[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"        "-oTHNSC-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/HNSC-TP/11541491/HNSC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/HNSC-TP/11544936/transformed.cor.cli.txt"

nPatients in clinical file=494, in cluster file=522, common to both=488
[1]  80 488
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               64               424 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               64               424 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              112               376 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              112               376 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               91               397 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               91               397 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               72               416 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               72               416 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               77               411 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               77               411 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              237               251 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              237               251 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               39               449 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               39               449 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               35               453 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               35               453 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              187               301 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              187               301 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               64               424 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               64               424 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               76               412 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               76               412 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               58               430 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               58               430 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              172               316 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              172               316 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              123               365 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              123               365 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              146               342 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              146               342 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              291               197 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              291               197 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               93               395 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               93               395 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
              129               359 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
              129               359 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                34                454 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                34                454 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                31                457 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                31                457 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                60                428 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                60                428 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                69                419 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                69                419 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               139                349 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               139                349 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                81                407 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                81                407 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                55                433 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                55                433 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
               139                349 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
               139                349 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                69                419 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                69                419 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
               103                385 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
               103                385 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
               104                384 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
               104                384 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                64                424 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                64                424 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                81                407 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                81                407 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
               112                376 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
               112                376 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                48                440 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                48                440 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                50                438 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                50                438 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                71                417 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                71                417 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               178                310 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               178                310 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               189                299 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               189                299 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                32                456 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                32                456 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
               108                380 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
               108                380 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               81               407 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               81               407 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               55               433 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               55               433 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               36               452 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               36               452 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               32               456 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               32               456 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               44               444 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               44               444 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              283               205 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              283               205 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               59               429 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               59               429 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              183               305 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              183               305 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              141               347 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              141               347 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               48               440 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               48               440 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              156               332 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              156               332 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               64               424 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               64               424 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               62               426 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               62               426 
[1] "7P LOSS MUTATION ANALYSIS"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               28               460 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               28               460 
[1] "7Q LOSS MUTATION ANALYSIS"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               39               449 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               39               449 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              175               313 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              175               313 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               28               460 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               28               460 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              175               313 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              175               313 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               81               407 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               81               407 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               149                339 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               149                339 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               104                384 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               104                384 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               135                353 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               135                353 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               160                328 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               160                328 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                33                455 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                33                455 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                29                459 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                29                459 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               154                334 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               154                334 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                53                435 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                53                435 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                95                393 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                95                393 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                57                431 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                57                431 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                72                416 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                72                416 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               101                387 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               101                387 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                32                456 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                32                456 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                96                392 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                96                392 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               198                290 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               198                290 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                90                398 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                90                398 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                79                409 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                79                409 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                46                442 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                46                442 
[1] "20Q LOSS MUTATION ANALYSIS"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                28                460 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                28                460 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               177                311 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               177                311 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                69                419 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                69                419 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               77               411 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               77               411 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDISEASE"                  
 [6] "NEOPLASM.DISEASESTAGE"                 
 [7] "PATHOLOGY.T.STAGE"                     
 [8] "PATHOLOGY.N.STAGE"                     
 [9] "PATHOLOGY.M.STAGE"                     
[10] "DCCUPLOADDATE"                         
[11] "GENDER"                                
[12] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[13] "DAYSTOLASTKNOWNALIVE"                  
[14] "RADIATIONTHERAPY"                      
[15] "HISTOLOGICALTYPE"                      
[16] "RADIATIONS.RADIATION.REGIMENINDICATION"
[17] "NUMBERPACKYEARSSMOKED"                 
[18] "YEAROFTOBACCOSMOKINGONSET"             
[19] "NUMBER.OF.LYMPH.NODES"                 
[20] "RACE"                                  
[21] "ETHNICITY"                             
[22] "BATCHNUMBER"                           

Input Data has 22 rows and 488 columns.

