILD-TYPE     2                         7   140
D53V14, multiclass
                           clus
vv                          9P LOSS MUTATED 9P LOSS WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 7
  WHITE                                   6               140
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(54) Variable = 9Q LOSS MUTATION ANALYSIS
D54V1, survival
                   sevent
clus2                 0   1
  9Q LOSS MUTATED     6   0
  9Q LOSS WILD-TYPE 349   6
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                6               355 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                0                 6 
$`9Q LOSS MUTATED`
TCGA-EJ-5514 TCGA-EJ-7781 TCGA-FC-7961 TCGA-HI-7168 TCGA-J9-A52E TCGA-YL-A9WY 
       36.23        23.90        15.42        78.61        10.62        28.34 

$`9Q LOSS WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 
        1.02         2.04         0.92        44.02        12.00         1.02 
TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 
       23.01         1.02        15.06        24.03         2.04        13.02 
TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 
       15.98        26.99         9.99        32.02        33.01         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        27.16        33.11        19.56        13.32        29.79 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        26.30        45.73        28.93        30.31 
TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 
       27.19        23.90        38.93        48.13        36.69        48.53 
TCGA-EJ-5512 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 
       38.53        60.23        46.55        47.80        52.27        64.50 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 
       51.88        68.35        43.07        36.66        38.76        39.75 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 
       60.23        41.85        47.87        29.06        27.02        49.02 
TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 
       61.15        83.57        21.80         9.70         9.50         9.37 
TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 
       16.77         7.66        17.52         5.75        27.68         6.28 
TCGA-EJ-7331 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 
        0.30        38.37        25.87        25.68        20.55        14.53 
TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 
       14.14        18.15        19.59        17.29         3.75        23.05 
TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8474 TCGA-EJ-A46B 
       19.92        64.47        63.98        26.99        10.32         5.33 
TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I 
        4.24        17.49         9.83         3.06         7.53        21.96 
TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J 
       17.62        12.92        13.71        18.41         9.14         2.99 
TCGA-EJ-A65M TCGA-FC-7708 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD 
        7.56        28.41        13.45         8.98        17.23        16.24 
TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 
        1.78        41.62        87.35        81.04        67.99        66.67 
TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 
       69.37        55.76        18.21        68.68        49.81        46.16 
TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 
       50.70        49.35        47.15        46.52        47.44        45.30 
TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 
       39.39        44.81         3.32        40.18        39.95        38.01 
TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 
       40.31        26.66        31.50        37.97        45.80        25.15 
TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 
       27.29        58.22        56.75        52.87        50.73        38.27 
TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 
       38.96        27.91        30.97        35.34        28.18        32.68 
TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 
       26.01        21.14         6.08        30.94         3.68        19.76 
TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 
        5.33         2.93         2.01         2.37        14.47        28.54 
TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 
        0.79        28.60         1.97         1.68         2.37         2.93 
TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 
        1.71         0.72         2.10         2.66         1.74         1.48 
TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 
        1.68         2.07        24.59        26.04         1.97         1.12 
TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 
        3.22        30.51         1.48        17.85        24.56         1.84 
TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 
       19.36        22.42         3.12        23.87         2.17         2.27 
TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 
        1.94        17.95        22.32         1.58        15.88         1.15 
TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN 
       22.36         0.76         1.78         2.01         2.20         1.61 
TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY 
        5.49         2.33         3.48         1.45         1.25         4.41 
TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K 
       88.24        82.92        43.69        20.19        12.30        21.76 
TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R 
       17.03        16.04        16.54        16.14        20.52        14.93 
TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I 
       17.19         6.02        13.32        17.36         9.17         9.17 
TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B 
       10.19         6.77        10.39        14.37        20.28        13.87 
TCGA-J9-A52C TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY 
        5.85        93.99        56.28        44.68        61.78       115.86 
TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 
       30.02        54.54       151.36        67.59        90.51        49.25 
TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 
      113.33        67.07        58.19        27.62        34.95        22.75 
TCGA-KK-A8IB TCGA-KK-A8IF TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 
        2.73        26.43        20.65         5.19         6.87         9.93 
TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL 
       13.15        27.02        25.08        15.88        18.84         3.19 
TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-TP-A8TT TCGA-TP-A8TV 
       41.00       114.64        47.21        86.14        11.90         8.19 
TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O 
        8.84        25.51        12.95         6.02        15.52        15.81 
TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 
       30.15        32.91        15.09         4.34       106.95        26.47 
TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D 
       84.69        94.65        23.93        75.91        55.56        60.92 
TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI 
       66.97        21.80        48.85        21.53        17.82         5.79 
TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK 
       37.18        27.81         3.91        38.04        48.03         9.04 
TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 
        2.99        25.97        31.96        31.50        31.96        28.54 
TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-Y6-A8TL 
       30.58        29.23        27.09        37.02        39.65        25.48 
TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 
       52.96        49.02        38.56        36.95        71.77        62.14 
TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH 
       60.56        16.83        45.50        41.46        45.14        28.77 
TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP 
       47.38        45.86        37.97        26.24       106.75        71.34 
TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK 
       62.79         7.00        14.04        41.39        60.99        62.37 
TCGA-YL-A9WL TCGA-YL-A9WX TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       24.33        49.91         1.64         4.93         1.12         7.86 
TCGA-ZG-A9ND 
        6.02 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            10.62              0.30 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            78.61            151.36 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            26.12             23.93 
[1] "10.6 - 78.6 (26.1)" "0.3 - 151.4 (23.9)"
[1] "hr="     "9200000"
D54V2, continuous
                   vv
clus                 T2  T3  T4
  9Q LOSS MUTATED     2   4   0
  9Q LOSS WILD-TYPE 148 202   5
D54V3, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T2               2               148
  T3               4               202
  T4               0                 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"
D54V4, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED     5   1
  9Q LOSS WILD-TYPE 258  43
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      5    1
  9Q LOSS WILD-TYPE  258   43
   clus
vv  9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  0               5               258
  1               1                43
[1] 2 2
[1] FALSE
D54V5, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED     0   6
  9Q LOSS WILD-TYPE  13 344
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      0    6
  9Q LOSS WILD-TYPE   13  344
                                        clus
vv                                       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE               0                13
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  6               344
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  9Q LOSS MUTATED     3   2   0   0
  9Q LOSS WILD-TYPE 240  88   5  11
D54V6, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  R0               3               240
  R1               2                88
  R2               0                 5
  RX               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"
D54V7, continuous
D54V8, continuous
D54V9, continuous
D54V10, continuous
D54V11, continuous
D54V12, continuous
D54V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9Q LOSS MUTATED       0                         0     4
  9Q LOSS WILD-TYPE     2                         7   142
D54V14, multiclass
                           clus
vv                          9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 7
  WHITE                                   4               142
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(55) Variable = 10P LOSS MUTATION ANALYSIS
D55V1, survival
                    sevent
clus2                  0   1
  10P LOSS MUTATED    29   1
  10P LOSS WILD-TYPE 326   5
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                30                331 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 1                  5 
$`10P LOSS MUTATED`
TCGA-CH-5751 TCGA-CH-5788 TCGA-CH-5790 TCGA-EJ-5518 TCGA-EJ-7784 TCGA-FC-7961 
       35.01        26.99        32.02        52.27        25.68        15.42 
TCGA-G9-6363 TCGA-G9-6377 TCGA-G9-7521 TCGA-HC-7213 TCGA-HC-7232 TCGA-HC-A48F 
       45.30        31.50        30.97         1.97         2.93        22.36 
TCGA-HI-7168 TCGA-HI-7171 TCGA-J9-A52B TCGA-KK-A59Z TCGA-KK-A6E6 TCGA-M7-A721 
       78.61        43.69        13.87        61.78       113.33        13.15 
TCGA-VP-A875 TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-XK-AAIV TCGA-XK-AAJ3 
       26.47        48.85        21.53        17.82        31.50        28.54 
TCGA-XK-AAJT TCGA-YL-A8HL TCGA-YL-A8SJ TCGA-YL-A8SL TCGA-YL-A8SQ TCGA-YL-A9WK 
       37.02        38.56        45.86        26.24        62.79        62.37 

$`10P LOSS WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5753 
        1.97        24.03         1.02        13.02        31.00         1.02 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 
        2.04         0.92        44.02        12.00         1.02        23.01 
TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 
        1.02        15.06        24.03         2.04        13.02        15.98 
TCGA-CH-5789 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 
        9.99        33.01         2.99        29.00        27.16        33.11 
TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 
       19.56        13.32        29.79        46.52        44.88        26.30 
TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 
       45.73        28.93        30.31        27.19        23.90        38.93 
TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 
       48.13        36.69        48.53        38.53        36.23        60.23 
TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 
       46.55        47.80        64.50        51.88        68.35        43.07 
TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 
       36.66        38.76        39.75        60.23        41.85        47.87 
TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 
       29.06        27.02        49.02        61.15        83.57        21.80 
TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 
        9.70         9.50         9.37        16.77         7.66        17.52 
TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 
        5.75        27.68         6.28         0.30        23.90        38.37 
TCGA-EJ-7783 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 
       25.87        20.55        14.53        14.14        18.15        19.59 
TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 
       17.29         3.75        23.05        19.92        64.47        63.98 
TCGA-EJ-8470 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F 
       26.99        10.32         5.33         4.24        17.49         9.83 
TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E 
        3.06         7.53        21.96        17.62        12.92        13.71 
TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-FC-7708 TCGA-FC-A4JI 
       18.41         9.14         2.99         7.56        28.41        13.45 
TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 
        8.98        17.23        16.24         1.78        41.62        87.35 
TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 
       81.04        67.99        66.67        69.37        55.76        18.21 
TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 
       68.68        49.81        46.16        50.70        49.35        47.15 
TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 
       46.52        47.44        39.39        44.81         3.32        40.18 
TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6378 TCGA-G9-6379 
       39.95        38.01        40.31        26.66        37.97        45.80 
TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 
       25.15        27.29        58.22        56.75        52.87        50.73 
TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 
       38.27        38.96        27.91        35.34        28.18        32.68 
TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 
       26.01        21.14         6.08        30.94         3.68        19.76 
TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 
        5.33         2.93         2.01         2.37        14.47        28.54 
TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7233 TCGA-HC-7736 
        0.79        28.60         1.68         2.37         1.71         0.72 
TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 
        2.10         2.66         1.74         1.48         1.68         2.07 
TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 
       24.59        26.04         1.97         1.12         3.22        30.51 
TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 
        1.48        17.85        24.56         1.84        19.36        22.42 
TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 
        3.12        23.87         2.17         2.27         1.94        17.95 
TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A4ZV TCGA-HC-A631 
       22.32         1.58        15.88         1.15         0.76         1.78 
TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ 
        2.01         2.20         1.61         5.49         2.33         3.48 
TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HI-7169 TCGA-HI-7170 TCGA-J4-8198 
        1.45         1.25         4.41        88.24        82.92        20.19 
TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O 
       12.30        21.76        17.03        16.04        16.54        16.14 
TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 
       20.52        14.93        17.19         6.02        13.32        17.36 
TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M 
        9.17         9.17        10.19         6.77        10.39        14.37 
TCGA-J4-A83N TCGA-J9-A52C TCGA-J9-A52E TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y 
       20.28         5.85        10.62        93.99        56.28        44.68 
TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 
      115.86        30.02        54.54       151.36        67.59        90.51 
TCGA-KK-A6E5 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 
       49.25        67.07        58.19        27.62        34.95        22.75 
TCGA-KK-A8IB TCGA-KK-A8IF TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 
        2.73        26.43        20.65         5.19         6.87         9.93 
TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM 
       27.02        25.08        15.88        18.84         3.19        41.00 
TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-TP-A8TT TCGA-TP-A8TV TCGA-VN-A88I 
      114.64        47.21        86.14        11.90         8.19         8.84 
TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P 
       25.51        12.95         6.02        15.52        15.81        30.15 
TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A876 TCGA-VP-A878 
       32.91        15.09         4.34       106.95        84.69        94.65 
TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H 
       23.93        75.91        55.56        60.92        66.97        21.80 
TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DI 
        5.79        37.18        27.81         3.91        38.04        48.03 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIW TCGA-XK-AAJA 
        9.04         2.99        25.97        31.96        31.96        30.58 
TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJU TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK 
       29.23        27.09        39.65        25.48        52.96        49.02 
TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB 
       36.95        71.77        62.14        60.56        16.83        45.50 
TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SK TCGA-YL-A8SO 
       41.46        45.14        28.77        47.38        37.97       106.75 
TCGA-YL-A8SP TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WL 
       71.34         7.00        14.04        41.39        60.99        24.33 
TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       49.91        28.34         1.64         4.93         1.12         7.86 
TCGA-ZG-A9ND 
        6.02 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              1.97               0.30 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            113.33             151.36 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             31.50              22.42 
[1] "2.0 - 113.3 (31.5)" "0.3 - 151.4 (22.4)"
[1] "hr=" "1.4"
D55V2, continuous
                    vv
clus                  T2  T3  T4
  10P LOSS MUTATED     6  21   3
  10P LOSS WILD-TYPE 144 185   2
D55V3, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  T2                6                144
  T3               21                185
  T4                3                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V4, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    20   8
  10P LOSS WILD-TYPE 243  36
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     20    8
  10P LOSS WILD-TYPE  243   36
   clus
vv  10P LOSS MUTATED 10P LOSS WILD-TYPE
  0               20                243
  1                8                 36
[1] 2 2
[1] FALSE
D55V5, binary
                    cls
clus                   0   1
  10P LOSS MUTATED     1  29
  10P LOSS WILD-TYPE  12 321
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      1   29
  10P LOSS WILD-TYPE   12  321
                                        clus
vv                                       10P LOSS MUTATED 10P LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                1                 12
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  29                321
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  10P LOSS MUTATED    15  13   1   0
  10P LOSS WILD-TYPE 228  77   4  11
D55V6, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  R0               15                228
  R1               13                 77
  R2                1                  4
  RX                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"
D55V7, continuous
D55V8, continuous
D55V9, continuous
D55V10, continuous
D55V11, continuous
D55V12, continuous
D55V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10P LOSS MUTATED       0                         0    12
  10P LOSS WILD-TYPE     2                         7   134
D55V14, multiclass
                           clus
vv                          10P LOSS MUTATED 10P LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  7
  WHITE                                   12                134
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(56) Variable = 10Q LOSS MUTATION ANALYSIS
D56V1, survival
                    sevent
clus2                  0   1
  10Q LOSS MUTATED    31   1
  10Q LOSS WILD-TYPE 324   5
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                32                329 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 1                  5 
$`10Q LOSS MUTATED`
TCGA-CH-5751 TCGA-CH-5790 TCGA-EJ-5507 TCGA-EJ-5518 TCGA-EJ-7784 TCGA-FC-7961 
       35.01        32.02        23.90        52.27        25.68        15.42 
TCGA-G9-6348 TCGA-G9-6377 TCGA-G9-6499 TCGA-G9-7521 TCGA-HC-7213 TCGA-HC-7232 
       49.81        31.50        50.73        30.97         1.97         2.93 
TCGA-HC-7737 TCGA-HC-8266 TCGA-HC-A48F TCGA-HI-7168 TCGA-HI-7171 TCGA-J9-A52B 
        2.10         1.15        22.36        78.61        43.69        13.87 
TCGA-KK-A59Z TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-M7-A721 TCGA-VP-A875 TCGA-VP-A87K 
       61.78       113.33        67.07        13.15        26.47        21.53 
TCGA-VP-AA1N TCGA-XK-AAIV TCGA-XK-AAJT TCGA-YL-A8HL TCGA-YL-A8SF TCGA-YL-A8SJ 
       17.82        31.50        37.02        38.56        45.14        45.86 
TCGA-YL-A8SL TCGA-YL-A9WK 
       26.24        62.37 

$`10Q LOSS WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5753 
        1.97        24.03         1.02        13.02        31.00         1.02 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 
        2.04         0.92        44.02        12.00         1.02        23.01 
TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 
        1.02        15.06        24.03         2.04        13.02        15.98 
TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 
       26.99         9.99        33.01         2.99        29.00        27.16 
TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 
       33.11        19.56        13.32        29.79        46.52        44.88 
TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5508 
       26.30        45.73        28.93        30.31        27.19        38.93 
TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 
       48.13        36.69        48.53        38.53        36.23        60.23 
TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 
       46.55        47.80        64.50        51.88        68.35        43.07 
TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 
       36.66        38.76        39.75        60.23        41.85        47.87 
TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 
       29.06        27.02        49.02        61.15        83.57        21.80 
TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 
        9.70         9.50         9.37        16.77         7.66        17.52 
TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 
        5.75        27.68         6.28         0.30        23.90        38.37 
TCGA-EJ-7783 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 
       25.87        20.55        14.53        14.14        18.15        19.59 
TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 
       17.29         3.75        23.05        19.92        64.47        63.98 
TCGA-EJ-8470 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F 
       26.99        10.32         5.33         4.24        17.49         9.83 
TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E 
        3.06         7.53        21.96        17.62        12.92        13.71 
TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-FC-7708 TCGA-FC-A4JI 
       18.41         9.14         2.99         7.56        28.41        13.45 
TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 
        8.98        17.23        16.24         1.78        41.62        87.35 
TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 
       81.04        67.99        66.67        69.37        55.76        18.21 
TCGA-G9-6347 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 
       68.68        46.16        50.70        49.35        47.15        46.52 
TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 
       47.44        45.30        39.39        44.81         3.32        40.18 
TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6378 TCGA-G9-6379 
       39.95        38.01        40.31        26.66        37.97        45.80 
TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-7509 
       25.15        27.29        58.22        56.75        52.87        38.27 
TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 
       38.96        27.91        35.34        28.18        32.68        26.01 
TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 
       21.14         6.08        30.94         3.68        19.76         5.33 
TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 
        2.93         2.01         2.37        14.47        28.54         0.79 
TCGA-HC-7212 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7738 
       28.60         1.68         2.37         1.71         0.72         2.66 
TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 
        1.74         1.48         1.68         2.07        24.59        26.04 
TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 
        1.97         1.12         3.22        30.51         1.48        17.85 
TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 
       24.56         1.84        19.36        22.42         3.12        23.87 
TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 
        2.17         2.27         1.94        17.95        22.32         1.58 
TCGA-HC-8265 TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN 
       15.88         0.76         1.78         2.01         2.20         1.61 
TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY 
        5.49         2.33         3.48         1.45         1.25         4.41 
TCGA-HI-7169 TCGA-HI-7170 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L 
       88.24        82.92        20.19        12.30        21.76        17.03 
TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S 
       16.04        16.54        16.14        20.52        14.93        17.19 
TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J 
        6.02        13.32        17.36         9.17         9.17        10.19 
TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52C TCGA-J9-A52E 
        6.77        10.39        14.37        20.28         5.85        10.62 
TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 
       93.99        56.28        44.68       115.86        30.02        54.54 
TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E8 TCGA-KK-A7AZ 
      151.36        67.59        90.51        49.25        58.19        27.62 
TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IB TCGA-KK-A8IF TCGA-KK-A8IL TCGA-M7-A71Y 
       34.95        22.75         2.73        26.43        20.65         5.19 
TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 
        6.87         9.93        27.02        25.08        15.88        18.84 
TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-TP-A8TT 
        3.19        41.00       114.64        47.21        86.14        11.90 
TCGA-TP-A8TV TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N 
        8.19         8.84        25.51        12.95         6.02        15.52 
TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 
       15.81        30.15        32.91        15.09         4.34       106.95 
TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D 
       84.69        94.65        23.93        75.91        55.56        60.92 
TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS 
       66.97        21.80        48.85         5.79        37.18        27.81 
TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX 
        3.91        38.04        48.03         9.04         2.99        25.97 
TCGA-XK-AAIR TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR 
       31.96        31.96        28.54        30.58        29.23        27.09 
TCGA-XK-AAJU TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HM TCGA-YL-A8HO 
       39.65        25.48        52.96        49.02        36.95        71.77 
TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SH 
       62.14        60.56        16.83        45.50        41.46        28.77 
TCGA-YL-A8SI TCGA-YL-A8SK TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR 
       47.38        37.97       106.75        71.34        62.79         7.00 
TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY 
       14.04        41.39        60.99        24.33        49.91        28.34 
TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9ND 
        1.64         4.93         1.12         7.86         6.02 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              1.15               0.30 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            113.33             151.36 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             31.50              22.75 
[1] "1.1 - 113.3 (31.5)" "0.3 - 151.4 (22.8)"
[1] "hr=" "1.4"
D56V2, continuous
                    vv
clus                  T2  T3  T4
  10Q LOSS MUTATED     8  22   2
  10Q LOSS WILD-TYPE 142 184   3
D56V3, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T2                8                142
  T3               22                184
  T4                2                  3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V4, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    21   9
  10Q LOSS WILD-TYPE 242  35
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     21    9
  10Q LOSS WILD-TYPE  242   35
   clus
vv  10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  0               21                242
  1                9                 35
[1] 2 2
[1] FALSE
D56V5, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     1  31
  10Q LOSS WILD-TYPE  12 319
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      1   31
  10Q LOSS WILD-TYPE   12  319
                                        clus
vv                                       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                1                 12
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  31                319
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  10Q LOSS MUTATED    16  15   0   0
  10Q LOSS WILD-TYPE 227  75   5  11
D56V6, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  R0               16                227
  R1               15                 75
  R2                0                  5
  RX                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"
D56V7, continuous
D56V8, continuous
D56V9, continuous
D56V10, continuous
D56V11, continuous
D56V12, continuous
D56V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10Q LOSS MUTATED       0                         1    13
  10Q LOSS WILD-TYPE     2                         6   133
D56V14, multiclass
                           clus
vv                          10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                1                  6
  WHITE                                   13                133
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(57) Variable = 11P LOSS MUTATION ANALYSIS
D57V1, survival
                    sevent
clus2                  0   1
  11P LOSS MUTATED     2   0
  11P LOSS WILD-TYPE 353   6
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 2                359 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 0                  6 
$`11P LOSS MUTATED`
TCGA-G9-6379 TCGA-VP-AA1N 
       45.80        17.82 