[1] "Batch" "22"   
[1] "Last Follow UP"
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 
         102          462          283          415           NA          276 
TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 
         248          722         1288         1762          520          725 
TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 
         623         1636         1747          190          644          451 
TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG 
          63          384          113          236          895          855 
TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DD 
         622          918          850          351          216           NA 
TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL 
         182           NA           NA           NA          314          623 
TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 
         142          187         2878          278          140          133 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 
         558          310          536          423          687          638 
TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A47Z 
        1153          428          436         2161          624            5 
TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 
           4          799          721         1157          142         1230 
TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 
        1151          392          817          993          642         1250 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 
         395          625           NA         1330          811         1268 
TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 
          NA         1007         1045          173           NA         1081 
TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 
          NA           NA           NA           NA           NA           NA 
TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 
          NA          683          290          630          933          629 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 
         628          594          629           45          432           98 
TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 
          NA          202         1110          224          318          611 
TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 
         394          735           NA          432          429           46 
TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T 
         443          535          391          904          645          225 
TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 
         526          484          348          175           NA          367 
TCGA-CN-A642 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
          NA          223          298         1466         1207          654 
TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 
          NA         1660         1422         1393         1399          317 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6221 TCGA-CQ-6223 
         341          129         1253           NA         1000         1057 
TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 
         985           NA           NA           NA         1179         1750 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 
        1560         1007          509         1309         1274          877 
TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB 
        1950         1353           NA          707           NA          893 
TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 
         998          785          391          303          950         2562 
TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 
         358         1663         1152          799         1777         1521 
TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 
          NA         1050         1125           NA          514           NA 
TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 
         362          311          345          354          234          379 
TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 
         350          479           NA         1435         1191         1440 
TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 
        1245           NA          105           NA          759          889 
TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 
          30          972           NA         1036           NA          796 
TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 
          NA          997         1430           NA          392          907 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 
         913          946          908          898          930          216 
TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 
         156          181         1077          911         1472         4241 
TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 
         522         3930         3295         1438          584          546 
TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 
        3270         2886         2327         2784         2437          519 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 
         406          701         2641         1478         1840          215 
TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6933 
        1315         1665          641         1899           NA           NA 
TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6939 
          NA           NA           NA           NA           NA           NA 
TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6948 
          NA           NA         3835           NA           NA           NA 
TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 
          NA           NA           NA           NA           NA           NA 
TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 
          NA           NA           NA           NA           NA           NA 
TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 
        3837         3381           NA           NA           NA           NA 
TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 
          NA           NA           NA           NA           NA           NA 
TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7242 
          NA         3497         2347           NA         1444         1095 
TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 
         954          797           NA           NA           NA           NA 
TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 
          NA           NA           NA         1099           NA           NA 
TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7414 
          NA           NA           NA           NA           NA           NA 
TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7423 
          NA           NA           NA           NA           NA           NA 
TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7429 TCGA-CV-7430 
          NA           NA           NA           NA           NA           NA 
TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7438 
          NA           NA           NA         4335           NA           NA 
TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U 
          NA          851           NA         5480           NA           NA 
TCGA-CV-A45V TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 
          NA           NA           NA           NA           NA           NA 
TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JD 
          NA           NA         1722           NA           NA           NA 
TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU 
        1075           NA          906           NA          670          110 
TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 
         646          714          606          685           NA          317 
TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 
         321          237          828           NA          773          292 
TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 
         701           77          491          154          568          106 
TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO 
         128          539          376          483          232          435 
TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 
         424          368          389          338         1778         1081 
TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 
         516         1030          548           NA          575          775 
TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
         622          299          369          368          324          340 
TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J 
        1131          490          658           15           92          585 
TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 
           3          384           14           13           NA            6 
TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 
          NA          407           58          133          414          403 
TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 
         206            2            5           25           NA           NA 
TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 
          37           55           44           24           25           11 
TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 
          49           10          111           33         1057          485 
TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61I 
         122          441          588          360          412           NA 
TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T 
         440           NA          351          360          224          552 
TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D 
         378          168           14           34          392           56 
TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 
         111          112           NA          254          240          910 
TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX 
          NA         1726         1559           NA         1120           NA 
TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 
         578         1917           NA           NA           NA           NA 
TCGA-P3-A6T7 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG 
          NA          400          553          357          245          218 
TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A8Z7 TCGA-QK-A8Z8 
         228          225          387          567          198           NA 
TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-UF-A718 
         149          135          135          157          168         1326 
TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 
        1663           NA         1319         1252         1278         1043 
TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ 
        1894          484          735         1497          665          214 
TCGA-UF-A7JS TCGA-UF-A7JV 
         413           NA 
Variable 1:'AGE':	nDistinctValues=60,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=168,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=316,	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=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=22,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=48,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 14:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'HISTOLOGICAL.TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NUMBERPACKYEARSSMOKED':	nDistinctValues=85,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'YEAROFTOBACCOSMOKINGONSET':	nDistinctValues=60,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=25,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 22:'BATCH.NUMBER':	nDistinctValues=23,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                                   
 [2] "NEOPLASM.DISEASESTAGE"                 
 [3] "PATHOLOGY.T.STAGE"                     
 [4] "PATHOLOGY.N.STAGE"                     
 [5] "PATHOLOGY.M.STAGE"                     
 [6] "GENDER"                                
 [7] "HISTOLOGICAL.TYPE"                     
 [8] "RADIATIONS.RADIATION.REGIMENINDICATION"
 [9] "NUMBERPACKYEARSSMOKED"                 
[10] "NUMBER.OF.LYMPH.NODES"                 
[11] "RACE"                                  
[12] "ETHNICITY"                             
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 488 columns, 1 survival variables, and 12 non-survival variables.
AGE, nv=60, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=6, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=5, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T0  T1  T2  T3  T4 
  1  46 127  94 162 
[1] "table(vv)"
vv
T0+T1    T2    T3    T4 
   47   127    94   162 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
 T0  T1  T2  T3  T4 
  1  46 127  94 162 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T0+T1    T2    T3    T4 
   47   127    94   162 
PATHOLOGY.N.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
170  63 152   8 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
170  63 152   8 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
 N0  N1  N2  N3 
170  63 152   8 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
170  63 152   8 
PATHOLOGY.M.STAGE, nv=3, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL.TYPE, nv=3, binary=FALSE, numeric=FALSE
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
NUMBERPACKYEARSSMOKED, nv=85, binary=FALSE, numeric=TRUE
NUMBER.OF.LYMPH.NODES, nv=25, binary=FALSE, numeric=TRUE
RACE, nv=4, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1P GAIN MUTATION ANALYSIS
D1V1, survival
                   sevent
clus2                 0   1
  1P GAIN MUTATED    37  15
  1P GAIN WILD-TYPE 264  98
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               52               362 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               15                98 
$`1P GAIN MUTATED`
TCGA-BA-5149 TCGA-BA-5555 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 TCGA-BB-8596 
         248          520          451          384          113         1955 
TCGA-BB-8601 TCGA-C9-A47Z TCGA-CN-4727 TCGA-CN-4739 TCGA-CN-5359 TCGA-CN-6020 
         624            5         1230         1330         1980           98 
TCGA-CN-6989 TCGA-CN-A49A TCGA-CQ-7067 TCGA-CR-6478 TCGA-CR-6482 TCGA-CR-7379 
         611          391          509         1969          345         1036 
TCGA-CR-7388 TCGA-CV-5431 TCGA-CV-5442 TCGA-CV-5444 TCGA-CV-5973 TCGA-CV-5977 
        1951          522         2327         2437         2641         1840 
TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7102 TCGA-CV-7235 TCGA-CV-7422 TCGA-CV-A45R 
        1959         1970         1945         1952         1957         5480 
TCGA-CV-A461 TCGA-CV-A6JE TCGA-CX-7082 TCGA-D6-A74Q TCGA-DQ-5625 TCGA-DQ-5629 
        1954         1075          317          338         1081          516 
TCGA-DQ-7588 TCGA-DQ-7596 TCGA-F7-8298 TCGA-H7-7774 TCGA-H7-A76A TCGA-IQ-A61O 
        1965          340          490          407          206          360 
TCGA-KU-A66T TCGA-P3-A5Q5 TCGA-P3-A6SW TCGA-P3-A6SX TCGA-QK-A8Z7 TCGA-QK-A8Z9 
         552          910         1120         1954          198          149 
TCGA-QK-A8ZA TCGA-UF-A719 TCGA-UF-A71E TCGA-UF-A7JH 
         135         1663         1278          665 

$`1P GAIN WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 
         102          462          283          415         1983          276 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 
         722         1288         1762          725          623         1636 
TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6871 TCGA-BA-7269 TCGA-BA-A4IF 
        1747          190          644           63          236          895 
TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB 
         855          622          918          850          351          216 
TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 
         182         1976          314          623          142          187 
TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 
        2878          278          140          133          558          310 
TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 
         536          423          687          638         1153          428 
TCGA-BB-7872 TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 
         436            4          799          721         1157          142 
TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 
        1151          392          817          993          642         1250 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 
         395          625         1960          811         1268         1988 
TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 
        1007         1045          173         1081         1977         1980 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 
        1966         1966         1975          683          290          630 
TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 
         933          629          628          594          629           45 
TCGA-CN-6019 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 
         432         1970          202         1110          224          318 
TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 
         394          735          432          429           46          443 
TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V 
         535          904          645          225          526          484 
TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 
         348          175          367          223          298         1466 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 
        1207          654         1660         1422         1393         1399 
TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 
         317          341          129         1253         1000         1057 
TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 
         985         1959         1959         1179         1750         1560 
TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 
        1007         1309         1274          877         1950         1353 
TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE 
        1960          707         1963          893          998          785 
TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 
         391          303          950         2562          358         1663 
TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 
        1152          799         1777         1521         1966         1050 
TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6484 
        1125         1971          514          362          311          354 
TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 
         234          379          350          479         1956         1435 
TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 