$`11P LOSS WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 
        1.02         2.04         0.92        44.02        12.00         1.02 
TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 
       23.01         1.02        15.06        24.03         2.04        13.02 
TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 
       15.98        26.99         9.99        32.02        33.01         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        27.16        33.11        19.56        13.32        29.79 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        26.30        45.73        28.93        30.31 
TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 
       27.19        23.90        38.93        48.13        36.69        48.53 
TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 
       38.53        36.23        60.23        46.55        47.80        52.27 
TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 
       64.50        51.88        68.35        43.07        36.66        38.76 
TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 
       39.75        60.23        41.85        47.87        29.06        27.02 
TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 
       49.02        61.15        83.57        21.80         9.70         9.50 
TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 
        9.37        16.77         7.66        17.52         5.75        27.68 
TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 
        6.28         0.30        23.90        38.37        25.87        25.68 
TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 
       20.55        14.53        14.14        18.15        19.59        17.29 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 
        3.75        23.05        19.92        64.47        63.98        26.99 
TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G 
       10.32         5.33         4.24        17.49         9.83         3.06 
TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F 
        7.53        21.96        17.62        12.92        13.71        18.41 
TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI 
        9.14         2.99         7.56        28.41        15.42        13.45 
TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 
        8.98        17.23        16.24         1.78        41.62        87.35 
TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 
       81.04        67.99        66.67        69.37        55.76        18.21 
TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 
       68.68        49.81        46.16        50.70        49.35        47.15 
TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 
       46.52        47.44        45.30        39.39        44.81         3.32 
TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 
       40.18        39.95        38.01        40.31        26.66        31.50 
TCGA-G9-6378 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 
       37.97        25.15        27.29        58.22        56.75        52.87 
TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 
       50.73        38.27        38.96        27.91        30.97        35.34 
TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX 
       28.18        32.68        26.01        21.14         6.08        30.94 
TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 
        3.68        19.76         5.33         2.93         2.01         2.37 
TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 
       14.47        28.54         0.79        28.60         1.97         1.68 
TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 
        2.37         2.93         1.71         0.72         2.10         2.66 
TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 
        1.74         1.48         1.68         2.07        24.59        26.04 
TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 
        1.97         1.12         3.22        30.51         1.48        17.85 
TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 
       24.56         1.84        19.36        22.42         3.12        23.87 
TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 
        2.17         2.27         1.94        17.95        22.32         1.58 
TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 
       15.88         1.15        22.36         0.76         1.78         2.01 
TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS 
        2.20         1.61         5.49         2.33         3.48         1.45 
TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
        1.25         4.41        78.61        88.24        82.92        43.69 
TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N 
       20.19        12.30        21.76        17.03        16.04        16.54 
TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 
       16.14        20.52        14.93        17.19         6.02        13.32 
TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L 
       17.36         9.17         9.17        10.19         6.77        10.39 
TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-KK-A59V 
       14.37        20.28        13.87         5.85        10.62        93.99 
TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 
       56.28        44.68        61.78       115.86        30.02        54.54 
TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 
      151.36        67.59        90.51        49.25       113.33        67.07 
TCGA-KK-A6E8 TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IB TCGA-KK-A8IF 
       58.19        27.62        34.95        22.75         2.73        26.43 
TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 
       20.65         5.19         6.87         9.93        13.15        27.02 
TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN 
       25.08        15.88        18.84         3.19        41.00       114.64 
TCGA-QU-A6IO TCGA-QU-A6IP TCGA-TP-A8TT TCGA-TP-A8TV TCGA-VN-A88I TCGA-VN-A88K 
       47.21        86.14        11.90         8.19         8.84        25.51 
TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q 
       12.95         6.02        15.52        15.81        30.15        32.91 
TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 
       15.09         4.34       106.95        26.47        84.69        94.65 
TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H 
       23.93        75.91        55.56        60.92        66.97        21.80 
TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR 
       48.85        21.53         5.79        37.18        27.81         3.91 
TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR 
       38.04        48.03         9.04         2.99        25.97        31.96 
TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR 
       31.50        31.96        28.54        30.58        29.23        27.09 
TCGA-XK-AAJT TCGA-XK-AAJU TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL 
       37.02        39.65        25.48        52.96        49.02        38.56 
TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB 
       36.95        71.77        62.14        60.56        16.83        45.50 
TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK 
       41.46        45.14        28.77        47.38        45.86        37.97 
TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH 
       26.24       106.75        71.34        62.79         7.00        14.04 
TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY 
       41.39        60.99        62.37        24.33        49.91        28.34 
TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9ND 
        1.64         4.93         1.12         7.86         6.02 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             17.82               0.30 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             45.80             151.36 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             31.81              23.93 
[1] "17.8 - 45.8 (31.8)" "0.3 - 151.4 (23.9)"
[1] "Remove cluster labels:" "11P LOSS MUTATED"      
D57V2, continuous
                    vv
clus                  T2  T3  T4
  11P LOSS MUTATED     0   3   0
  11P LOSS WILD-TYPE 150 203   5
D57V3, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  T2                0                150
  T3                3                203
  T4                0                  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"
D57V4, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     3   0
  11P LOSS WILD-TYPE 260  44
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      3    0
  11P LOSS WILD-TYPE  260   44
   clus
vv  11P LOSS MUTATED 11P LOSS WILD-TYPE
  0                3                260
  1                0                 44
[1] 2 2
[1] FALSE
D57V5, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     0   3
  11P LOSS WILD-TYPE  13 347
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      0    3
  11P LOSS WILD-TYPE   13  347
                                        clus
vv                                       11P LOSS MUTATED 11P LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                0                 13
  PROSTATE ADENOCARCINOMA ACINAR TYPE                   3                347
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  11P LOSS MUTATED     1   2   0   0
  11P LOSS WILD-TYPE 242  88   5  11
D57V6, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  R0                1                242
  R1                2                 88
  R2                0                  5
  RX                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"
D57V7, continuous
D57V8, continuous
D57V9, continuous
D57V10, continuous
D57V11, continuous
D57V12, continuous
D57V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11P LOSS MUTATED       0                         0     0
  11P LOSS WILD-TYPE     2                         7   146
D57V14, multiclass

Clustering(58) Variable = 12P LOSS MUTATION ANALYSIS
D58V1, survival
                    sevent
clus2                  0   1
  12P LOSS MUTATED    30   0
  12P LOSS WILD-TYPE 325   6
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                30                331 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 0                  6 
$`12P LOSS MUTATED`
TCGA-2A-A8W3 TCGA-CH-5744 TCGA-CH-5751 TCGA-CH-5766 TCGA-EJ-5510 TCGA-EJ-5514 
       25.35         1.97        35.01         1.02        36.69        36.23 
TCGA-EJ-5519 TCGA-EJ-5522 TCGA-EJ-5526 TCGA-EJ-7781 TCGA-EJ-7784 TCGA-G9-6364 
       64.50        68.35        38.76        23.90        25.68        39.39 
TCGA-G9-6379 TCGA-G9-7521 TCGA-HC-8262 TCGA-HC-A48F TCGA-HC-A6AL TCGA-HI-7168 
       45.80        30.97        22.32        22.36         2.20        78.61 
TCGA-J4-A67M TCGA-J9-A52B TCGA-KK-A6E1 TCGA-KK-A6E6 TCGA-KK-A7AZ TCGA-M7-A725 
       16.04        13.87        54.54       113.33        27.62        18.84 
TCGA-VP-A87J TCGA-VP-AA1N TCGA-X4-A8KQ TCGA-YL-A8SC TCGA-YL-A8SJ TCGA-YL-A9WK 
       48.85        17.82        37.18        41.46        45.86        62.37 

$`12P LOSS WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-CH-5737 
       20.42        43.79        22.06        33.96         3.68         2.99 
TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5746 
        6.97        22.06         1.02        12.99        13.97        24.03 
TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 
        1.02        13.02        31.00         1.02         2.04         0.92 
TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5767 TCGA-CH-5768 
       44.02        12.00         1.02        23.01        15.06        24.03 
TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 
        2.04        13.02        15.98        26.99         9.99        32.02 
TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 
       33.01         2.99        29.00        27.16        33.11        19.56 
TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 
       13.32        29.79        46.52        44.88        26.30        45.73 
TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 
       28.93        30.31        27.19        23.90        38.93        48.13 
TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 
       48.53        38.53        60.23        46.55        47.80        52.27 
TCGA-EJ-5521 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 
       51.88        43.07        36.66        39.75        60.23        41.85 
TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 
       47.87        29.06        27.02        49.02        61.15        83.57 
TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 
       21.80         9.70         9.50         9.37        16.77         7.66 
TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7782 
       17.52         5.75        27.68         6.28         0.30        38.37 
TCGA-EJ-7783 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 
       25.87        20.55        14.53        14.14        18.15        19.59 
TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 
       17.29         3.75        23.05        19.92        64.47        63.98 
TCGA-EJ-8470 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F 
       26.99        10.32         5.33         4.24        17.49         9.83 
TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E 
        3.06         7.53        21.96        17.62        12.92        13.71 
TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-FC-7708 TCGA-FC-7961 
       18.41         9.14         2.99         7.56        28.41        15.42 
TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 
       13.45         8.98        17.23        16.24         1.78        41.62 
TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 
       87.35        81.04        67.99        66.67        69.37        55.76 
TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 
       18.21        68.68        49.81        46.16        50.70        49.35 
TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6365 TCGA-G9-6366 
       47.15        46.52        47.44        45.30        44.81         3.32 
TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 
       40.18        39.95        38.01        40.31        26.66        31.50 
TCGA-G9-6378 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 
       37.97        25.15        27.29        58.22        56.75        52.87 
TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7522 TCGA-G9-7523 
       50.73        38.27        38.96        27.91        35.34        28.18 
TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY 
       32.68        26.01        21.14         6.08        30.94         3.68 
TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 
       19.76         5.33         2.93         2.01         2.37        14.47 
TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 
       28.54         0.79        28.60         1.97         1.68         2.37 
TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 
        2.93         1.71         0.72         2.10         2.66         1.74 
TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 
        1.48         1.68         2.07        24.59        26.04         1.97 
TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 
        1.12         3.22        30.51         1.48        17.85        24.56 
TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 
        1.84        19.36        22.42         3.12        23.87         2.17 
TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 
        2.27         1.94        17.95         1.58        15.88         1.15 
TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP 
        0.76         1.78         2.01         1.61         5.49         2.33 
TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HI-7169 TCGA-HI-7170 
        3.48         1.45         1.25         4.41        88.24        82.92 
TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67N 
       43.69        20.19        12.30        21.76        17.03        16.54 
TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 
       16.14        20.52        14.93        17.19         6.02        13.32 
TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L 
       17.36         9.17         9.17        10.19         6.77        10.39 
TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52C TCGA-J9-A52E TCGA-KK-A59V TCGA-KK-A59X 
       14.37        20.28         5.85        10.62        93.99        56.28 
TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E2 TCGA-KK-A6E3 
       44.68        61.78       115.86        30.02       151.36        67.59 
TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7B1 TCGA-KK-A7B2 
       90.51        49.25        67.07        58.19        34.95        22.75 
TCGA-KK-A8IB TCGA-KK-A8IF TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 
        2.73        26.43        20.65         5.19         6.87         9.93 
TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-QU-A6IL TCGA-QU-A6IM 
       13.15        27.02        25.08        15.88         3.19        41.00 
TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-TP-A8TT TCGA-TP-A8TV TCGA-VN-A88I 
      114.64        47.21        86.14        11.90         8.19         8.84 
TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P 
       25.51        12.95         6.02        15.52        15.81        30.15 
TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 
       32.91        15.09         4.34       106.95        26.47        84.69 
TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E 
       94.65        23.93        75.91        55.56        60.92        66.97 
TCGA-VP-A87H TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83G 
       21.80        21.53         5.79        27.81         3.91        38.04 
TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV 
       48.03         9.04         2.99        25.97        31.96        31.50 
TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT 
       31.96        28.54        30.58        29.23        27.09        37.02 
TCGA-XK-AAJU TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM 
       39.65        25.48        52.96        49.02        38.56        36.95 
TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SF 
       71.77        62.14        60.56        16.83        45.50        45.14 
TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP 
       28.77        47.38        37.97        26.24       106.75        71.34 
TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WL 
       62.79         7.00        14.04        41.39        60.99        24.33 
TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       49.91        28.34         1.64         4.93         1.12         7.86 
TCGA-ZG-A9ND 
        6.02 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              1.02               0.30 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
            113.33             151.36 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             35.62              22.75 
[1] "1.0 - 113.3 (35.6)" "0.3 - 151.4 (22.8)"
[1] "hr="   "8e+07"
D58V2, continuous
                    vv
clus                  T2  T3  T4
  12P LOSS MUTATED     9  21   1
  12P LOSS WILD-TYPE 141 185   4
D58V3, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  T2                9                141
  T3               21                185
  T4                1                  4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V4, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    23   8
  12P LOSS WILD-TYPE 240  36
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     23    8
  12P LOSS WILD-TYPE  240   36
   clus
vv  12P LOSS MUTATED 12P LOSS WILD-TYPE
  0               23                240
  1                8                 36
[1] 2 2
[1] FALSE
D58V5, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     0  31
  12P LOSS WILD-TYPE  13 319
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      0   31
  12P LOSS WILD-TYPE   13  319
                                        clus
vv                                       12P LOSS MUTATED 12P LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                0                 13
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  31                319
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  12P LOSS MUTATED    20   8   1   2
  12P LOSS WILD-TYPE 223  82   4   9
D58V6, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  R0               20                223
  R1                8                 82
  R2                1                  4
  RX                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"
D58V7, continuous
D58V8, continuous
D58V9, continuous
D58V10, continuous
D58V11, continuous
D58V12, continuous
D58V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12P LOSS MUTATED       0                         0    12
  12P LOSS WILD-TYPE     2                         7   134
D58V14, multiclass
                           clus
vv                          12P LOSS MUTATED 12P LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  7
  WHITE                                   12                134
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(59) Variable = 12Q LOSS MUTATION ANALYSIS
D59V1, survival
                    sevent
clus2                  0   1
  12Q LOSS MUTATED    13   0
  12Q LOSS WILD-TYPE 342   6
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                13                348 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 0                  6 
$`12Q LOSS MUTATED`
TCGA-CH-5751 TCGA-EJ-5510 TCGA-EJ-5514 TCGA-EJ-5526 TCGA-EJ-7781 TCGA-EJ-7784 
       35.01        36.69        36.23        38.76        23.90        25.68 
TCGA-G9-7521 TCGA-HC-8216 TCGA-HI-7168 TCGA-J9-A52B TCGA-KK-A6E1 TCGA-KK-A7AZ 
       30.97        22.42        78.61        13.87        54.54        27.62 
TCGA-VP-AA1N 
       17.82 

$`12Q LOSS WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5753 
        1.97        24.03         1.02        13.02        31.00         1.02 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 
        2.04         0.92        44.02        12.00         1.02        23.01 
TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 
        1.02        15.06        24.03         2.04        13.02        15.98 
TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 
       26.99         9.99        32.02        33.01         2.99        29.00 
TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
       27.16        33.11        19.56        13.32        29.79        46.52 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       44.88        26.30        45.73        28.93        30.31        27.19 
TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5515 
       23.90        38.93        48.13        48.53        38.53        60.23 
TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 
       46.55        47.80        52.27        64.50        51.88        68.35 
TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 
       43.07        36.66        39.75        60.23        41.85        47.87 
TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 
       29.06        27.02        49.02        61.15        83.57        21.80 
TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 
        9.70         9.50         9.37        16.77         7.66        17.52 
TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7782 TCGA-EJ-7783 
        5.75        27.68         6.28         0.30        38.37        25.87 
TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 
       20.55        14.53        14.14        18.15        19.59        17.29 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 
        3.75        23.05        19.92        64.47        63.98        26.99 
TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G 
       10.32         5.33         4.24        17.49         9.83         3.06 
TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F 
        7.53        21.96        17.62        12.92        13.71        18.41 
TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI 
        9.14         2.99         7.56        28.41        15.42        13.45 
TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 
        8.98        17.23        16.24         1.78        41.62        87.35 
TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 
       81.04        67.99        66.67        69.37        55.76        18.21 
TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 
       68.68        49.81        46.16        50.70        49.35        47.15 
TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 
       46.52        47.44        45.30        39.39        44.81         3.32 
TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 
       40.18        39.95        38.01        40.31        26.66        31.50 
TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 
       37.97        45.80        25.15        27.29        58.22        56.75 
TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7522 
       52.87        50.73        38.27        38.96        27.91        35.34 
TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX 
       28.18        32.68        26.01        21.14         6.08        30.94 
TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 
        3.68        19.76         5.33         2.93         2.01         2.37 
TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 
       14.47        28.54         0.79        28.60         1.97         1.68 
TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 
        2.37         2.93         1.71         0.72         2.10         2.66 
TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 
        1.74         1.48         1.68         2.07        24.59        26.04 
TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 
        1.97         1.12         3.22        30.51         1.48        17.85 
TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 
       24.56         1.84        19.36         3.12        23.87         2.17 
TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 
        2.27         1.94        17.95        22.32         1.58        15.88 
TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL 
        1.15        22.36         0.76         1.78         2.01         2.20 
TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX 
        1.61         5.49         2.33         3.48         1.45         1.25 
TCGA-HC-A6HY TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 
        4.41        88.24        82.92        43.69        20.19        12.30 
TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q 
       21.76        17.03        16.04        16.54        16.14        20.52 
TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 
       14.93        17.19         6.02        13.32        17.36         9.17 
TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N 
        9.17        10.19         6.77        10.39        14.37        20.28 
TCGA-J9-A52C TCGA-J9-A52E TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z 
        5.85        10.62        93.99        56.28        44.68        61.78 
TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 
      115.86        30.02       151.36        67.59        90.51        49.25 
TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IB 
      113.33        67.07        58.19        34.95        22.75         2.73 
TCGA-KK-A8IF TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 
       26.43        20.65         5.19         6.87         9.93        13.15 
TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM 
       27.02        25.08        15.88        18.84         3.19        41.00 
TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-TP-A8TT TCGA-TP-A8TV TCGA-VN-A88I 
      114.64        47.21        86.14        11.90         8.19         8.84 
TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P 
       25.51        12.95         6.02        15.52        15.81        30.15 
TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 
       32.91        15.09         4.34       106.95        26.47        84.69 
TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E 
       94.65        23.93        75.91        55.56        60.92        66.97 
TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS 
       21.80        48.85        21.53         5.79        37.18        27.81 
TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX 
        3.91        38.04        48.03         9.04         2.99        25.97 
TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP 
       31.96        31.50        31.96        28.54        30.58        29.23 
TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK 
       27.09        37.02        39.65        25.48        52.96        49.02 
TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA 
       38.56        36.95        71.77        62.14        60.56        16.83 
TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ 
       45.50        41.46        45.14        28.77        47.38        45.86 
TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR 
       37.97        26.24       106.75        71.34        62.79         7.00 
TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX 
       14.04        41.39        60.99        62.37        24.33        49.91 
TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9ND 
       28.34         1.64         4.93         1.12         7.86         6.02 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             13.87               0.30 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             78.61             151.36 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             30.97              23.46 
[1] "13.9 - 78.6 (31.0)" "0.3 - 151.4 (23.5)"
[1] "hr="     "2.6e+07"
D59V2, continuous
                    vv
clus                  T2  T3  T4
  12Q LOSS MUTATED     4   8   1
  12Q LOSS WILD-TYPE 146 198   4
D59V3, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  T2                4                146
  T3                8                198
  T4                1                  4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V4, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     9   4
  12Q LOSS WILD-TYPE 254  40
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      9    4
  12Q LOSS WILD-TYPE  254   40
   clus
vv  12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  0                9                254
  1                4                 40
[1] 2 2
[1] FALSE
D59V5, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     0  13
  12Q LOSS WILD-TYPE  13 337
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      0   13
  12Q LOSS WILD-TYPE   13  337
                                        clus
vv                                       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                0                 13
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  13                337
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  12Q LOSS MUTATED     9   3   0   1
  12Q LOSS WILD-TYPE 234  87   5  10
D59V6, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  R0                9                234
  R1                3                 87
  R2                0                  5
  RX                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"
D59V7, continuous
D59V8, continuous
D59V9, continuous
D59V10, continuous
D59V11, continuous
D59V12, continuous
D59V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12Q LOSS MUTATED       0                         0     7
  12Q LOSS WILD-TYPE     2                         7   139
D59V14, multiclass
                           clus
vv                          12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  7
  WHITE                                    7                139
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(60) Variable = 13Q LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                  0   1
  13Q LOSS MUTATED    52   0
  13Q LOSS WILD-TYPE 303   6
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                52                309 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 0                  6 
$`13Q LOSS MUTATED`
TCGA-CH-5737 TCGA-CH-5751 TCGA-CH-5771 TCGA-CH-5788 TCGA-EJ-5495 TCGA-EJ-5504 
        2.99        35.01        13.02        26.99        33.11        28.93 
TCGA-EJ-5507 TCGA-EJ-5511 TCGA-EJ-5514 TCGA-EJ-5516 TCGA-EJ-5521 TCGA-EJ-5525 
       23.90        48.53        36.23        46.55        51.88        36.66 
TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7781 TCGA-EJ-7783 TCGA-EJ-7786 TCGA-EJ-A46D 
        9.37        16.77        23.90        25.87        14.53         4.24 
TCGA-FC-7961 TCGA-G9-6329 TCGA-G9-6378 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 
       15.42        41.62        37.97        38.96        27.91        30.97 
TCGA-HC-7213 TCGA-HC-8266 TCGA-HC-A4ZV TCGA-HC-A632 TCGA-HC-A6AN TCGA-HC-A6AS 
        1.97         1.15         0.76         2.01         1.61         1.45 
TCGA-HI-7168 TCGA-J9-A52B TCGA-J9-A52E TCGA-KK-A6E1 TCGA-KK-A6E6 TCGA-KK-A6E7 
       78.61        13.87        10.62        54.54       113.33        67.07 
TCGA-KK-A6E8 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A87D TCGA-XJ-A9DI TCGA-XK-AAIV 
       58.19        26.47        84.69        60.92        48.03        31.50 
TCGA-YL-A8S9 TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SJ TCGA-YL-A8SK 
       60.56        45.50        41.46        45.14        45.86        37.97 
TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SQ TCGA-YL-A9WK 
       26.24       106.75        62.79        62.37 

$`13Q LOSS WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 
        6.97        22.06         1.02        12.99        13.97         1.97 
TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 
       24.03         1.02        13.02        31.00         1.02         2.04 
TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 
        0.92        44.02        12.00         1.02        23.01         1.02 
TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5772 TCGA-CH-5789 TCGA-CH-5790 
       15.06        24.03         2.04        15.98         9.99        32.02 
TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5496 TCGA-EJ-5497 
       33.01         2.99        29.00        27.16        19.56        13.32 
TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5505 
       29.79        46.52        44.88        26.30        45.73        30.31 
TCGA-EJ-5506 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5512 TCGA-EJ-5515 
       27.19        38.93        48.13        36.69        38.53        60.23 
TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5526 
       47.80        52.27        64.50        68.35        43.07        38.76 
TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 
       39.75        60.23        41.85        47.87        29.06        27.02 
TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 
       49.02        61.15        83.57        21.80         9.70         9.50 
TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 
        7.66        17.52         5.75        27.68         6.28         0.30 
TCGA-EJ-7782 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 
       38.37        25.68        20.55        14.14        18.15        19.59 
TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 
       17.29         3.75        23.05        19.92        64.47        63.98 
TCGA-EJ-8470 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G 
       26.99        10.32         5.33        17.49         9.83         3.06 
TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F 
        7.53        21.96        17.62        12.92        13.71        18.41 
TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-FC-7708 TCGA-FC-A4JI TCGA-FC-A5OB 
        9.14         2.99         7.56        28.41        13.45         8.98 
TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 
       17.23        16.24         1.78        87.35        81.04        67.99 
TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 
       66.67        69.37        55.76        18.21        68.68        49.81 
TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 
       46.16        50.70        49.35        47.15        46.52        47.44 
TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 
       45.30        39.39        44.81         3.32        40.18        39.95 
TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6379 TCGA-G9-6384 
       38.01        40.31        26.66        31.50        45.80        25.15 
TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 
       27.29        58.22        56.75        52.87        50.73        38.27 
TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 
       35.34        28.18        32.68        26.01        21.14         6.08 
TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 
       30.94         3.68        19.76         5.33         2.93         2.01 
TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7230 
        2.37        14.47        28.54         0.79        28.60         1.68 
TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 
        2.37         2.93         1.71         0.72         2.10         2.66 
TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 
        1.74         1.48         1.68         2.07        24.59        26.04 
TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 
        1.97         1.12         3.22        30.51         1.48        17.85 
TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 
       24.56         1.84        19.36        22.42         3.12        23.87 
TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 
        2.17         2.27         1.94        17.95        22.32         1.58 
TCGA-HC-8265 TCGA-HC-A48F TCGA-HC-A631 TCGA-HC-A6AL TCGA-HC-A6AO TCGA-HC-A6AP 
       15.88        22.36         1.78         2.20         5.49         2.33 
TCGA-HC-A6AQ TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
        3.48         1.25         4.41        88.24        82.92        43.69 
TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N 
       20.19        12.30        21.76        17.03        16.04        16.54 
TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 
       16.14        20.52        14.93        17.19         6.02        13.32 
TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L 
       17.36         9.17         9.17        10.19         6.77        10.39 
TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52C TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y 
       14.37        20.28         5.85        93.99        56.28        44.68 
TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 
       61.78       115.86        30.02       151.36        67.59        90.51 
TCGA-KK-A6E5 TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IB TCGA-KK-A8IF 
       49.25        27.62        34.95        22.75         2.73        26.43 
TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 
       20.65         5.19         6.87         9.93        13.15        27.02 
TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN 
       25.08        15.88        18.84         3.19        41.00       114.64 
TCGA-QU-A6IO TCGA-QU-A6IP TCGA-TP-A8TT TCGA-TP-A8TV TCGA-VN-A88I TCGA-VN-A88K 
       47.21        86.14        11.90         8.19         8.84        25.51 
TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q 
       12.95         6.02        15.52        15.81        30.15        32.91 
TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B 
       15.09         4.34       106.95        94.65        23.93        75.91 
TCGA-VP-A87C TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N 
       55.56        66.97        21.80        48.85        21.53        17.82 
TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DK 
        5.79        37.18        27.81         3.91        38.04         9.04 
TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA 
        2.99        25.97        31.96        31.96        28.54        30.58 
TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-Y6-A8TL TCGA-YL-A8HJ 
       29.23        27.09        37.02        39.65        25.48        52.96 
TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8SA 
       49.02        38.56        36.95        71.77        62.14        16.83 
TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SP TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI 
       28.77        47.38        71.34         7.00        14.04        41.39 
TCGA-YL-A9WJ TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX 
       60.99        24.33        49.91        28.34         1.64         4.93 
TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9ND 
        1.12         7.86         6.02 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              0.76               0.30 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            113.33             151.36 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             34.06              22.06 
[1] "0.8 - 113.3 (34.1)" "0.3 - 151.4 (22.1)"
[1] "hr="     "9.4e+07"
D60V2, continuous
                    vv
clus                  T2  T3  T4
  13Q LOSS MUTATED    14  38   1
  13Q LOSS WILD-TYPE 136 168   4
D60V3, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T2               14                136
  T3               38                168
  T4                1                  4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V4, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    36  12
  13Q LOSS WILD-TYPE 227  32
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     36   12
  13Q LOSS WILD-TYPE  227   32
   clus
vv  13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  0               36                227
  1               12                 32
[1] 2 2
[1] FALSE
D60V5, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     1  52
  13Q LOSS WILD-TYPE  12 298
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      1   52
  13Q LOSS WILD-TYPE   12  298
                                        clus
vv                                       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                1                 12
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  52                298
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  13Q LOSS MUTATED    30  19   0   2
  13Q LOSS WILD-TYPE 213  71   5   9
D60V6, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  R0               30                213
  R1               19                 71
  R2                0                  5
  RX                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"
D60V7, continuous
D60V8, continuous
D60V9, continuous
D60V10, continuous
D60V11, continuous
D60V12, continuous
D60V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  13Q LOSS MUTATED       0                         2    19
  13Q LOSS WILD-TYPE     2                         5   127
D60V14, multiclass
                           clus
vv                          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                2                  5
  WHITE                                   19                127
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(61) Variable = 14Q LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                  0   1
  14Q LOSS MUTATED    17   1
  14Q LOSS WILD-TYPE 338   5
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                18                343 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                 1                  5 
$`14Q LOSS MUTATED`
TCGA-EJ-7783 TCGA-EJ-7784 TCGA-G9-6361 TCGA-G9-6499 TCGA-G9-7521 TCGA-G9-7523 
       25.87        25.68        46.52        50.73        30.97        28.18 
TCGA-HC-7213 TCGA-HC-7821 TCGA-HI-7171 TCGA-J4-A67O TCGA-VP-A875 TCGA-VP-A87K 
        1.97         1.84        43.69        16.14        26.47        21.53 
TCGA-YL-A8HO TCGA-YL-A8SB TCGA-YL-A8SJ TCGA-YL-A8SL TCGA-YL-A8SQ TCGA-YL-A9WX 
       71.77        45.50        45.86        26.24        62.79        49.91 

$`14Q LOSS WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 
        1.02         2.04         0.92        44.02        12.00         1.02 
TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 
       23.01         1.02        15.06        24.03         2.04        13.02 
TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 
       15.98        26.99         9.99        32.02        33.01         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        27.16        33.11        19.56        13.32        29.79 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        26.30        45.73        28.93        30.31 
TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 
       27.19        23.90        38.93        48.13        36.69        48.53 
TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 
       38.53        36.23        60.23        46.55        47.80        52.27 
TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 
       64.50        51.88        68.35        43.07        36.66        38.76 
TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 
       39.75        60.23        41.85        47.87        29.06        27.02 
TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 
       49.02        61.15        83.57        21.80         9.70         9.50 
TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 
        9.37        16.77         7.66        17.52         5.75        27.68 
TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7785 TCGA-EJ-7786 
        6.28         0.30        23.90        38.37        20.55        14.53 
TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 
       14.14        18.15        19.59        17.29         3.75        23.05 
TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8474 TCGA-EJ-A46B 
       19.92        64.47        63.98        26.99        10.32         5.33 
TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I 
        4.24        17.49         9.83         3.06         7.53        21.96 
TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J 
       17.62        12.92        13.71        18.41         9.14         2.99 
TCGA-EJ-A65M TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V 
        7.56        28.41        15.42        13.45         8.98        17.23 
TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 
       16.24         1.78        41.62        87.35        81.04        67.99 
TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 
       66.67        69.37        55.76        18.21        68.68        49.81 
TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6362 TCGA-G9-6363 
       46.16        50.70        49.35        47.15        47.44        45.30 
TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 
       39.39        44.81         3.32        40.18        39.95        38.01 
TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 
       40.31        26.66        31.50        37.97        45.80        25.15 
TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-7509 TCGA-G9-7510 
       27.29        58.22        56.75        52.87        38.27        38.96 
TCGA-G9-7519 TCGA-G9-7522 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 
       27.91        35.34        32.68        26.01        21.14         6.08 
TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 
       30.94         3.68        19.76         5.33         2.93         2.01 
TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7230 
        2.37        14.47        28.54         0.79        28.60         1.68 
TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 
        2.37         2.93         1.71         0.72         2.10         2.66 
TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 
        1.74         1.48         1.68         2.07        24.59        26.04 
TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 
        1.97         1.12         3.22        30.51         1.48        17.85 
TCGA-HC-7820 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 
       24.56        19.36        22.42         3.12        23.87         2.17 
TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 
        2.27         1.94        17.95        22.32         1.58        15.88 
TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL 
        1.15        22.36         0.76         1.78         2.01         2.20 
TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX 
        1.61         5.49         2.33         3.48         1.45         1.25 
TCGA-HC-A6HY TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-J4-8198 TCGA-J4-8200 
        4.41        78.61        88.24        82.92        20.19        12.30 
TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67Q TCGA-J4-A67R 
       21.76        17.03        16.04        16.54        20.52        14.93 
TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I 
       17.19         6.02        13.32        17.36         9.17         9.17 
TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B 
       10.19         6.77        10.39        14.37        20.28        13.87 
TCGA-J9-A52C TCGA-J9-A52E TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z 
        5.85        10.62        93.99        56.28        44.68        61.78 
TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 
      115.86        30.02        54.54       151.36        67.59        90.51 
TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AZ TCGA-KK-A7B1 
       49.25       113.33        67.07        58.19        27.62        34.95 
TCGA-KK-A7B2 TCGA-KK-A8IB TCGA-KK-A8IF TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z 
       22.75         2.73        26.43        20.65         5.19         6.87 
TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 
        9.93        13.15        27.02        25.08        15.88        18.84 
TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-TP-A8TT 
        3.19        41.00       114.64        47.21        86.14        11.90 
TCGA-TP-A8TV TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N 
        8.19         8.84        25.51        12.95         6.02        15.52 
TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 
       15.81        30.15        32.91        15.09         4.34       106.95 
TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D 
       84.69        94.65        23.93        75.91        55.56        60.92 
TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ 
       66.97        21.80        48.85        17.82         5.79        37.18 
TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ 
       27.81         3.91        38.04        48.03         9.04         2.99 
TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA 
       25.97        31.96        31.50        31.96        28.54        30.58 
TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-Y6-A8TL TCGA-YL-A8HJ 
       29.23        27.09        37.02        39.65        25.48        52.96 
TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA 
       49.02        38.56        36.95        62.14        60.56        16.83 
TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SK TCGA-YL-A8SO 
       41.46        45.14        28.77        47.38        37.97       106.75 
TCGA-YL-A8SP TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK 
       71.34         7.00        14.04        41.39        60.99        62.37 
TCGA-YL-A9WL TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       24.33        28.34         1.64         4.93         1.12         7.86 
TCGA-ZG-A9ND 
        6.02 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              1.84               0.30 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             71.77             151.36 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            29.575             23.010 
[1] "1.8 - 71.8 (29.6)"  "0.3 - 151.4 (23.0)"
[1] "hr=" "2.6"
D61V2, continuous
                    vv
clus                  T2  T3  T4
  14Q LOSS MUTATED     2  16   0
  14Q LOSS WILD-TYPE 148 190   5
D61V3, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  T2                2                148
  T3               16                190
  T4                0                  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"
D61V4, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    14   4
  14Q LOSS WILD-TYPE 249  40
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     14    4
  14Q LOSS WILD-TYPE  249   40
   clus
vv  14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  0               14                249
  1                4                 40
[1] 2 2
[1] FALSE
D61V5, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED     1  17
  14Q LOSS WILD-TYPE  12 333
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      1   17
  14Q LOSS WILD-TYPE   12  333
                                        clus
vv                                       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                1                 12
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  17                333
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  14Q LOSS MUTATED     9   8   0   0
  14Q LOSS WILD-TYPE 234  82   5  11
D61V6, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  R0                9                234
  R1                8                 82
  R2                0                  5
  RX                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"
D61V7, continuous
D61V8, continuous
D61V9, continuous
D61V10, continuous
D61V11, continuous
D61V12, continuous
D61V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  14Q LOSS MUTATED       0                         0     7
  14Q LOSS WILD-TYPE     2                         7   139
D61V14, multiclass
                           clus
vv                          14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  7
  WHITE                                    7                139
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(62) Variable = 15Q LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                  0   1
  15Q LOSS MUTATED    21   1
  15Q LOSS WILD-TYPE 334   5
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                22                339 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 1                  5 
$`15Q LOSS MUTATED`
TCGA-CH-5751 TCGA-CH-5753 TCGA-EJ-5507 TCGA-EJ-7783 TCGA-FC-A4JI TCGA-G9-7521 
       35.01         1.02        23.90        25.87        13.45        30.97 
TCGA-HC-7213 TCGA-HC-7749 TCGA-HC-7752 TCGA-HC-7821 TCGA-HC-8216 TCGA-HI-7168 
        1.97         1.97         3.22         1.84        22.42        78.61 
TCGA-HI-7171 TCGA-J9-A52E TCGA-KK-A59Z TCGA-KK-A6E0 TCGA-VP-A872 TCGA-XK-AAJA 
       43.69        10.62        61.78        30.02       106.95        30.58 
TCGA-XK-AAJT TCGA-YL-A8HO TCGA-YL-A8SB TCGA-YL-A8SQ 
       37.02        71.77        45.50        62.79 