        1191         1440         1245         1960          105         1979 
TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7382 
         759          889           30          972         1968          796 
TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 
        1954          997         1430          392          907          913 
TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 
         946          908          898          930          216          156 
TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5432 
         181         1077          911         1472         1955         1950 
TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 
        3295         1438          584          546         1978         2886 
TCGA-CV-5443 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5976 TCGA-CV-5978 
        1958          519          406          701         1478          215 
TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 
        1315         1665          641         1899         1970         1948 
TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 
        1969         1952         1959         3835         1948         1969 
TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7097 
        1966         1957         1969         1959         3837         1970 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7238 
        1936         1959         1939         1987         1979         1444 
TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7254 
        1095          954          797         1967         1960         1976 
TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7424 TCGA-CV-7427 
        1099         1974         1948         1955         1947         1937 
TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 
        1973         1972         1937         1984         1958         1959 
TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 
        1981          851         1945         1960         1940         1946 
TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT 
        1722         1977         1970          906         1959          670 
TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 
         110          646          714          606          685         1950 
TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 
         321          237          828          773          292          701 
TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 
          77          491          154          568          106          128 
TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP 
         539          376          483          232          435          424 
TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-DQ-5624 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7589 
         368          389         1778         1030          548          575 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 
         775          622          299          369          368          324 
TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S 
        1131          658           15           92          585            3 
TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-8501 TCGA-H7-8502 
         384           14           13            6           58          133 
TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 
         414          403            2            5           25           37 
TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 
          55           44           24           25           11           49 
TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 
          10          111           33         1057          485          122 
TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61L 
         441          588          360          412          440          351 
TCGA-KU-A66S TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A 
         224          378          168           14           34          392 
TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5QA 
          56          111          112          254          240         1726 
TCGA-P3-A5QE TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A64Z 
        1559          578         1917         1968          400          553 
TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ 
         357          245          218          228          225          387 
TCGA-QK-A6V9 TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-UF-A718 TCGA-UF-A71B 
         567          135          157          168         1326         1319 
TCGA-UF-A71D TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF 
        1252         1043         1894          484          735         1497 
TCGA-UF-A7JJ TCGA-UF-A7JS 
         214          413 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                5                 2 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             5480              3837 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            787.5             701.0 
[1] "5.0 - 5480.0 (787.5)" "2.0 - 3837.0 (701.0)"
[1] "hr=" "1.3"
D1V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  1P GAIN MUTATED         3        6         7        33         2         0
  1P GAIN WILD-TYPE      23       69        67       202        10         1
D1V3, multiclass
           clus
vv          1P GAIN MUTATED 1P GAIN WILD-TYPE
  STAGE I                 3                23
  STAGE II                6                69
  STAGE III               7                67
  STAGE IVA              33               202
  STAGE IVB               2                10
  STAGE IVC               0                 1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  1P GAIN MUTATED       3  15  12  21
  1P GAIN WILD-TYPE    44 112  82 141
D1V4, multiclass
       clus
vv      1P GAIN MUTATED 1P GAIN WILD-TYPE
  T0+T1               3                44
  T2                 15               112
  T3                 12                82
  T4                 21               141
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  1P GAIN MUTATED    16   9  22   1
  1P GAIN WILD-TYPE 154  54 130   7
D1V5, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  N0              16               154
  N1               9                54
  N2              22               130
  N3               1                 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"