$`15Q LOSS WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5754 
        1.97        24.03         1.02        13.02        31.00         2.04 
TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 
        0.92        44.02        12.00         1.02        23.01         1.02 
TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 
       15.06        24.03         2.04        13.02        15.98        26.99 
TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 
        9.99        32.02        33.01         2.99        29.00        27.16 
TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 
       33.11        19.56        13.32        29.79        46.52        44.88 
TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5508 
       26.30        45.73        28.93        30.31        27.19        38.93 
TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 
       48.13        36.69        48.53        38.53        36.23        60.23 
TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 
       46.55        47.80        52.27        64.50        51.88        68.35 
TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 
       43.07        36.66        38.76        39.75        60.23        41.85 
TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 
       47.87        29.06        27.02        49.02        61.15        83.57 
TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 
       21.80         9.70         9.50         9.37        16.77         7.66 
TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 
       17.52         5.75        27.68         6.28         0.30        23.90 
TCGA-EJ-7782 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 
       38.37        25.68        20.55        14.53        14.14        18.15 
TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 
       19.59        17.29         3.75        23.05        19.92        64.47 
TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E 
       63.98        26.99        10.32         5.33         4.24        17.49 
TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D 
        9.83         3.06         7.53        21.96        17.62        12.92 
TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-FC-7708 
       13.71        18.41         9.14         2.99         7.56        28.41 
TCGA-FC-7961 TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 
       15.42         8.98        17.23        16.24         1.78        41.62 
TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 
       87.35        81.04        67.99        66.67        69.37        55.76 
TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 
       18.21        68.68        49.81        46.16        50.70        49.35 
TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 
       47.15        46.52        47.44        45.30        39.39        44.81 
TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 
        3.32        40.18        39.95        38.01        40.31        26.66 
TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 
       31.50        37.97        45.80        25.15        27.29        58.22 
TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 
       56.75        52.87        50.73        38.27        38.96        27.91 
TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 
       35.34        28.18        32.68        26.01        21.14         6.08 
TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 
       30.94         3.68        19.76         5.33         2.93         2.01 
TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7230 
        2.37        14.47        28.54         0.79        28.60         1.68 
TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 
        2.37         2.93         1.71         0.72         2.10         2.66 
TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 
        1.74         1.48         1.68         2.07        24.59        26.04 
TCGA-HC-7750 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-8213 
        1.12        30.51         1.48        17.85        24.56        19.36 
TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 
        3.12        23.87         2.17         2.27         1.94        17.95 
TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV 
       22.32         1.58        15.88         1.15        22.36         0.76 
TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP 
        1.78         2.01         2.20         1.61         5.49         2.33 
TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HI-7169 TCGA-HI-7170 
        3.48         1.45         1.25         4.41        88.24        82.92 
TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N 
       20.19        12.30        21.76        17.03        16.04        16.54 
TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 
       16.14        20.52        14.93        17.19         6.02        13.32 
TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L 
       17.36         9.17         9.17        10.19         6.77        10.39 
TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52C TCGA-KK-A59V TCGA-KK-A59X 
       14.37        20.28        13.87         5.85        93.99        56.28 
TCGA-KK-A59Y TCGA-KK-A6DY TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 
       44.68       115.86        54.54       151.36        67.59        90.51 
TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AZ TCGA-KK-A7B1 
       49.25       113.33        67.07        58.19        27.62        34.95 
TCGA-KK-A7B2 TCGA-KK-A8IB TCGA-KK-A8IF TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z 
       22.75         2.73        26.43        20.65         5.19         6.87 
TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 
        9.93        13.15        27.02        25.08        15.88        18.84 
TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-TP-A8TT 
        3.19        41.00       114.64        47.21        86.14        11.90 
TCGA-TP-A8TV TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N 
        8.19         8.84        25.51        12.95         6.02        15.52 
TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A875 
       15.81        30.15        32.91        15.09         4.34        26.47 
TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D 
       84.69        94.65        23.93        75.91        55.56        60.92 
TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI 
       66.97        21.80        48.85        21.53        17.82         5.79 
TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK 
       37.18        27.81         3.91        38.04        48.03         9.04 
TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 
        2.99        25.97        31.96        31.50        31.96        28.54 
TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJU TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK 
       29.23        27.09        39.65        25.48        52.96        49.02 
TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SC 
       38.56        36.95        62.14        60.56        16.83        41.46 
TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL 
       45.14        28.77        47.38        45.86        37.97        26.24 
TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ 
      106.75        71.34         7.00        14.04        41.39        60.99 
TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX 
       62.37        24.33        49.91        28.34         1.64         4.93 
TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9ND 
        1.12         7.86         6.02 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              1.02               0.30 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            106.95             151.36 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             30.30              23.87 
[1] "1.0 - 107.0 (30.3)" "0.3 - 151.4 (23.9)"
[1] "hr=" "2.1"
D62V2, continuous
                    vv
clus                  T2  T3  T4
  15Q LOSS MUTATED     2  19   1
  15Q LOSS WILD-TYPE 148 187   4
D62V3, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T2                2                148
  T3               19                187
  T4                1                  4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V4, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED    16   5
  15Q LOSS WILD-TYPE 247  39
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     16    5
  15Q LOSS WILD-TYPE  247   39
   clus
vv  15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  0               16                247
  1                5                 39
[1] 2 2
[1] FALSE
D62V5, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     1  21
  15Q LOSS WILD-TYPE  12 329
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      1   21
  15Q LOSS WILD-TYPE   12  329
                                        clus
vv                                       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                1                 12
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  21                329
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  15Q LOSS MUTATED    14   7   0   0
  15Q LOSS WILD-TYPE 229  83   5  11
D62V6, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  R0               14                229
  R1                7                 83
  R2                0                  5
  RX                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"
D62V7, continuous
D62V8, continuous
D62V9, continuous
D62V10, continuous
D62V11, continuous
D62V12, continuous
D62V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  15Q LOSS MUTATED       0                         0    10
  15Q LOSS WILD-TYPE     2                         7   136
D62V14, multiclass
                           clus
vv                          15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  7
  WHITE                                   10                136
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(63) Variable = 16P LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                  0   1
  16P LOSS MUTATED    21   0
  16P LOSS WILD-TYPE 334   6
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                21                340 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 0                  6 
$`16P LOSS MUTATED`
TCGA-CH-5739 TCGA-EJ-5498 TCGA-EJ-5514 TCGA-EJ-7123 TCGA-EJ-7781 TCGA-EJ-7784 
       22.06        29.79        36.23        49.02        23.90        25.68 
TCGA-EJ-8469 TCGA-G9-6329 TCGA-G9-7523 TCGA-HC-7078 TCGA-HC-7749 TCGA-HC-A4ZV 
       63.98        41.62        28.18         5.33         1.97         0.76 
TCGA-HC-A6HX TCGA-HC-A6HY TCGA-J4-A83I TCGA-KK-A59Z TCGA-KK-A6E7 TCGA-VP-AA1N 
        1.25         4.41         9.17        61.78        67.07        17.82 
TCGA-YL-A8HO TCGA-YL-A8SJ TCGA-YL-A8SQ 
       71.77        45.86        62.79 

$`16P LOSS WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 
        2.99         6.97         1.02        12.99        13.97         1.97 
TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 
       24.03         1.02        13.02        35.01        31.00         1.02 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 
        2.04         0.92        44.02        12.00         1.02        23.01 
TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 
        1.02        15.06        24.03         2.04        13.02        15.98 
TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 
       26.99         9.99        32.02        33.01         2.99        29.00 
TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5499 TCGA-EJ-5501 
       27.16        33.11        19.56        13.32        46.52        44.88 
TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 
       26.30        45.73        28.93        30.31        27.19        23.90 
TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5515 
       38.93        48.13        36.69        48.53        38.53        60.23 
TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 
       46.55        47.80        52.27        64.50        51.88        68.35 
TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 
       43.07        36.66        38.76        39.75        60.23        41.85 
TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 
       47.87        29.06        27.02        61.15        83.57        21.80 
TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 
        9.70         9.50         9.37        16.77         7.66        17.52 
TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7782 TCGA-EJ-7783 
        5.75        27.68         6.28         0.30        38.37        25.87 
TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 
       20.55        14.53        14.14        18.15        19.59        17.29 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8470 TCGA-EJ-8474 
        3.75        23.05        19.92        64.47        26.99        10.32 
TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H 
        5.33         4.24        17.49         9.83         3.06         7.53 
TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G 
       21.96        17.62        12.92        13.71        18.41         9.14 
TCGA-EJ-A65J TCGA-EJ-A65M TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB 
        2.99         7.56        28.41        15.42        13.45         8.98 
TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 
       17.23        16.24         1.78        87.35        81.04        67.99 
TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 
       66.67        69.37        55.76        18.21        68.68        49.81 
TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 
       46.16        50.70        49.35        47.15        46.52        47.44 
TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 
       45.30        39.39        44.81         3.32        40.18        39.95 
TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 
       38.01        40.31        26.66        31.50        37.97        45.80 
TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 
       25.15        27.29        58.22        56.75        52.87        50.73 
TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7525 
       38.27        38.96        27.91        30.97        35.34        32.68 
TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 
       26.01        21.14         6.08        30.94         3.68        19.76 
TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 
        2.93         2.01         2.37        14.47        28.54         0.79 
TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 
       28.60         1.97         1.68         2.37         2.93         1.71 
TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 
        0.72         2.10         2.66         1.74         1.48         1.68 
TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 
        2.07        24.59        26.04         1.12         3.22        30.51 
TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 
        1.48        17.85        24.56         1.84        19.36        22.42 
TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 
        3.12        23.87         2.17         2.27         1.94        17.95 
TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A631 
       22.32         1.58        15.88         1.15        22.36         1.78 
TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ 
        2.01         2.20         1.61         5.49         2.33         3.48 
TCGA-HC-A6AS TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 
        1.45        78.61        88.24        82.92        43.69        20.19 
TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O 
       12.30        21.76        17.03        16.04        16.54        16.14 
TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 
       20.52        14.93        17.19         6.02        13.32        17.36 
TCGA-J4-A6M7 TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N 
        9.17        10.19         6.77        10.39        14.37        20.28 
TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y 
       13.87         5.85        10.62        93.99        56.28        44.68 
TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 
      115.86        30.02        54.54       151.36        67.59        90.51 
TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E8 TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 
       49.25       113.33        58.19        27.62        34.95        22.75 
TCGA-KK-A8IB TCGA-KK-A8IF TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 
        2.73        26.43        20.65         5.19         6.87         9.93 
TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL 
       13.15        27.02        25.08        15.88        18.84         3.19 
TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-TP-A8TT TCGA-TP-A8TV 
       41.00       114.64        47.21        86.14        11.90         8.19 
TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O 
        8.84        25.51        12.95         6.02        15.52        15.81 
TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 
       30.15        32.91        15.09         4.34       106.95        26.47 
TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D 
       84.69        94.65        23.93        75.91        55.56        60.92 
TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KQ 
       66.97        21.80        48.85        21.53         5.79        37.18 
TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ 
       27.81         3.91        38.04        48.03         9.04         2.99 
TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA 
       25.97        31.96        31.50        31.96        28.54        30.58 
TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-Y6-A8TL TCGA-YL-A8HJ 
       29.23        27.09        37.02        39.65        25.48        52.96 
TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA 
       49.02        38.56        36.95        62.14        60.56        16.83 
TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SK 
       45.50        41.46        45.14        28.77        47.38        37.97 
TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI 
       26.24       106.75        71.34         7.00        14.04        41.39 
TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW 
       60.99        62.37        24.33        49.91        28.34         1.64 
TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9ND 
        4.93         1.12         7.86         6.02 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              0.76               0.30 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             71.77             151.36 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
            28.180             23.885 
[1] "0.8 - 71.8 (28.2)"  "0.3 - 151.4 (23.9)"
[1] "hr="     "7.6e+07"
D63V2, continuous
                    vv
clus                  T2  T3  T4
  16P LOSS MUTATED     9  12   0
  16P LOSS WILD-TYPE 141 194   5
D63V3, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  T2                9                141
  T3               12                194
  T4                0                  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"
D63V4, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    18   1
  16P LOSS WILD-TYPE 245  43
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     18    1
  16P LOSS WILD-TYPE  245   43
   clus
vv  16P LOSS MUTATED 16P LOSS WILD-TYPE
  0               18                245
  1                1                 43
[1] 2 2
[1] FALSE
D63V5, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     0  21
  16P LOSS WILD-TYPE  13 329
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      0   21
  16P LOSS WILD-TYPE   13  329
                                        clus
vv                                       16P LOSS MUTATED 16P LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                0                 13
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  21                329
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  16P LOSS MUTATED    14   6   0   1
  16P LOSS WILD-TYPE 229  84   5  10
D63V6, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  R0               14                229
  R1                6                 84
  R2                0                  5
  RX                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"
D63V7, continuous
D63V8, continuous
D63V9, continuous
D63V10, continuous
D63V11, continuous
D63V12, continuous
D63V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16P LOSS MUTATED       0                         0     9
  16P LOSS WILD-TYPE     2                         7   137
D63V14, multiclass
                           clus
vv                          16P LOSS MUTATED 16P LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  7
  WHITE                                    9                137
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(64) Variable = 16Q LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                  0   1
  16Q LOSS MUTATED    68   1
  16Q LOSS WILD-TYPE 287   5
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                69                292 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 1                  5 
$`16Q LOSS MUTATED`
TCGA-CH-5739 TCGA-CH-5751 TCGA-CH-5764 TCGA-CH-5788 TCGA-CH-5791 TCGA-EJ-5495 
       22.06        35.01         1.02        26.99        33.01        33.11 
TCGA-EJ-5498 TCGA-EJ-5514 TCGA-EJ-5525 TCGA-EJ-5527 TCGA-EJ-7123 TCGA-EJ-7312 
       29.79        36.23        36.66        39.75        49.02        21.80 
TCGA-EJ-7318 TCGA-EJ-7327 TCGA-EJ-7781 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7789 
       16.77         5.75        23.90        25.87        25.68        18.15 
TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-A46F TCGA-FC-7961 TCGA-FC-A5OB TCGA-G9-6329 
       63.98        26.99         9.83        15.42         8.98        41.62 
TCGA-G9-6343 TCGA-G9-6362 TCGA-G9-6384 TCGA-G9-6496 TCGA-G9-7521 TCGA-G9-7523 
       18.21        47.44        25.15        56.75        30.97        28.18 
TCGA-HC-7078 TCGA-HC-7213 TCGA-HC-7736 TCGA-HC-7742 TCGA-HC-7749 TCGA-HC-7821 
        5.33         1.97         0.72         1.48         1.97         1.84 
TCGA-HC-8216 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A632 TCGA-HC-A6HX TCGA-HC-A6HY 
       22.42        22.36         0.76         2.01         1.25         4.41 
TCGA-HI-7168 TCGA-HI-7171 TCGA-J4-A83I TCGA-J9-A52B TCGA-KK-A59Z TCGA-KK-A6DY 
       78.61        43.69         9.17        13.87        61.78       115.86 
TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A8IF TCGA-QU-A6IO TCGA-VN-A88M TCGA-VN-A88N 
      113.33        67.07        26.43        47.21         6.02        15.52 
TCGA-VN-A88Q TCGA-VP-A87K TCGA-VP-AA1N TCGA-X4-A8KQ TCGA-XK-AAIR TCGA-XK-AAJP 
       32.91        21.53        17.82        37.18        31.96        29.23 
TCGA-XK-AAJR TCGA-YL-A8HO TCGA-YL-A8SC TCGA-YL-A8SJ TCGA-YL-A8SL TCGA-YL-A8SQ 
       27.09        71.77        41.46        45.86        26.24        62.79 
TCGA-YL-A8SR TCGA-YL-A9WK TCGA-YL-A9WX 
        7.00        62.37        49.91 

$`16Q LOSS WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 
        2.99         6.97         1.02        12.99        13.97         1.97 
TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 
       24.03         1.02        13.02        31.00         1.02         2.04 
TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 
        0.92        44.02        12.00        23.01         1.02        15.06 
TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5789 TCGA-CH-5790 
       24.03         2.04        13.02        15.98         9.99        32.02 
TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5499 
        2.99        29.00        27.16        19.56        13.32        46.52 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       44.88        26.30        45.73        28.93        30.31        27.19 
TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       23.90        38.93        48.13        36.69        48.53        38.53 
TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 
       60.23        46.55        47.80        52.27        64.50        51.88 
TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5526 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 
       68.35        43.07        38.76        60.23        41.85        47.87 
TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7314 TCGA-EJ-7315 
       29.06        27.02        61.15        83.57         9.70         9.50 
TCGA-EJ-7317 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 
        9.37         7.66        17.52        27.68         6.28         0.30 
TCGA-EJ-7782 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7791 TCGA-EJ-7792 
       38.37        20.55        14.53        14.14        19.59        17.29 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8474 TCGA-EJ-A46B 
        3.75        23.05        19.92        64.47        10.32         5.33 
TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B 
        4.24        17.49         3.06         7.53        21.96        17.62 
TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M 
       12.92        13.71        18.41         9.14         2.99         7.56 
TCGA-FC-7708 TCGA-FC-A4JI TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6332 
       28.41        13.45        17.23        16.24         1.78        87.35 
TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6347 
       81.04        67.99        66.67        69.37        55.76        68.68 
TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 
       49.81        46.16        50.70        49.35        47.15        46.52 
TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 
       45.30        39.39        44.81         3.32        40.18        39.95 
TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 
       38.01        40.31        26.66        31.50        37.97        45.80 
TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 
       27.29        58.22        52.87        50.73        38.27        38.96 
TCGA-G9-7519 TCGA-G9-7522 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 
       27.91        35.34        32.68        26.01        21.14         6.08 
TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 
       30.94         3.68        19.76         2.93         2.01         2.37 
TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7230 TCGA-HC-7231 
       14.47        28.54         0.79        28.60         1.68         2.37 
TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7744 
        2.93         1.71         2.10         2.66         1.74         1.68 
TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 
        2.07        24.59        26.04         1.12         3.22        30.51 
TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-8213 TCGA-HC-8256 TCGA-HC-8257 
        1.48        17.85        24.56        19.36         3.12        23.87 
TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 
        2.17         2.27         1.94        17.95        22.32         1.58 
TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A631 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO 
       15.88         1.15         1.78         2.20         1.61         5.49 
TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HI-7169 TCGA-HI-7170 TCGA-J4-8198 
        2.33         3.48         1.45        88.24        82.92        20.19 
TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O 
       12.30        21.76        17.03        16.04        16.54        16.14 
TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 
       20.52        14.93        17.19         6.02        13.32        17.36 
TCGA-J4-A6M7 TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N 
        9.17        10.19         6.77        10.39        14.37        20.28 
TCGA-J9-A52C TCGA-J9-A52E TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A6E0 
        5.85        10.62        93.99        56.28        44.68        30.02 
TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E8 
       54.54       151.36        67.59        90.51        49.25        58.19 
TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IB TCGA-KK-A8IL TCGA-M7-A71Y 
       27.62        34.95        22.75         2.73        20.65         5.19 
TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 
        6.87         9.93        13.15        27.02        25.08        15.88 
TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IP TCGA-TP-A8TT 
       18.84         3.19        41.00       114.64        86.14        11.90 
TCGA-TP-A8TV TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88O TCGA-VN-A88P 
        8.19         8.84        25.51        12.95        15.81        30.15 
TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 
       15.09         4.34       106.95        26.47        84.69        94.65 
TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H 
       23.93        75.91        55.56        60.92        66.97        21.80 
TCGA-VP-A87J TCGA-WW-A8ZI TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DI 
       48.85         5.79        27.81         3.91        38.04        48.03 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 
        9.04         2.99        25.97        31.50        31.96        28.54 
TCGA-XK-AAJA TCGA-XK-AAJT TCGA-XK-AAJU TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK 
       30.58        37.02        39.65        25.48        52.96        49.02 
TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB 
       38.56        36.95        62.14        60.56        16.83        45.50 
TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SK TCGA-YL-A8SO TCGA-YL-A8SP 
       45.14        28.77        47.38        37.97       106.75        71.34 
TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WL TCGA-YL-A9WY TCGA-ZG-A8QW 
       14.04        41.39        60.99        24.33        28.34         1.64 
TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9ND 
        4.93         1.12         7.86         6.02 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              0.72               0.30 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
            115.86             151.36 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             26.43              22.88 
[1] "0.7 - 115.9 (26.4)" "0.3 - 151.4 (22.9)"
[1] "hr=" "1.4"
D64V2, continuous
                    vv
clus                  T2  T3  T4
  16Q LOSS MUTATED    21  47   1
  16Q LOSS WILD-TYPE 129 159   4
D64V3, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  T2               21                129
  T3               47                159
  T4                1                  4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V4, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    55  10
  16Q LOSS WILD-TYPE 208  34
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     55   10
  16Q LOSS WILD-TYPE  208   34
   clus
vv  16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  0               55                208
  1               10                 34
[1] 2 2
[1] FALSE
D64V5, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED     2  67
  16Q LOSS WILD-TYPE  11 283
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      2   67
  16Q LOSS WILD-TYPE   11  283
                                        clus
vv                                       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                2                 11
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  67                283
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  16Q LOSS MUTATED    43  20   0   2
  16Q LOSS WILD-TYPE 200  70   5   9
D64V6, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  R0               43                200
  R1               20                 70
  R2                0                  5
  RX                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"
D64V7, continuous
D64V8, continuous
D64V9, continuous
D64V10, continuous
D64V11, continuous
D64V12, continuous
D64V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16Q LOSS MUTATED       0                         1    29
  16Q LOSS WILD-TYPE     2                         6   117
D64V14, multiclass
                           clus
vv                          16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                1                  6
  WHITE                                   29                117
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(65) Variable = 17P LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                  0   1
  17P LOSS MUTATED    53   0
  17P LOSS WILD-TYPE 302   6
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                53                308 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 0                  6 
$`17P LOSS MUTATED`
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5764 TCGA-CH-5790 TCGA-EJ-5507 TCGA-EJ-5514 
        2.04         0.92         1.02        32.02        23.90        36.23 
TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5526 TCGA-EJ-7315 TCGA-EJ-7781 TCGA-EJ-7797 
       64.50        51.88        38.76         9.50        23.90        19.92 
TCGA-EJ-A46F TCGA-FC-A4JI TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6494 TCGA-G9-6499 
        9.83        13.45        26.66        31.50        58.22        50.73 
TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7521 TCGA-G9-A9S7 TCGA-HC-7078 TCGA-HC-7213 
       38.27        38.96        30.97        21.14         5.33         1.97 
TCGA-HC-7230 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV 
        1.68         1.48         1.68         1.15        22.36         0.76 
TCGA-HI-7168 TCGA-J9-A52B TCGA-J9-A52E TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E1 
       78.61        13.87        10.62        61.78       115.86        54.54 
TCGA-KK-A6E4 TCGA-KK-A6E6 TCGA-M7-A725 TCGA-VP-A875 TCGA-VP-A87C TCGA-VP-A87D 
       90.51       113.33        18.84        26.47        55.56        60.92 
TCGA-VP-A87K TCGA-VP-AA1N TCGA-XK-AAJA TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HO 
       21.53        17.82        30.58        49.02        38.56        71.77 
TCGA-YL-A8SB TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SQ TCGA-YL-A9WH 
       45.50        37.97        26.24        62.79        14.04 

$`17P LOSS WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5753 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 
        1.02        44.02        12.00        23.01         1.02        15.06 
TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 
       24.03         2.04        13.02        15.98        26.99         9.99 
TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 
       33.01         2.99        29.00        27.16        33.11        19.56 
TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 
       13.32        29.79        46.52        44.88        26.30        45.73 
TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 
       28.93        30.31        27.19        38.93        48.13        36.69 
TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 
       48.53        38.53        60.23        46.55        47.80        52.27 
TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 
       68.35        43.07        36.66        39.75        60.23        41.85 
TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 
       47.87        29.06        27.02        49.02        61.15        83.57 
TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 
       21.80         9.70         9.37        16.77         7.66        17.52 
TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7782 TCGA-EJ-7783 
        5.75        27.68         6.28         0.30        38.37        25.87 
TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 
       25.68        20.55        14.53        14.14        18.15        19.59 
TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 
       17.29         3.75        23.05        64.47        63.98        26.99 
TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46G TCGA-EJ-A46H 
       10.32         5.33         4.24        17.49         3.06         7.53 
TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G 
       21.96        17.62        12.92        13.71        18.41         9.14 
TCGA-EJ-A65J TCGA-EJ-A65M TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A5OB TCGA-FC-A66V 
        2.99         7.56        28.41        15.42         8.98        17.23 
TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 
       16.24         1.78        41.62        87.35        81.04        67.99 
TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 
       66.67        69.37        55.76        18.21        68.68        49.81 
TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 
       46.16        50.70        49.35        47.15        46.52        47.44 
TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 
       45.30        39.39        44.81         3.32        40.18        39.95 
TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 
       38.01        40.31        37.97        45.80        25.15        27.29 
TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-7519 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 
       56.75        52.87        27.91        35.34        28.18        32.68 
TCGA-G9-A9S0 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7079 
       26.01         6.08        30.94         3.68        19.76         2.93 
TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 
        2.01         2.37        14.47        28.54         0.79        28.60 
TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 
        2.37         2.93         1.71         0.72         2.10         2.66 
TCGA-HC-7740 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 
        1.74         2.07        24.59        26.04         1.97         1.12 
TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 
        3.22        30.51         1.48        17.85        24.56         1.84 
TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 
       19.36        22.42         3.12        23.87         2.17         2.27 
TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-A631 
        1.94        17.95        22.32         1.58        15.88         1.78 
TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ 
        2.01         2.20         1.61         5.49         2.33         3.48 
TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
        1.45         1.25         4.41        88.24        82.92        43.69 
TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N 
       20.19        12.30        21.76        17.03        16.04        16.54 
TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 
       16.14        20.52        14.93        17.19         6.02        13.32 
TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L 
       17.36         9.17         9.17        10.19         6.77        10.39 
TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52C TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y 
       14.37        20.28         5.85        93.99        56.28        44.68 
TCGA-KK-A6E0 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E5 TCGA-KK-A6E7 TCGA-KK-A6E8 
       30.02       151.36        67.59        49.25        67.07        58.19 
TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IB TCGA-KK-A8IF TCGA-KK-A8IL 
       27.62        34.95        22.75         2.73        26.43        20.65 
TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 
        5.19         6.87         9.93        13.15        27.02        25.08 
TCGA-M7-A724 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP 
       15.88         3.19        41.00       114.64        47.21        86.14 
TCGA-TP-A8TT TCGA-TP-A8TV TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M 
       11.90         8.19         8.84        25.51        12.95         6.02 
TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 
       15.52        15.81        30.15        32.91        15.09         4.34 
TCGA-VP-A872 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87E 
      106.95        84.69        94.65        23.93        75.91        66.97 
TCGA-VP-A87H TCGA-VP-A87J TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR 
       21.80        48.85         5.79        37.18        27.81         3.91 
TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR 
       38.04        48.03         9.04         2.99        25.97        31.96 
TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT 
       31.50        31.96        28.54        29.23        27.09        37.02 
TCGA-XK-AAJU TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HM TCGA-YL-A8S8 TCGA-YL-A8S9 
       39.65        25.48        52.96        36.95        62.14        60.56 
TCGA-YL-A8SA TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ 
       16.83        41.46        45.14        28.77        47.38        45.86 
TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SR TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK 
      106.75        71.34         7.00        41.39        60.99        62.37 
TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY 
       24.33        49.91        28.34         1.64         4.93         1.12 
TCGA-ZG-A8QZ TCGA-ZG-A9ND 
        7.86         6.02 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.76               0.30 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            115.86             151.36 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             26.66              23.03 
[1] "0.8 - 115.9 (26.7)" "0.3 - 151.4 (23.0)"
[1] "hr="     "9.1e+07"
D65V2, continuous
                    vv
clus                  T2  T3  T4
  17P LOSS MUTATED    12  40   1
  17P LOSS WILD-TYPE 138 166   4
D65V3, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  T2               12                138
  T3               40                166
  T4                1                  4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V4, binary
                    cls
clus                   0   1
  17P LOSS MUTATED    37  13
  17P LOSS WILD-TYPE 226  31
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     37   13
  17P LOSS WILD-TYPE  226   31
   clus
vv  17P LOSS MUTATED 17P LOSS WILD-TYPE
  0               37                226
  1               13                 31
[1] 2 2
[1] FALSE
D65V5, binary
                    cls
clus                   0   1
  17P LOSS MUTATED     1  52
  17P LOSS WILD-TYPE  12 298
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      1   52
  17P LOSS WILD-TYPE   12  298
                                        clus
vv                                       17P LOSS MUTATED 17P LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                1                 12
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  52                298
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  17P LOSS MUTATED    32  20   0   1
  17P LOSS WILD-TYPE 211  70   5  10
D65V6, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  R0               32                211
  R1               20                 70
  R2                0                  5
  RX                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"
D65V7, continuous
D65V8, continuous
D65V9, continuous
D65V10, continuous
D65V11, continuous
D65V12, continuous
D65V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17P LOSS MUTATED       0                         0    22
  17P LOSS WILD-TYPE     2                         7   124
D65V14, multiclass
                           clus
vv                          17P LOSS MUTATED 17P LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  7
  WHITE                                   22                124
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(66) Variable = 17Q LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                  0   1
  17Q LOSS MUTATED    12   0
  17Q LOSS WILD-TYPE 343   6
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                12                349 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 0                  6 
$`17Q LOSS MUTATED`
TCGA-G9-6499 TCGA-HC-7213 TCGA-HC-7744 TCGA-HC-A48F TCGA-J9-A52E TCGA-KK-A6E4 
       50.73         1.97         1.68        22.36        10.62        90.51 
TCGA-M7-A725 TCGA-VP-A875 TCGA-VP-AA1N TCGA-XK-AAJA TCGA-YL-A8HO TCGA-YL-A8SQ 
       18.84        26.47        17.82        30.58        71.77        62.79 

$`17Q LOSS WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 
        1.02         2.04         0.92        44.02        12.00         1.02 
TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 
       23.01         1.02        15.06        24.03         2.04        13.02 
TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 
       15.98        26.99         9.99        32.02        33.01         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        27.16        33.11        19.56        13.32        29.79 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        26.30        45.73        28.93        30.31 
TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 
       27.19        23.90        38.93        48.13        36.69        48.53 
TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 
       38.53        36.23        60.23        46.55        47.80        52.27 
TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 
       64.50        51.88        68.35        43.07        36.66        38.76 
TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 
       39.75        60.23        41.85        47.87        29.06        27.02 
TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 
       49.02        61.15        83.57        21.80         9.70         9.50 
TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 
        9.37        16.77         7.66        17.52         5.75        27.68 
TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 
        6.28         0.30        23.90        38.37        25.87        25.68 
TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 
       20.55        14.53        14.14        18.15        19.59        17.29 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 
        3.75        23.05        19.92        64.47        63.98        26.99 
TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G 
       10.32         5.33         4.24        17.49         9.83         3.06 
TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F 
        7.53        21.96        17.62        12.92        13.71        18.41 
TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI 
        9.14         2.99         7.56        28.41        15.42        13.45 
TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 
        8.98        17.23        16.24         1.78        41.62        87.35 
TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 
       81.04        67.99        66.67        69.37        55.76        18.21 
TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 
       68.68        49.81        46.16        50.70        49.35        47.15 
TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 
       46.52        47.44        45.30        39.39        44.81         3.32 
TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 
       40.18        39.95        38.01        40.31        26.66        31.50 
TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 
       37.97        45.80        25.15        27.29        58.22        56.75 
TCGA-G9-6498 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 
       52.87        38.27        38.96        27.91        30.97        35.34 
TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX 
       28.18        32.68        26.01        21.14         6.08        30.94 
TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 
        3.68        19.76         5.33         2.93         2.01         2.37 
TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7230 TCGA-HC-7231 
       14.47        28.54         0.79        28.60         1.68         2.37 
TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 
        2.93         1.71         0.72         2.10         2.66         1.74 
TCGA-HC-7742 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 
        1.48         2.07        24.59        26.04         1.97         1.12 
TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 
        3.22        30.51         1.48        17.85        24.56         1.84 
TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 
       19.36        22.42         3.12        23.87         2.17         2.27 
TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 
        1.94        17.95        22.32         1.58        15.88         1.15 
TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO 
        0.76         1.78         2.01         2.20         1.61         5.49 
TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HI-7168 
        2.33         3.48         1.45         1.25         4.41        78.61 
TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K 
       88.24        82.92        43.69        20.19        12.30        21.76 
TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R 
       17.03        16.04        16.54        16.14        20.52        14.93 
TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I 
       17.19         6.02        13.32        17.36         9.17         9.17 
TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B 
       10.19         6.77        10.39        14.37        20.28        13.87 
TCGA-J9-A52C TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY 
        5.85        93.99        56.28        44.68        61.78       115.86 
TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E5 TCGA-KK-A6E6 
       30.02        54.54       151.36        67.59        49.25       113.33 
TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IB 
       67.07        58.19        27.62        34.95        22.75         2.73 
TCGA-KK-A8IF TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 
       26.43        20.65         5.19         6.87         9.93        13.15 
TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN 
       27.02        25.08        15.88         3.19        41.00       114.64 
TCGA-QU-A6IO TCGA-QU-A6IP TCGA-TP-A8TT TCGA-TP-A8TV TCGA-VN-A88I TCGA-VN-A88K 
       47.21        86.14        11.90         8.19         8.84        25.51 
TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q 
       12.95         6.02        15.52        15.81        30.15        32.91 
TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 
       15.09         4.34       106.95        84.69        94.65        23.93 
TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J 
       75.91        55.56        60.92        66.97        21.80        48.85 
TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83G 
       21.53         5.79        37.18        27.81         3.91        38.04 
TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV 
       48.03         9.04         2.99        25.97        31.96        31.50 
TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU 
       31.96        28.54        29.23        27.09        37.02        39.65 
TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8S8 
       25.48        52.96        49.02        38.56        36.95        62.14 
TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH 
       60.56        16.83        45.50        41.46        45.14        28.77 
TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP 
       47.38        45.86        37.97        26.24       106.75        71.34 
TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL 
        7.00        14.04        41.39        60.99        62.37        24.33 
TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       49.91        28.34         1.64         4.93         1.12         7.86 
TCGA-ZG-A9ND 
        6.02 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              1.68               0.30 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             90.51             151.36 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
            24.415             23.930 
[1] "1.7 - 90.5 (24.4)"  "0.3 - 151.4 (23.9)"
[1] "hr="     "2.6e+07"
D66V2, continuous
                    vv
clus                  T2  T3  T4
  17Q LOSS MUTATED     2  10   0
  17Q LOSS WILD-TYPE 148 196   5
D66V3, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  T2                2                148
  T3               10                196
  T4                0                  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"
D66V4, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    11   1
  17Q LOSS WILD-TYPE 252  43
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     11    1
  17Q LOSS WILD-TYPE  252   43
   clus
vv  17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  0               11                252
  1                1                 43
[1] 2 2
[1] FALSE
D66V5, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     0  12
  17Q LOSS WILD-TYPE  13 338
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      0   12
  17Q LOSS WILD-TYPE   13  338
                                        clus
vv                                       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                0                 13
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  12                338
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  17Q LOSS MUTATED     5   7   0   0
  17Q LOSS WILD-TYPE 238  83   5  11
D66V6, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  R0                5                238
  R1                7                 83
  R2                0                  5
  RX                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"
D66V7, continuous
D66V8, continuous
D66V9, continuous
D66V10, continuous
D66V11, continuous
D66V12, continuous
D66V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17Q LOSS MUTATED       0                         0     3
  17Q LOSS WILD-TYPE     2                         7   143
D66V14, multiclass
                           clus
vv                          17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  7
  WHITE                                    3                143
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(67) Variable = 18P LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                  0   1
  18P LOSS MUTATED    45   2
  18P LOSS WILD-TYPE 310   4
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                47                314 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 2                  4 
$`18P LOSS MUTATED`
TCGA-CH-5751 TCGA-CH-5761 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5791 TCGA-EJ-5514 
       35.01         0.92        15.98        26.99        33.01        36.23 
TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-7781 TCGA-EJ-A65B TCGA-G9-6354 TCGA-G9-6373 
       52.27        64.50        23.90        17.62        49.35        26.66 
TCGA-G9-6377 TCGA-G9-7523 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-HC-7078 TCGA-HC-7211 
       31.50        28.18        26.01        21.14         5.33         0.79 
TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7736 TCGA-HC-7745 TCGA-HC-7820 TCGA-HC-7821 
        1.97         1.68         0.72         2.07        24.56         1.84 
TCGA-HC-A48F TCGA-HC-A631 TCGA-HC-A632 TCGA-HI-7168 TCGA-HI-7170 TCGA-HI-7171 
       22.36         1.78         2.01        78.61        82.92        43.69 
TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E7 TCGA-KK-A8IB TCGA-M7-A724 TCGA-TP-A8TV 
       61.78       115.86        67.07         2.73        15.88         8.19 
TCGA-VN-A88P TCGA-VP-A872 TCGA-WW-A8ZI TCGA-XJ-A83G TCGA-XK-AAIV TCGA-YL-A8HK 
       30.15       106.95         5.79        38.04        31.50        49.02 
TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8SJ TCGA-YL-A8SO TCGA-YL-A9WK 
       36.95        71.77        45.86       106.75        62.37 

$`18P LOSS WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5753 
        1.97        24.03         1.02        13.02        31.00         1.02 
TCGA-CH-5754 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 
        2.04        44.02        12.00         1.02        23.01         1.02 
TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5789 TCGA-CH-5790 
       15.06        24.03         2.04        13.02         9.99        32.02 
TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 
        2.99        29.00        27.16        33.11        19.56        13.32 
TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 
       29.79        46.52        44.88        26.30        45.73        28.93 
TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 
       30.31        27.19        23.90        38.93        48.13        36.69 
TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5521 
       48.53        38.53        60.23        46.55        47.80        51.88 
TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 
       68.35        43.07        36.66        38.76        39.75        60.23 
TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 
       41.85        47.87        29.06        27.02        49.02        61.15 
TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 
       83.57        21.80         9.70         9.50         9.37        16.77 
TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 
        7.66        17.52         5.75        27.68         6.28         0.30 
TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 
       38.37        25.87        25.68        20.55        14.53        14.14 
TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 
       18.15        19.59        17.29         3.75        23.05        19.92 
TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D 
       64.47        63.98        26.99        10.32         5.33         4.24 
TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65D 
       17.49         9.83         3.06         7.53        21.96        12.92 
TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-FC-7708 
       13.71        18.41         9.14         2.99         7.56        28.41 
TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 
       15.42        13.45         8.98        17.23        16.24         1.78 
TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 
       41.62        87.35        81.04        67.99        66.67        69.37 
TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 
       55.76        18.21        68.68        49.81        46.16        50.70 
TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 
       47.15        46.52        47.44        45.30        39.39        44.81 
TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6378 
        3.32        40.18        39.95        38.01        40.31        37.97 
TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 
       45.80        25.15        27.29        58.22        56.75        52.87 
TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 
       50.73        38.27        38.96        27.91        30.97        35.34 
TCGA-G9-7525 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7079 
       32.68         6.08        30.94         3.68        19.76         2.93 
TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7212 TCGA-HC-7231 
        2.01         2.37        14.47        28.54        28.60         2.37 
TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 
        2.93         1.71         2.10         2.66         1.74         1.48 
TCGA-HC-7744 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 
        1.68        24.59        26.04         1.97         1.12         3.22 
TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 
       30.51         1.48        17.85        19.36        22.42         3.12 
TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 
       23.87         2.17         2.27         1.94        17.95        22.32 
TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A4ZV TCGA-HC-A6AL TCGA-HC-A6AN 
        1.58        15.88         1.15         0.76         2.20         1.61 
TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY 
        5.49         2.33         3.48         1.45         1.25         4.41 
TCGA-HI-7169 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M 
       88.24        20.19        12.30        21.76        17.03        16.04 
TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T 
       16.54        16.14        20.52        14.93        17.19         6.02 
TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K 
       13.32        17.36         9.17         9.17        10.19         6.77 
TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E 
       10.39        14.37        20.28        13.87         5.85        10.62 
TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 
       93.99        56.28        44.68        30.02        54.54       151.36 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E8 TCGA-KK-A7AZ 
       67.59        90.51        49.25       113.33        58.19        27.62 
TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IF TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z 
       34.95        22.75        26.43        20.65         5.19         6.87 
TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A725 TCGA-QU-A6IL 
        9.93        13.15        27.02        25.08        18.84         3.19 
TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-TP-A8TT TCGA-VN-A88I 
       41.00       114.64        47.21        86.14        11.90         8.84 
TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88Q 
       25.51        12.95         6.02        15.52        15.81        32.91 
TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 
       15.09         4.34        26.47        84.69        94.65        23.93 
TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J 
       75.91        55.56        60.92        66.97        21.80        48.85 
TCGA-VP-A87K TCGA-VP-AA1N TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A9DI 
       21.53        17.82        37.18        27.81         3.91        48.03 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIW TCGA-XK-AAJ3 
        9.04         2.99        25.97        31.96        31.96        28.54 
TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-Y6-A8TL 
       30.58        29.23        27.09        37.02        39.65        25.48 
TCGA-YL-A8HJ TCGA-YL-A8HL TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB 
       52.96        38.56        62.14        60.56        16.83        45.50 
TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SK TCGA-YL-A8SL 
       41.46        45.14        28.77        47.38        37.97        26.24 
TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ 
       71.34        62.79         7.00        14.04        41.39        60.99 
TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY 
       24.33        49.91        28.34         1.64         4.93         1.12 
TCGA-ZG-A8QZ TCGA-ZG-A9ND 
        7.86         6.02 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              0.72               0.30 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            115.86             151.36 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             28.18              22.88 
[1] "0.7 - 115.9 (28.2)" "0.3 - 151.4 (22.9)"
[1] "hr=" "2.3"
D67V2, continuous
                    vv
clus                  T2  T3  T4
  18P LOSS MUTATED    16  30   2
  18P LOSS WILD-TYPE 134 176   3
D67V3, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  T2               16                134
  T3               30                176
  T4                2                  3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V4, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    36   8
  18P LOSS WILD-TYPE 227  36
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     36    8
  18P LOSS WILD-TYPE  227   36
   clus
vv  18P LOSS MUTATED 18P LOSS WILD-TYPE
  0               36                227
  1                8                 36
[1] 2 2
[1] FALSE
D67V5, binary
                    cls
clus                   0   1
  18P LOSS MUTATED     2  46
  18P LOSS WILD-TYPE  11 304
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      2   46
  18P LOSS WILD-TYPE   11  304
                                        clus
vv                                       18P LOSS MUTATED 18P LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                2                 11
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  46                304
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  18P LOSS MUTATED    26  19   0   0
  18P LOSS WILD-TYPE 217  71   5  11
D67V6, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  R0               26                217
  R1               19                 71
  R2                0                  5
  RX                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"
D67V7, continuous
D67V8, continuous
D67V9, continuous
D67V10, continuous
D67V11, continuous
D67V12, continuous
D67V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18P LOSS MUTATED       0                         0    22
  18P LOSS WILD-TYPE     2                         7   124
D67V14, multiclass
                           clus
vv                          18P LOSS MUTATED 18P LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  7
  WHITE                                   22                124
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(68) Variable = 18Q LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                  0   1
  18Q LOSS MUTATED    67   2
  18Q LOSS WILD-TYPE 288   4
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                69                292 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 2                  4 
$`18Q LOSS MUTATED`
TCGA-CH-5751 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5772 TCGA-CH-5791 TCGA-EJ-5504 
       35.01         2.04         0.92        15.98        33.01        28.93 
TCGA-EJ-5507 TCGA-EJ-5514 TCGA-EJ-5518 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-7781 
       23.90        36.23        52.27        43.07        36.66        23.90 
TCGA-EJ-7794 TCGA-EJ-A65B TCGA-G9-6329 TCGA-G9-6348 TCGA-G9-6354 TCGA-G9-6373 
       23.05        17.62        41.62        49.81        49.35        26.66 
TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-7521 TCGA-G9-7523 TCGA-G9-A9S0 TCGA-HC-7078 
       31.50        37.97        30.97        28.18        26.01         5.33 
TCGA-HC-7211 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7742 TCGA-HC-7745 TCGA-HC-7820 
        0.79         1.97         1.68         1.48         2.07        24.56 
TCGA-HC-7821 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A6HY TCGA-HI-7168 
        1.84        22.36         0.76         1.78         4.41        78.61 
TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-A67N TCGA-KK-A59X TCGA-KK-A59Z TCGA-KK-A6DY 
       82.92        43.69        16.54        56.28        61.78       115.86 
TCGA-KK-A6E1 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A8IB TCGA-M7-A724 TCGA-M7-A725 
       54.54       113.33        67.07         2.73        15.88        18.84 
TCGA-TP-A8TV TCGA-VN-A88K TCGA-VN-A88P TCGA-VP-A872 TCGA-VP-A87C TCGA-WW-A8ZI 
        8.19        25.51        30.15       106.95        55.56         5.79 
TCGA-XJ-A83G TCGA-XK-AAIV TCGA-XK-AAJT TCGA-YL-A8HK TCGA-YL-A8HM TCGA-YL-A8HO 
       38.04        31.50        37.02        49.02        36.95        71.77 
TCGA-YL-A8SA TCGA-YL-A8SJ TCGA-YL-A8SO TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH 
       16.83        45.86       106.75        62.79         7.00        14.04 
TCGA-YL-A9WK TCGA-YL-A9WX TCGA-YL-A9WY 
       62.37        49.91        28.34 

$`18Q LOSS WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5753 
        1.97        24.03         1.02        13.02        31.00         1.02 
TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 
       44.02        12.00         1.02        23.01         1.02        15.06 
TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 
       24.03         2.04        13.02        26.99         9.99        32.02 
TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 
        2.99        29.00        27.16        33.11        19.56        13.32 
TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5505 
       29.79        46.52        44.88        26.30        45.73        30.31 
TCGA-EJ-5506 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       27.19        38.93        48.13        36.69        48.53        38.53 
TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 
       60.23        46.55        47.80        64.50        51.88        68.35 
TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 
       38.76        39.75        60.23        41.85        47.87        29.06 
TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 
       27.02        49.02        61.15        83.57        21.80         9.70 
TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 
        9.50         9.37        16.77         7.66        17.52         5.75 
TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 
       27.68         6.28         0.30        38.37        25.87        25.68 
TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 
       20.55        14.53        14.14        18.15        19.59        17.29 
TCGA-EJ-7793 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8474 
        3.75        19.92        64.47        63.98        26.99        10.32 
TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H 
        5.33         4.24        17.49         9.83         3.06         7.53 
TCGA-EJ-A46I TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J 
       21.96        12.92        13.71        18.41         9.14         2.99 
TCGA-EJ-A65M TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V 
        7.56        28.41        15.42        13.45         8.98        17.23 
TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 
       16.24         1.78        87.35        81.04        67.99        66.67 
TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6351 TCGA-G9-6353 
       69.37        55.76        18.21        68.68        46.16        50.70 
TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 
       47.15        46.52        47.44        45.30        39.39        44.81 
TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6379 
        3.32        40.18        39.95        38.01        40.31        45.80 
TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 
       25.15        27.29        58.22        56.75        52.87        50.73 
TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7522 TCGA-G9-7525 TCGA-G9-A9S7 
       38.27        38.96        27.91        35.34        32.68        21.14 
TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7079 TCGA-HC-7080 
        6.08        30.94         3.68        19.76         2.93         2.01 
TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7212 TCGA-HC-7231 TCGA-HC-7232 
        2.37        14.47        28.54        28.60         2.37         2.93 
TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7744 
        1.71         0.72         2.10         2.66         1.74         1.68 
TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 
       24.59        26.04         1.97         1.12         3.22        30.51 
TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 
        1.48        17.85        19.36        22.42         3.12        23.87 
TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 
        2.17         2.27         1.94        17.95        22.32         1.58 
TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO 
       15.88         1.15         2.01         2.20         1.61         5.49 
TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HI-7169 TCGA-J4-8198 
        2.33         3.48         1.45         1.25        88.24        20.19 
TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67O TCGA-J4-A67Q 
       12.30        21.76        17.03        16.04        16.14        20.52 
TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 
       14.93        17.19         6.02        13.32        17.36         9.17 
TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N 
        9.17        10.19         6.77        10.39        14.37        20.28 
TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-KK-A59V TCGA-KK-A59Y TCGA-KK-A6E0 
       13.87         5.85        10.62        93.99        44.68        30.02 
TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E8 TCGA-KK-A7AZ 
      151.36        67.59        90.51        49.25        58.19        27.62 
TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IF TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z 
       34.95        22.75        26.43        20.65         5.19         6.87 
TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-QU-A6IL TCGA-QU-A6IM 
        9.93        13.15        27.02        25.08         3.19        41.00 
TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-TP-A8TT TCGA-VN-A88I TCGA-VN-A88L 
      114.64        47.21        86.14        11.90         8.84        12.95 
TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 
        6.02        15.52        15.81        32.91        15.09         4.34 
TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87D 
       26.47        84.69        94.65        23.93        75.91        60.92 
TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-X4-A8KQ 
       66.97        21.80        48.85        21.53        17.82        37.18 
TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX 
       27.81         3.91        48.03         9.04         2.99        25.97 
TCGA-XK-AAIR TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR 
       31.96        31.96        28.54        30.58        29.23        27.09 
TCGA-XK-AAJU TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HL TCGA-YL-A8S8 TCGA-YL-A8S9 
       39.65        25.48        52.96        38.56        62.14        60.56 
TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SK 
       45.50        41.46        45.14        28.77        47.38        37.97 
TCGA-YL-A8SL TCGA-YL-A8SP TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WL TCGA-ZG-A8QW 
       26.24        71.34        41.39        60.99        24.33         1.64 
TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9ND 
        4.93         1.12         7.86         6.02 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              0.76               0.30 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            115.86             151.36 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             30.15              22.01 
[1] "0.8 - 115.9 (30.1)" "0.3 - 151.4 (22.0)"
[1] "hr=" "1.5"
D68V2, continuous
                    vv
clus                  T2  T3  T4
  18Q LOSS MUTATED    22  47   2
  18Q LOSS WILD-TYPE 128 159   3
D68V3, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T2               22                128
  T3               47                159
  T4                2                  3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V4, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED    47  16
  18Q LOSS WILD-TYPE 216  28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     47   16
  18Q LOSS WILD-TYPE  216   28
   clus
vv  18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  0               47                216
  1               16                 28
[1] 2 2
[1] FALSE
D68V5, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED     2  69
  18Q LOSS WILD-TYPE  11 281
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      2   69
  18Q LOSS WILD-TYPE   11  281
                                        clus
vv                                       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                2                 11
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  69                281
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  18Q LOSS MUTATED    36  32   0   1
  18Q LOSS WILD-TYPE 207  58   5  10
D68V6, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  R0               36                207
  R1               32                 58
  R2                0                  5
  RX                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"
D68V7, continuous
D68V8, continuous
D68V9, continuous
D68V10, continuous
D68V11, continuous
D68V12, continuous
D68V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18Q LOSS MUTATED       0                         2    28
  18Q LOSS WILD-TYPE     2                         5   118
D68V14, multiclass
                           clus
vv                          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                2                  5
  WHITE                                   28                118
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(69) Variable = 19P LOSS MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                  0   1
  19P LOSS MUTATED    13   0
  19P LOSS WILD-TYPE 342   6
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                13                348 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 0                  6 
$`19P LOSS MUTATED`
TCGA-EJ-7328 TCGA-EJ-7781 TCGA-HC-7080 TCGA-J9-A52B TCGA-J9-A52E TCGA-KK-A6E5 
       27.68        23.90         2.01        13.87        10.62        49.25 
TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-TP-A8TV TCGA-XK-AAJA TCGA-YL-A8HM TCGA-YL-A8SL 
      113.33        67.07         8.19        30.58        36.95        26.24 
TCGA-YL-A9WK 
       62.37 

$`19P LOSS WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 
        1.02         2.04         0.92        44.02        12.00         1.02 
TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 
       23.01         1.02        15.06        24.03         2.04        13.02 
TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 
       15.98        26.99         9.99        32.02        33.01         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        27.16        33.11        19.56        13.32        29.79 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        26.30        45.73        28.93        30.31 
TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 
       27.19        23.90        38.93        48.13        36.69        48.53 
TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 
       38.53        36.23        60.23        46.55        47.80        52.27 
TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 
       64.50        51.88        68.35        43.07        36.66        38.76 
TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 
       39.75        60.23        41.85        47.87        29.06        27.02 
TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 
       49.02        61.15        83.57        21.80         9.70         9.50 
TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7330 
        9.37        16.77         7.66        17.52         5.75         6.28 
TCGA-EJ-7331 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 
        0.30        38.37        25.87        25.68        20.55        14.53 
TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 
       14.14        18.15        19.59        17.29         3.75        23.05 
TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8474 TCGA-EJ-A46B 
       19.92        64.47        63.98        26.99        10.32         5.33 
TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I 
        4.24        17.49         9.83         3.06         7.53        21.96 
TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J 
       17.62        12.92        13.71        18.41         9.14         2.99 
TCGA-EJ-A65M TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V 
        7.56        28.41        15.42        13.45         8.98        17.23 
TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 
       16.24         1.78        41.62        87.35        81.04        67.99 
TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 
       66.67        69.37        55.76        18.21        68.68        49.81 
TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 
       46.16        50.70        49.35        47.15        46.52        47.44 
TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 
       45.30        39.39        44.81         3.32        40.18        39.95 
TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 
       38.01        40.31        26.66        31.50        37.97        45.80 
TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 
       25.15        27.29        58.22        56.75        52.87        50.73 
TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 
       38.27        38.96        27.91        30.97        35.34        28.18 
TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY 
       32.68        26.01        21.14         6.08        30.94         3.68 
TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 
       19.76         5.33         2.93         2.37        14.47        28.54 
TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 
        0.79        28.60         1.97         1.68         2.37         2.93 
TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 
        1.71         0.72         2.10         2.66         1.74         1.48 
TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 
        1.68         2.07        24.59        26.04         1.97         1.12 
TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 
        3.22        30.51         1.48        17.85        24.56         1.84 
TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 
       19.36        22.42         3.12        23.87         2.17         2.27 
TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 
        1.94        17.95        22.32         1.58        15.88         1.15 
TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN 
       22.36         0.76         1.78         2.01         2.20         1.61 
TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY 
        5.49         2.33         3.48         1.45         1.25         4.41 
TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 
       78.61        88.24        82.92        43.69        20.19        12.30 
TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q 
       21.76        17.03        16.04        16.54        16.14        20.52 
TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 
       14.93        17.19         6.02        13.32        17.36         9.17 
TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N 
        9.17        10.19         6.77        10.39        14.37        20.28 
TCGA-J9-A52C TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY 
        5.85        93.99        56.28        44.68        61.78       115.86 
TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E8 
       30.02        54.54       151.36        67.59        90.51        58.19 
TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IB TCGA-KK-A8IF TCGA-KK-A8IL 
       27.62        34.95        22.75         2.73        26.43        20.65 
TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 
        5.19         6.87         9.93        13.15        27.02        25.08 
TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO 
       15.88        18.84         3.19        41.00       114.64        47.21 
TCGA-QU-A6IP TCGA-TP-A8TT TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M 
       86.14        11.90         8.84        25.51        12.95         6.02 
TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 
       15.52        15.81        30.15        32.91        15.09         4.34 
TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B 
      106.95        26.47        84.69        94.65        23.93        75.91 
TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K 
       55.56        60.92        66.97        21.80        48.85        21.53 
TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83G 
       17.82         5.79        37.18        27.81         3.91        38.04 
TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV 
       48.03         9.04         2.99        25.97        31.96        31.50 
TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU 
       31.96        28.54        29.23        27.09        37.02        39.65 
TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HO TCGA-YL-A8S8 
       25.48        52.96        49.02        38.56        71.77        62.14 
TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH 
       60.56        16.83        45.50        41.46        45.14        28.77 
TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ 
       47.38        45.86        37.97       106.75        71.34        62.79 
TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WL TCGA-YL-A9WX 
        7.00        14.04        41.39        60.99        24.33        49.91 
TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9ND 
       28.34         1.64         4.93         1.12         7.86         6.02 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              2.01               0.30 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
            113.33             151.36 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
            27.680             23.885 
[1] "2.0 - 113.3 (27.7)" "0.3 - 151.4 (23.9)"
[1] "hr="     "2.6e+07"
D69V2, continuous
                    vv
clus                  T2  T3  T4
  19P LOSS MUTATED     3  10   0
  19P LOSS WILD-TYPE 147 196   5
D69V3, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  T2                3                147
  T3               10                196
  T4                0                  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"
D69V4, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    11   2
  19P LOSS WILD-TYPE 252  42
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     11    2
  19P LOSS WILD-TYPE  252   42
   clus
vv  19P LOSS MUTATED 19P LOSS WILD-TYPE
  0               11                252
  1                2                 42
[1] 2 2
[1] FALSE
D69V5, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     0  13
  19P LOSS WILD-TYPE  13 337
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      0   13
  19P LOSS WILD-TYPE   13  337
                                        clus
vv                                       19P LOSS MUTATED 19P LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                0                 13
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  13                337
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  19P LOSS MUTATED     8   5   0   0
  19P LOSS WILD-TYPE 235  85   5  11
D69V6, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  R0                8                235
  R1                5                 85
  R2                0                  5
  RX                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"
D69V7, continuous
D69V8, continuous
D69V9, continuous
D69V10, continuous
D69V11, continuous
D69V12, continuous
D69V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19P LOSS MUTATED       0                         0     3
  19P LOSS WILD-TYPE     2                         7   143
D69V14, multiclass
                           clus
vv                          19P LOSS MUTATED 19P LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  7
  WHITE                                    3                143
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(70) Variable = 19Q LOSS MUTATION ANALYSIS
D70V1, survival
                    sevent
clus2                  0   1
  19Q LOSS MUTATED    13   0
  19Q LOSS WILD-TYPE 342   6
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                13                348 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 0                  6 
$`19Q LOSS MUTATED`
TCGA-EJ-7328 TCGA-EJ-7781 TCGA-HC-7080 TCGA-J9-A52B TCGA-J9-A52E TCGA-KK-A6E5 
       27.68        23.90         2.01        13.87        10.62        49.25 
TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-TP-A8TV TCGA-XK-AAJA TCGA-YL-A8HM TCGA-YL-A8SL 
      113.33        67.07         8.19        30.58        36.95        26.24 
TCGA-YL-A9WK 
       62.37 

$`19Q LOSS WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 
        1.02         2.04         0.92        44.02        12.00         1.02 
TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 
       23.01         1.02        15.06        24.03         2.04        13.02 
TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 
       15.98        26.99         9.99        32.02        33.01         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        27.16        33.11        19.56        13.32        29.79 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        26.30        45.73        28.93        30.31 
TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 
       27.19        23.90        38.93        48.13        36.69        48.53 
TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 
       38.53        36.23        60.23        46.55        47.80        52.27 
TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 
       64.50        51.88        68.35        43.07        36.66        38.76 
TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 
       39.75        60.23        41.85        47.87        29.06        27.02 
TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 
       49.02        61.15        83.57        21.80         9.70         9.50 
TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7330 
        9.37        16.77         7.66        17.52         5.75         6.28 
TCGA-EJ-7331 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 
        0.30        38.37        25.87        25.68        20.55        14.53 
TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 
       14.14        18.15        19.59        17.29         3.75        23.05 
TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8474 TCGA-EJ-A46B 
       19.92        64.47        63.98        26.99        10.32         5.33 
TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I 
        4.24        17.49         9.83         3.06         7.53        21.96 
TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J 
       17.62        12.92        13.71        18.41         9.14         2.99 
TCGA-EJ-A65M TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V 
        7.56        28.41        15.42        13.45         8.98        17.23 
TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 
       16.24         1.78        41.62        87.35        81.04        67.99 
TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 
       66.67        69.37        55.76        18.21        68.68        49.81 
TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 
       46.16        50.70        49.35        47.15        46.52        47.44 
TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 
       45.30        39.39        44.81         3.32        40.18        39.95 
TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 
       38.01        40.31        26.66        31.50        37.97        45.80 
TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 
       25.15        27.29        58.22        56.75        52.87        50.73 
TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 
       38.27        38.96        27.91        30.97        35.34        28.18 
TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY 
       32.68        26.01        21.14         6.08        30.94         3.68 
TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 
       19.76         5.33         2.93         2.37        14.47        28.54 
TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 
        0.79        28.60         1.97         1.68         2.37         2.93 
TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 
        1.71         0.72         2.10         2.66         1.74         1.48 
TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 
        1.68         2.07        24.59        26.04         1.97         1.12 
TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 
        3.22        30.51         1.48        17.85        24.56         1.84 
TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 
       19.36        22.42         3.12        23.87         2.17         2.27 
TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 
        1.94        17.95        22.32         1.58        15.88         1.15 
TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN 
       22.36         0.76         1.78         2.01         2.20         1.61 
TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY 
        5.49         2.33         3.48         1.45         1.25         4.41 
TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 
       78.61        88.24        82.92        43.69        20.19        12.30 
TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q 
       21.76        17.03        16.04        16.54        16.14        20.52 
TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 
       14.93        17.19         6.02        13.32        17.36         9.17 
TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N 
        9.17        10.19         6.77        10.39        14.37        20.28 
TCGA-J9-A52C TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY 
        5.85        93.99        56.28        44.68        61.78       115.86 
TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E8 
       30.02        54.54       151.36        67.59        90.51        58.19 
TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IB TCGA-KK-A8IF TCGA-KK-A8IL 
       27.62        34.95        22.75         2.73        26.43        20.65 
TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 
        5.19         6.87         9.93        13.15        27.02        25.08 
TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO 
       15.88        18.84         3.19        41.00       114.64        47.21 
TCGA-QU-A6IP TCGA-TP-A8TT TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M 
       86.14        11.90         8.84        25.51        12.95         6.02 
TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 
       15.52        15.81        30.15        32.91        15.09         4.34 
TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B 
      106.95        26.47        84.69        94.65        23.93        75.91 
TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K 
       55.56        60.92        66.97        21.80        48.85        21.53 
TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83G 
       17.82         5.79        37.18        27.81         3.91        38.04 
TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV 
       48.03         9.04         2.99        25.97        31.96        31.50 
TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU 
       31.96        28.54        29.23        27.09        37.02        39.65 
TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HO TCGA-YL-A8S8 
       25.48        52.96        49.02        38.56        71.77        62.14 
TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH 
       60.56        16.83        45.50        41.46        45.14        28.77 
TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ 
       47.38        45.86        37.97       106.75        71.34        62.79 
TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WL TCGA-YL-A9WX 
        7.00        14.04        41.39        60.99        24.33        49.91 
TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9ND 
       28.34         1.64         4.93         1.12         7.86         6.02 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              2.01               0.30 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            113.33             151.36 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            27.680             23.885 
[1] "2.0 - 113.3 (27.7)" "0.3 - 151.4 (23.9)"
[1] "hr="     "2.6e+07"
D70V2, continuous
                    vv
clus                  T2  T3  T4
  19Q LOSS MUTATED     3  10   0
  19Q LOSS WILD-TYPE 147 196   5
D70V3, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  T2                3                147
  T3               10                196
  T4                0                  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"
D70V4, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    11   2
  19Q LOSS WILD-TYPE 252  42
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     11    2
  19Q LOSS WILD-TYPE  252   42
   clus
vv  19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  0               11                252
  1                2                 42
[1] 2 2
[1] FALSE
D70V5, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     0  13
  19Q LOSS WILD-TYPE  13 337
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      0   13
  19Q LOSS WILD-TYPE   13  337
                                        clus
vv                                       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                0                 13
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  13                337
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  19Q LOSS MUTATED     8   5   0   0
  19Q LOSS WILD-TYPE 235  85   5  11
D70V6, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  R0                8                235
  R1                5                 85
  R2                0                  5
  RX                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"
D70V7, continuous
D70V8, continuous
D70V9, continuous
D70V10, continuous
D70V11, continuous
D70V12, continuous
D70V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19Q LOSS MUTATED       0                         0     3
  19Q LOSS WILD-TYPE     2                         7   143
D70V14, multiclass
                           clus
vv                          19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  7
  WHITE                                    3                143
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(71) Variable = 20P LOSS MUTATION ANALYSIS
D71V1, survival
                    sevent
clus2                  0   1
  20P LOSS MUTATED    11   1
  20P LOSS WILD-TYPE 344   5
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                12                349 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 1                  5 
$`20P LOSS MUTATED`
TCGA-CH-5772 TCGA-EJ-5532 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7784 TCGA-FC-A4JI 
       15.98        47.87        21.80         9.70        25.68        13.45 
TCGA-G9-6339 TCGA-G9-6494 TCGA-G9-A9S0 TCGA-HC-7821 TCGA-VP-A87C TCGA-YL-A8SL 
       69.37        58.22        26.01         1.84        55.56        26.24 

$`20P LOSS WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 
        1.02         2.04         0.92        44.02        12.00         1.02 
TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 
       23.01         1.02        15.06        24.03         2.04        13.02 
TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 
       26.99         9.99        32.02        33.01         2.99        29.00 
TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
       27.16        33.11        19.56        13.32        29.79        46.52 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       44.88        26.30        45.73        28.93        30.31        27.19 
TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       23.90        38.93        48.13        36.69        48.53        38.53 
TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 
       36.23        60.23        46.55        47.80        52.27        64.50 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 
       51.88        68.35        43.07        36.66        38.76        39.75 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 
       60.23        41.85        29.06        27.02        49.02        61.15 
TCGA-EJ-7218 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 
       83.57         9.50         9.37        16.77         7.66        17.52 
TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 
        5.75        27.68         6.28         0.30        23.90        38.37 
TCGA-EJ-7783 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 
       25.87        20.55        14.53        14.14        18.15        19.59 
TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 
       17.29         3.75        23.05        19.92        64.47        63.98 
TCGA-EJ-8470 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F 
       26.99        10.32         5.33         4.24        17.49         9.83 
TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E 
        3.06         7.53        21.96        17.62        12.92        13.71 
TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-FC-7708 TCGA-FC-7961 
       18.41         9.14         2.99         7.56        28.41        15.42 
TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 
        8.98        17.23        16.24         1.78        41.62        87.35 
TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 
       81.04        67.99        66.67        55.76        18.21        68.68 
TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 
       49.81        46.16        50.70        49.35        47.15        46.52 
TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 
       47.44        45.30        39.39        44.81         3.32        40.18 
TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 
       39.95        38.01        40.31        26.66        31.50        37.97 
TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 
       45.80        25.15        27.29        56.75        52.87        50.73 
TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 
       38.27        38.96        27.91        30.97        35.34        28.18 
TCGA-G9-7525 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 
       32.68        21.14         6.08        30.94         3.68        19.76 
TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 
        5.33         2.93         2.01         2.37        14.47        28.54 
TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 
        0.79        28.60         1.97         1.68         2.37         2.93 
TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 
        1.71         0.72         2.10         2.66         1.74         1.48 
TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 
        1.68         2.07        24.59        26.04         1.97         1.12 
TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-8213 
        3.22        30.51         1.48        17.85        24.56        19.36 
TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 
       22.42         3.12        23.87         2.17         2.27         1.94 
TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F 
       17.95        22.32         1.58        15.88         1.15        22.36 
TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO 
        0.76         1.78         2.01         2.20         1.61         5.49 
TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HI-7168 
        2.33         3.48         1.45         1.25         4.41        78.61 
TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K 
       88.24        82.92        43.69        20.19        12.30        21.76 
TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R 
       17.03        16.04        16.54        16.14        20.52        14.93 
TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I 
       17.19         6.02        13.32        17.36         9.17         9.17 
TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B 
       10.19         6.77        10.39        14.37        20.28        13.87 
TCGA-J9-A52C TCGA-J9-A52E TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z 
        5.85        10.62        93.99        56.28        44.68        61.78 
TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 
      115.86        30.02        54.54       151.36        67.59        90.51 
TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AZ TCGA-KK-A7B1 
       49.25       113.33        67.07        58.19        27.62        34.95 
TCGA-KK-A7B2 TCGA-KK-A8IB TCGA-KK-A8IF TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z 
       22.75         2.73        26.43        20.65         5.19         6.87 
TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 
        9.93        13.15        27.02        25.08        15.88        18.84 
TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-TP-A8TT 
        3.19        41.00       114.64        47.21        86.14        11.90 
TCGA-TP-A8TV TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N 
        8.19         8.84        25.51        12.95         6.02        15.52 
TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 
       15.81        30.15        32.91        15.09         4.34       106.95 
TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87D 
       26.47        84.69        94.65        23.93        75.91        60.92 
TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI 
       66.97        21.80        48.85        21.53        17.82         5.79 
TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK 
       37.18        27.81         3.91        38.04        48.03         9.04 
TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 
        2.99        25.97        31.96        31.50        31.96        28.54 
TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-Y6-A8TL 
       30.58        29.23        27.09        37.02        39.65        25.48 
TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 
       52.96        49.02        38.56        36.95        71.77        62.14 
TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH 
       60.56        16.83        45.50        41.46        45.14        28.77 
TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ 
       47.38        45.86        37.97       106.75        71.34        62.79 
TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL 
        7.00        14.04        41.39        60.99        62.37        24.33 
TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       49.91        28.34         1.64         4.93         1.12         7.86 
TCGA-ZG-A9ND 
        6.02 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
              1.84               0.30 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             69.37             151.36 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
            25.845             23.900 
[1] "1.8 - 69.4 (25.8)"  "0.3 - 151.4 (23.9)"
[1] "hr=" "5.4"
D71V2, continuous
                    vv
clus                  T2  T3  T4
  20P LOSS MUTATED     2  10   1
  20P LOSS WILD-TYPE 148 196   4
D71V3, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  T2                2                148
  T3               10                196
  T4                1                  4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V4, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     8   3
  20P LOSS WILD-TYPE 255  41
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      8    3
  20P LOSS WILD-TYPE  255   41
   clus
vv  20P LOSS MUTATED 20P LOSS WILD-TYPE
  0                8                255
  1                3                 41
[1] 2 2
[1] FALSE
D71V5, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     0  13
  20P LOSS WILD-TYPE  13 337
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      0   13
  20P LOSS WILD-TYPE   13  337
                                        clus
vv                                       20P LOSS MUTATED 20P LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                0                 13
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  13                337
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  20P LOSS MUTATED     9   3   0   0
  20P LOSS WILD-TYPE 234  87   5  11
D71V6, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  R0                9                234
  R1                3                 87
  R2                0                  5
  RX                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"
D71V7, continuous
D71V8, continuous
D71V9, continuous
D71V10, continuous
D71V11, continuous
D71V12, continuous
D71V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20P LOSS MUTATED       0                         1     6
  20P LOSS WILD-TYPE     2                         6   140
D71V14, multiclass
                           clus
vv                          20P LOSS MUTATED 20P LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                1                  6
  WHITE                                    6                140
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(72) Variable = 20Q LOSS MUTATION ANALYSIS
D72V1, survival
                    sevent
clus2                  0   1
  20Q LOSS MUTATED     7   0
  20Q LOSS WILD-TYPE 348   6
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 7                354 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 0                  6 
$`20Q LOSS MUTATED`
TCGA-CH-5772 TCGA-EJ-5532 TCGA-EJ-7784 TCGA-FC-A4JI TCGA-G9-6494 TCGA-HC-A632 
       15.98        47.87        25.68        13.45        58.22         2.01 
TCGA-YL-A8SL 
       26.24 

$`20Q LOSS WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 
        1.02         2.04         0.92        44.02        12.00         1.02 
TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 
       23.01         1.02        15.06        24.03         2.04        13.02 
TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 
       26.99         9.99        32.02        33.01         2.99        29.00 
TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
       27.16        33.11        19.56        13.32        29.79        46.52 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       44.88        26.30        45.73        28.93        30.31        27.19 
TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       23.90        38.93        48.13        36.69        48.53        38.53 
TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 
       36.23        60.23        46.55        47.80        52.27        64.50 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 
       51.88        68.35        43.07        36.66        38.76        39.75 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 
       60.23        41.85        29.06        27.02        49.02        61.15 
TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 
       83.57        21.80         9.70         9.50         9.37        16.77 
TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 
        7.66        17.52         5.75        27.68         6.28         0.30 
TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 
       23.90        38.37        25.87        20.55        14.53        14.14 
TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 
       18.15        19.59        17.29         3.75        23.05        19.92 
TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D 
       64.47        63.98        26.99        10.32         5.33         4.24 
TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B 
       17.49         9.83         3.06         7.53        21.96        17.62 
TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M 
       12.92        13.71        18.41         9.14         2.99         7.56 
TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 
       28.41        15.42         8.98        17.23        16.24         1.78 
TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 
       41.62        87.35        81.04        67.99        66.67        69.37 
TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 
       55.76        18.21        68.68        49.81        46.16        50.70 
TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 
       49.35        47.15        46.52        47.44        45.30        39.39 
TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 
       44.81         3.32        40.18        39.95        38.01        40.31 
TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 
       26.66        31.50        37.97        45.80        25.15        27.29 
TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 
       56.75        52.87        50.73        38.27        38.96        27.91 
TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 
       30.97        35.34        28.18        32.68        26.01        21.14 
TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 
        6.08        30.94         3.68        19.76         5.33         2.93 
TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 
        2.01         2.37        14.47        28.54         0.79        28.60 
TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 
        1.97         1.68         2.37         2.93         1.71         0.72 
TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 
        2.10         2.66         1.74         1.48         1.68         2.07 
TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 
       24.59        26.04         1.97         1.12         3.22        30.51 
TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 
        1.48        17.85        24.56         1.84        19.36        22.42 
TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 
        3.12        23.87         2.17         2.27         1.94        17.95 
TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV 
       22.32         1.58        15.88         1.15        22.36         0.76 
TCGA-HC-A631 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ 
        1.78         2.20         1.61         5.49         2.33         3.48 
TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 
        1.45         1.25         4.41        78.61        88.24        82.92 
TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M 
       43.69        20.19        12.30        21.76        17.03        16.04 
TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T 
       16.54        16.14        20.52        14.93        17.19         6.02 
TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K 
       13.32        17.36         9.17         9.17        10.19         6.77 
TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E 
       10.39        14.37        20.28        13.87         5.85        10.62 
TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 
       93.99        56.28        44.68        61.78       115.86        30.02 
TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 
       54.54       151.36        67.59        90.51        49.25       113.33 
TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IB 
       67.07        58.19        27.62        34.95        22.75         2.73 
TCGA-KK-A8IF TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 
       26.43        20.65         5.19         6.87         9.93        13.15 
TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM 
       27.02        25.08        15.88        18.84         3.19        41.00 
TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-TP-A8TT TCGA-TP-A8TV TCGA-VN-A88I 
      114.64        47.21        86.14        11.90         8.19         8.84 
TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P 
       25.51        12.95         6.02        15.52        15.81        30.15 
TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 
       32.91        15.09         4.34       106.95        26.47        84.69 
TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E 
       94.65        23.93        75.91        55.56        60.92        66.97 
TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ 
       21.80        48.85        21.53        17.82         5.79        37.18 
TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ 
       27.81         3.91        38.04        48.03         9.04         2.99 
TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 TCGA-XK-AAJA 
       25.97        31.96        31.50        31.96        28.54        30.58 
TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-Y6-A8TL TCGA-YL-A8HJ 
       29.23        27.09        37.02        39.65        25.48        52.96 
TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 
       49.02        38.56        36.95        71.77        62.14        60.56 
TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI 
       16.83        45.50        41.46        45.14        28.77        47.38 
TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR 
       45.86        37.97       106.75        71.34        62.79         7.00 
TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX 
       14.04        41.39        60.99        62.37        24.33        49.91 
TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9ND 
       28.34         1.64         4.93         1.12         7.86         6.02 

  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
              2.01               0.30 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             58.22             151.36 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
            25.680             23.915 
[1] "2.0 - 58.2 (25.7)"  "0.3 - 151.4 (23.9)"
[1] "hr="     "9200000"
D72V2, continuous
                    vv
clus                  T2  T3  T4
  20Q LOSS MUTATED     1   5   1
  20Q LOSS WILD-TYPE 149 201   4
D72V3, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  T2                1                149
  T3                5                201
  T4                1                  4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V4, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     5   1
  20Q LOSS WILD-TYPE 258  43
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      5    1
  20Q LOSS WILD-TYPE  258   43
   clus
vv  20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  0                5                258
  1                1                 43
[1] 2 2
[1] FALSE
D72V5, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     0   7
  20Q LOSS WILD-TYPE  13 343
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      0    7
  20Q LOSS WILD-TYPE   13  343
                                        clus
vv                                       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                0                 13
  PROSTATE ADENOCARCINOMA ACINAR TYPE                   7                343
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  20Q LOSS MUTATED     5   2   0   0
  20Q LOSS WILD-TYPE 238  88   5  11
D72V6, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  R0                5                238
  R1                2                 88
  R2                0                  5
  RX                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"
D72V7, continuous
D72V8, continuous
D72V9, continuous
D72V10, continuous
D72V11, continuous
D72V12, continuous
D72V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20Q LOSS MUTATED       0                         0     4
  20Q LOSS WILD-TYPE     2                         7   142
D72V14, multiclass
                           clus
vv                          20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  7
  WHITE                                    4                142
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(73) Variable = 21Q LOSS MUTATION ANALYSIS
D73V1, survival
                    sevent
clus2                  0   1
  21Q LOSS MUTATED    13   0
  21Q LOSS WILD-TYPE 342   6
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                13                348 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 0                  6 
$`21Q LOSS MUTATED`
TCGA-CH-5751 TCGA-CH-5761 TCGA-EJ-5519 TCGA-G9-6329 TCGA-G9-7521 TCGA-HC-7748 
       35.01         0.92        64.50        41.62        30.97        26.04 
TCGA-HC-7821 TCGA-J9-A52B TCGA-VP-A87K TCGA-XK-AAIW TCGA-YL-A8SJ TCGA-YL-A9WL 
        1.84        13.87        21.53        31.96        45.86        24.33 
TCGA-YL-A9WY 
       28.34 

$`21Q LOSS WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5753 
        1.97        24.03         1.02        13.02        31.00         1.02 
TCGA-CH-5754 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 
        2.04        44.02        12.00         1.02        23.01         1.02 
TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 
       15.06        24.03         2.04        13.02        15.98        26.99 
TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 
        9.99        32.02        33.01         2.99        29.00        27.16 
TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 
       33.11        19.56        13.32        29.79        46.52        44.88 
TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 
       26.30        45.73        28.93        30.31        27.19        23.90 
TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 
       38.93        48.13        36.69        48.53        38.53        36.23 
TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5521 TCGA-EJ-5522 
       60.23        46.55        47.80        52.27        51.88        68.35 
TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 
       43.07        36.66        38.76        39.75        60.23        41.85 
TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 
       47.87        29.06        27.02        49.02        61.15        83.57 
TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 
       21.80         9.70         9.50         9.37        16.77         7.66 
TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 
       17.52         5.75        27.68         6.28         0.30        23.90 
TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 
       38.37        25.87        25.68        20.55        14.53        14.14 
TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 
       18.15        19.59        17.29         3.75        23.05        19.92 
TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D 
       64.47        63.98        26.99        10.32         5.33         4.24 
TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B 
       17.49         9.83         3.06         7.53        21.96        17.62 
TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M 
       12.92        13.71        18.41         9.14         2.99         7.56 
TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD 
       28.41        15.42        13.45         8.98        17.23        16.24 
TCGA-FC-A8O0 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 
        1.78        87.35        81.04        67.99        66.67        69.37 
TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 
       55.76        18.21        68.68        49.81        46.16        50.70 
TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 
       49.35        47.15        46.52        47.44        45.30        39.39 
TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 
       44.81         3.32        40.18        39.95        38.01        40.31 
TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 
       26.66        31.50        37.97        45.80        25.15        27.29 
TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 
       58.22        56.75        52.87        50.73        38.27        38.96 
TCGA-G9-7519 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 
       27.91        35.34        28.18        32.68        26.01        21.14 
TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 
        6.08        30.94         3.68        19.76         5.33         2.93 
TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 
        2.01         2.37        14.47        28.54         0.79        28.60 
TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 
        1.97         1.68         2.37         2.93         1.71         0.72 
TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 
        2.10         2.66         1.74         1.48         1.68         2.07 
TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 
       24.59         1.97         1.12         3.22        30.51         1.48 
TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 
       17.85        24.56        19.36        22.42         3.12        23.87 
TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 
        2.17         2.27         1.94        17.95        22.32         1.58 
TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 
       15.88         1.15        22.36         0.76         1.78         2.01 
TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS 
        2.20         1.61         5.49         2.33         3.48         1.45 
TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
        1.25         4.41        78.61        88.24        82.92        43.69 
TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N 
       20.19        12.30        21.76        17.03        16.04        16.54 
TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 
       16.14        20.52        14.93        17.19         6.02        13.32 
TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L 
       17.36         9.17         9.17        10.19         6.77        10.39 
TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52C TCGA-J9-A52E TCGA-KK-A59V TCGA-KK-A59X 
       14.37        20.28         5.85        10.62        93.99        56.28 
TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 
       44.68        61.78       115.86        30.02        54.54       151.36 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 
       67.59        90.51        49.25       113.33        67.07        58.19 
TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IB TCGA-KK-A8IF TCGA-KK-A8IL 
       27.62        34.95        22.75         2.73        26.43        20.65 
TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 
        5.19         6.87         9.93        13.15        27.02        25.08 
TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO 
       15.88        18.84         3.19        41.00       114.64        47.21 
TCGA-QU-A6IP TCGA-TP-A8TT TCGA-TP-A8TV TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L 
       86.14        11.90         8.19         8.84        25.51        12.95 
TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R 
        6.02        15.52        15.81        30.15        32.91        15.09 
TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 
        4.34       106.95        26.47        84.69        94.65        23.93 
TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J 
       75.91        55.56        60.92        66.97        21.80        48.85 
TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83G 
       17.82         5.79        37.18        27.81         3.91        38.04 
TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV 
       48.03         9.04         2.99        25.97        31.96        31.50 
TCGA-XK-AAJ3 TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU 
       28.54        30.58        29.23        27.09        37.02        39.65 
TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO 
       25.48        52.96        49.02        38.56        36.95        71.77 
TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF 
       62.14        60.56        16.83        45.50        41.46        45.14 
TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP 
       28.77        47.38        37.97        26.24       106.75        71.34 
TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK 
       62.79         7.00        14.04        41.39        60.99        62.37 
TCGA-YL-A9WX TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9ND 
       49.91         1.64         4.93         1.12         7.86         6.02 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              0.92               0.30 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             64.50             151.36 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            28.340             23.885 
[1] "0.9 - 64.5 (28.3)"  "0.3 - 151.4 (23.9)"
[1] "hr="     "2.6e+07"
D73V2, continuous
                    vv
clus                  T2  T3  T4
  21Q LOSS MUTATED     2  11   1
  21Q LOSS WILD-TYPE 148 195   4
D73V3, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  T2                2                148
  T3               11                195
  T4                1                  4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V4, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     8   5
  21Q LOSS WILD-TYPE 255  39
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      8    5
  21Q LOSS WILD-TYPE  255   39
   clus
vv  21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  0                8                255
  1                5                 39
[1] 2 2
[1] FALSE
D73V5, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     1  13
  21Q LOSS WILD-TYPE  12 337
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      1   13
  21Q LOSS WILD-TYPE   12  337
                                        clus
vv                                       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                1                 12
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  13                337
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  21Q LOSS MUTATED     8   5   0   0
  21Q LOSS WILD-TYPE 235  85   5  11
D73V6, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  R0                8                235
  R1                5                 85
  R2                0                  5
  RX                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"
D73V7, continuous
D73V8, continuous
D73V9, continuous
D73V10, continuous
D73V11, continuous
D73V12, continuous
D73V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  21Q LOSS MUTATED       0                         0     6
  21Q LOSS WILD-TYPE     2                         7   140
D73V14, multiclass
                           clus
vv                          21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  7
  WHITE                                    6                140
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(74) Variable = 22Q LOSS MUTATION ANALYSIS
D74V1, survival
                    sevent
clus2                  0   1
  22Q LOSS MUTATED    30   1
  22Q LOSS WILD-TYPE 325   5
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                31                330 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 1                  5 
$`22Q LOSS MUTATED`
TCGA-CH-5751 TCGA-CH-5753 TCGA-CH-5761 TCGA-CH-5766 TCGA-CH-5772 TCGA-EJ-5511 
       35.01         1.02         0.92         1.02        15.98        48.53 
TCGA-EJ-7783 TCGA-G9-6356 TCGA-G9-7521 TCGA-HC-7080 TCGA-HC-8216 TCGA-HC-A48F 
       25.87        47.15        30.97         2.01        22.42        22.36 
TCGA-HC-A631 TCGA-HI-7168 TCGA-HI-7171 TCGA-J9-A52E TCGA-M7-A71Y TCGA-M7-A725 
        1.78        78.61        43.69        10.62         5.19        18.84 
TCGA-VN-A88K TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A87K TCGA-XJ-A9DX TCGA-XK-AAJA 
       25.51       106.95        26.47        21.53        25.97        30.58 
TCGA-YL-A8HM TCGA-YL-A8SB TCGA-YL-A8SQ TCGA-YL-A9WH TCGA-YL-A9WK TCGA-YL-A9WL 
       36.95        45.50        62.79        14.04        62.37        24.33 
TCGA-ZG-A8QW 
        1.64 

$`22Q LOSS WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5754 
        1.97        24.03         1.02        13.02        31.00         2.04 
TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5767 TCGA-CH-5768 
       44.02        12.00         1.02        23.01        15.06        24.03 
TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 
        2.04        13.02        26.99         9.99        32.02        33.01 
TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 
        2.99        29.00        27.16        33.11        19.56        13.32 
TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 
       29.79        46.52        44.88        26.30        45.73        28.93 
TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 
       30.31        27.19        23.90        38.93        48.13        36.69 
TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 
       38.53        36.23        60.23        46.55        47.80        52.27 
TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 
       64.50        51.88        68.35        43.07        36.66        38.76 
TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 
       39.75        60.23        41.85        47.87        29.06        27.02 
TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 
       49.02        61.15        83.57        21.80         9.70         9.50 
TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 
        9.37        16.77         7.66        17.52         5.75        27.68 
TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7784 TCGA-EJ-7785 
        6.28         0.30        23.90        38.37        25.68        20.55 
TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 
       14.53        14.14        18.15        19.59        17.29         3.75 
TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8474 
       23.05        19.92        64.47        63.98        26.99        10.32 
TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H 
        5.33         4.24        17.49         9.83         3.06         7.53 
TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G 
       21.96        17.62        12.92        13.71        18.41         9.14 
TCGA-EJ-A65J TCGA-EJ-A65M TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB 
        2.99         7.56        28.41        15.42        13.45         8.98 
TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 
       17.23        16.24         1.78        41.62        87.35        81.04 
TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 
       67.99        66.67        69.37        55.76        18.21        68.68 
TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6361 TCGA-G9-6362 
       49.81        46.16        50.70        49.35        46.52        47.44 
TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 
       45.30        39.39        44.81         3.32        40.18        39.95 
TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 
       38.01        40.31        26.66        31.50        37.97        45.80 
TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 
       25.15        27.29        58.22        56.75        52.87        50.73 
TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 
       38.27        38.96        27.91        35.34        28.18        32.68 
TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 
       26.01        21.14         6.08        30.94         3.68        19.76 
TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 
        5.33         2.93         2.37        14.47        28.54         0.79 
TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 
       28.60         1.97         1.68         2.37         2.93         1.71 
TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 
        0.72         2.10         2.66         1.74         1.48         1.68 
TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 
        2.07        24.59        26.04         1.97         1.12         3.22 
TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 
       30.51         1.48        17.85        24.56         1.84        19.36 
TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 
        3.12        23.87         2.17         2.27         1.94        17.95 
TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A4ZV TCGA-HC-A632 
       22.32         1.58        15.88         1.15         0.76         2.01 
TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS 
        2.20         1.61         5.49         2.33         3.48         1.45 
TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HI-7169 TCGA-HI-7170 TCGA-J4-8198 TCGA-J4-8200 
        1.25         4.41        88.24        82.92        20.19        12.30 
TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q 
       21.76        17.03        16.04        16.54        16.14        20.52 
TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 
       14.93        17.19         6.02        13.32        17.36         9.17 
TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N 
        9.17        10.19         6.77        10.39        14.37        20.28 
TCGA-J9-A52B TCGA-J9-A52C TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z 
       13.87         5.85        93.99        56.28        44.68        61.78 
TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 
      115.86        30.02        54.54       151.36        67.59        90.51 
TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AZ TCGA-KK-A7B1 
       49.25       113.33        67.07        58.19        27.62        34.95 
TCGA-KK-A7B2 TCGA-KK-A8IB TCGA-KK-A8IF TCGA-KK-A8IL TCGA-M7-A71Z TCGA-M7-A720 
       22.75         2.73        26.43        20.65         6.87         9.93 
TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-QU-A6IL TCGA-QU-A6IM 
       13.15        27.02        25.08        15.88         3.19        41.00 
TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-TP-A8TT TCGA-TP-A8TV TCGA-VN-A88I 
      114.64        47.21        86.14        11.90         8.19         8.84 
TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q 
       12.95         6.02        15.52        15.81        30.15        32.91 
TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B 
       15.09         4.34        84.69        94.65        23.93        75.91 
TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-AA1N 
       55.56        60.92        66.97        21.80        48.85        17.82 
TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DI 
        5.79        37.18        27.81         3.91        38.04        48.03 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 
        9.04         2.99        31.96        31.50        31.96        28.54 
TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-Y6-A8TL TCGA-YL-A8HJ 
       29.23        27.09        37.02        39.65        25.48        52.96 
TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA 
       49.02        38.56        71.77        62.14        60.56        16.83 
TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK 
       41.46        45.14        28.77        47.38        45.86        37.97 
TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SR TCGA-YL-A9WI TCGA-YL-A9WJ 
       26.24       106.75        71.34         7.00        41.39        60.99 
TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9ND 
       49.91        28.34         4.93         1.12         7.86         6.02 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              0.92               0.30 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            106.95             151.36 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             25.51              23.90 
[1] "0.9 - 107.0 (25.5)" "0.3 - 151.4 (23.9)"
[1] "hr=" "2"  
D74V2, continuous
                    vv
clus                  T2  T3  T4
  22Q LOSS MUTATED     4  27   1
  22Q LOSS WILD-TYPE 146 179   4
D74V3, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T2                4                146
  T3               27                179
  T4                1                  4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V4, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    22   9
  22Q LOSS WILD-TYPE 241  35
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     22    9
  22Q LOSS WILD-TYPE  241   35
   clus
vv  22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  0               22                241
  1                9                 35
[1] 2 2
[1] FALSE
D74V5, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED     3  29
  22Q LOSS WILD-TYPE  10 321
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      3   29
  22Q LOSS WILD-TYPE   10  321
                                        clus
vv                                       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE                3                 10
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  29                321
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  22Q LOSS MUTATED    18  14   0   0
  22Q LOSS WILD-TYPE 225  76   5  11
D74V6, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  R0               18                225
  R1               14                 76
  R2                0                  5
  RX                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"
D74V7, continuous
D74V8, continuous
D74V9, continuous
D74V10, continuous
D74V11, continuous
D74V12, continuous
D74V13, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  22Q LOSS MUTATED       0                         1    10
  22Q LOSS WILD-TYPE     2                         6   136
D74V14, multiclass
                           clus
vv                          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                1                  6
  WHITE                                   10                136
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(75) Variable = XQ LOSS MUTATION ANALYSIS
D75V1, survival
                   sevent
clus2                 0   1
  XQ LOSS MUTATED    28   1
  XQ LOSS WILD-TYPE 327   5
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               29               332 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                1                 5 
$`XQ LOSS MUTATED`
TCGA-CH-5753 TCGA-EJ-5507 TCGA-EJ-7312 TCGA-EJ-7783 TCGA-EJ-7789 TCGA-EJ-A65D 
        1.02        23.90        21.80        25.87        18.15        12.92 
TCGA-G9-6369 TCGA-G9-6499 TCGA-HC-7213 TCGA-HC-A48F TCGA-HI-7171 TCGA-J4-A67N 
       39.95        50.73         1.97        22.36        43.69        16.54 
TCGA-KK-A59X TCGA-KK-A59Z TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E6 TCGA-KK-A6E8 
       56.28        61.78        30.02        54.54       113.33        58.19 
TCGA-TP-A8TV TCGA-VN-A943 TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-XK-AAJP 
        8.19         4.34        21.53        17.82         5.79        29.23 
TCGA-YL-A8SC TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A9WL TCGA-ZG-A9ND 
       41.46        37.97        26.24        24.33         6.02 

$`XQ LOSS WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 
        2.04         0.92        44.02        12.00         1.02        23.01 
TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 
        1.02        15.06        24.03         2.04        13.02        15.98 
TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 
       26.99         9.99        32.02        33.01         2.99        29.00 
TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
       27.16        33.11        19.56        13.32        29.79        46.52 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       44.88        26.30        45.73        28.93        30.31        27.19 
TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 
       38.93        48.13        36.69        48.53        38.53        36.23 
TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 
       60.23        46.55        47.80        52.27        64.50        51.88 
TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 
       68.35        43.07        36.66        38.76        39.75        60.23 
TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 
       41.85        47.87        29.06        27.02        49.02        61.15 
TCGA-EJ-7218 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 
       83.57         9.70         9.50         9.37        16.77         7.66 
TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 
       17.52         5.75        27.68         6.28         0.30        23.90 
TCGA-EJ-7782 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7791 
       38.37        25.68        20.55        14.53        14.14        19.59 
TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 
       17.29         3.75        23.05        19.92        64.47        63.98 
TCGA-EJ-8470 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F 
       26.99        10.32         5.33         4.24        17.49         9.83 
TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65E TCGA-EJ-A65F 
        3.06         7.53        21.96        17.62        13.71        18.41 
TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI 
        9.14         2.99         7.56        28.41        15.42        13.45 
TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 
        8.98        17.23        16.24         1.78        41.62        87.35 
TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 
       81.04        67.99        66.67        69.37        55.76        18.21 
TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 
       68.68        49.81        46.16        50.70        49.35        47.15 
TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 
       46.52        47.44        45.30        39.39        44.81         3.32 
TCGA-G9-6367 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 
       40.18        38.01        40.31        26.66        31.50        37.97 
TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 
       45.80        25.15        27.29        58.22        56.75        52.87 
TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 
       38.27        38.96        27.91        30.97        35.34        28.18 
TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY 
       32.68        26.01        21.14         6.08        30.94         3.68 
TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 
       19.76         5.33         2.93         2.01         2.37        14.47 
TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 
       28.54         0.79        28.60         1.68         2.37         2.93 
TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 
        1.71         0.72         2.10         2.66         1.74         1.48 
TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 
        1.68         2.07        24.59        26.04         1.97         1.12 
TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 
        3.22        30.51         1.48        17.85        24.56         1.84 
TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 
       19.36        22.42         3.12        23.87         2.17         2.27 
TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 
        1.94        17.95        22.32         1.58        15.88         1.15 
TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO 
        0.76         1.78         2.01         2.20         1.61         5.49 
TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HI-7168 
        2.33         3.48         1.45         1.25         4.41        78.61 
TCGA-HI-7169 TCGA-HI-7170 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L 
       88.24        82.92        20.19        12.30        21.76        17.03 
TCGA-J4-A67M TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T 
       16.04        16.14        20.52        14.93        17.19         6.02 
TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K 
       13.32        17.36         9.17         9.17        10.19         6.77 
TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E 
       10.39        14.37        20.28        13.87         5.85        10.62 
TCGA-KK-A59V TCGA-KK-A59Y TCGA-KK-A6DY TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 
       93.99        44.68       115.86       151.36        67.59        90.51 
TCGA-KK-A6E5 TCGA-KK-A6E7 TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8IB 
       49.25        67.07        27.62        34.95        22.75         2.73 
TCGA-KK-A8IF TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 
       26.43        20.65         5.19         6.87         9.93        13.15 
TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM 
       27.02        25.08        15.88        18.84         3.19        41.00 
TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-TP-A8TT TCGA-VN-A88I TCGA-VN-A88K 
      114.64        47.21        86.14        11.90         8.84        25.51 
TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q 
       12.95         6.02        15.52        15.81        30.15        32.91 
TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 
       15.09       106.95        26.47        84.69        94.65        23.93 
TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J 
       75.91        55.56        60.92        66.97        21.80        48.85 
TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK 
       37.18        27.81         3.91        38.04        48.03         9.04 
TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJ3 
        2.99        25.97        31.96        31.50        31.96        28.54 
TCGA-XK-AAJA TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-Y6-A8TL TCGA-YL-A8HJ 
       30.58        27.09        37.02        39.65        25.48        52.96 
TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 
       49.02        38.56        36.95        71.77        62.14        60.56 
TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ 
       16.83        45.50        45.14        28.77        47.38        45.86 
TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI 
      106.75        71.34        62.79         7.00        14.04        41.39 
TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX 
       60.99        62.37        49.91        28.34         1.64         4.93 
TCGA-ZG-A8QY TCGA-ZG-A8QZ 
        1.12         7.86 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             1.02              0.30 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           113.33            151.36 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           24.330            23.915 
[1] "1.0 - 113.3 (24.3)" "0.3 - 151.4 (23.9)"
[1] "hr=" "2.3"
D75V2, continuous
                   vv
clus                 T2  T3  T4
  XQ LOSS MUTATED     7  22   0
  XQ LOSS WILD-TYPE 143 184   5
D75V3, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T2               7               143
  T3              22               184
  T4               0                 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"
D75V4, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    22   7
  XQ LOSS WILD-TYPE 241  37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     22    7
  XQ LOSS WILD-TYPE  241   37
   clus
vv  XQ LOSS MUTATED XQ LOSS WILD-TYPE
  0              22               241
  1               7                37
[1] 2 2
[1] FALSE
D75V5, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     2  27
  XQ LOSS WILD-TYPE  11 323
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      2   27
  XQ LOSS WILD-TYPE   11  323
                                        clus
vv                                       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE               2                11
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 27               323
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  XQ LOSS MUTATED    19   8   0   2
  XQ LOSS WILD-TYPE 224  82   5   9
D75V6, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  R0              19               224
  R1               8                82
  R2               0                 5
  RX               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"
D75V7, continuous
D75V8, continuous
D75V9, continuous
D75V10, continuous
D75V11, continuous
D75V12, continuous
D75V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XQ LOSS MUTATED       0                         1     7
  XQ LOSS WILD-TYPE     2                         6   139
D75V14, multiclass
                           clus
vv                          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               1                 6
  WHITE                                   7               139
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