                   vv
clus                 M0  M1  MX
  1P GAIN MUTATED    15   0  12
  1P GAIN WILD-TYPE 152   1  46
D1V6, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  M0              15               152
  M1               0                 1
  MX              12                46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V7, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    18  46
  1P GAIN WILD-TYPE 114 310
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     18   46
  1P GAIN WILD-TYPE  114  310
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE              18               114
  MALE                46               310
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  1P GAIN MUTATED                                      59
  1P GAIN WILD-TYPE                                   418
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  1P GAIN MUTATED                                                             1
  1P GAIN WILD-TYPE                                                           0
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  1P GAIN MUTATED                                                     4
  1P GAIN WILD-TYPE                                                   6
D1V8, multiclass
                                                             clus
vv                                                            1P GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    59
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       4
                                                             clus
vv                                                            1P GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     418
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                 0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V9, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    11  53
  1P GAIN WILD-TYPE  68 356
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     11   53
  1P GAIN WILD-TYPE   68  356
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  NO               11                68
  YES              53               356
[1] 2 2
[1] FALSE
D1V10, continuous
D1V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1P GAIN MUTATED                                  0     1
  1P GAIN WILD-TYPE                                2    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1P GAIN MUTATED                          12    48
  1P GAIN WILD-TYPE                        32   367
D1V12, multiclass
                                  clus
vv                                 1P GAIN MUTATED 1P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                     12                32
  WHITE                                         48               367
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V13, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     5  55
  1P GAIN WILD-TYPE  19 376
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      5   55
  1P GAIN WILD-TYPE   19  376
                        clus
vv                       1P GAIN MUTATED 1P GAIN WILD-TYPE
  HISPANIC OR LATINO                   5                19
  NOT HISPANIC OR LATINO              55               376
[1] 2 2
[1] FALSE

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                 0   1
  1Q GAIN MUTATED    67  24
  1Q GAIN WILD-TYPE 234  89
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               91               323 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               24                89 
$`1Q GAIN MUTATED`
TCGA-BA-5555 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-7269 TCGA-BB-4224 
         520          451           63          384          236          278 
TCGA-BB-4227 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-8596 TCGA-BB-8601 TCGA-CN-4727 
         133         1153          428         1955          624         1230 
TCGA-CN-4728 TCGA-CN-4739 TCGA-CN-5359 TCGA-CN-5367 TCGA-CN-5374 TCGA-CN-6010 
        1151         1330         1980         1966          290          630 
TCGA-CN-6013 TCGA-CN-6020 TCGA-CN-6023 TCGA-CN-6997 TCGA-CN-A49A TCGA-CN-A63U 
         628           98         1110          429          391          526 
TCGA-CQ-7064 TCGA-CQ-7067 TCGA-CQ-A4C9 TCGA-CQ-A4CD TCGA-CQ-A4CI TCGA-CR-6478 
        1560          509          707          998          950         1969 
TCGA-CR-6482 TCGA-CR-7370 TCGA-CR-7379 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 
         345          105         1036         1951          392          907 
TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5434 TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5444 
        1955          522         3295         1978         2327         2437 
TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6941 
        1840          215         1315         1969         1952         1959 
TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7235 TCGA-CV-7243 
        1959         1970         1939         1945         1952          954 
TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7422 TCGA-CV-7440 TCGA-CV-A45R 
        1960         1976         1099         1957         1981         5480 
TCGA-CV-A461 TCGA-CV-A6JE TCGA-CX-7082 TCGA-CX-7086 TCGA-D6-6827 TCGA-D6-A6EP 
        1954         1075          317          237          568          424 
TCGA-D6-A74Q TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-7589 TCGA-DQ-7596 TCGA-F7-8298 
         338         1081          516          575          340          490 
TCGA-H7-7774 TCGA-H7-A76A TCGA-HD-7754 TCGA-HD-7917 TCGA-HL-7533 TCGA-IQ-A61H 
         407          206           25           37         1057          412 
TCGA-IQ-A61O TCGA-KU-A66T TCGA-P3-A5Q5 TCGA-P3-A6SW TCGA-QK-A8Z7 TCGA-QK-A8Z9 
         360          552          910         1120          198          149 
TCGA-QK-A8ZA TCGA-QK-AA3J TCGA-UF-A719 TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7JD 
         135          157         1663         1252         1278          735 
TCGA-UF-A7JH 
         665 

$`1Q GAIN WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 
         102          462          283          415         1983          276 
TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5557 
         248          722         1288         1762          725          623 
TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6873 TCGA-BA-A4IF 
        1636         1747          190          644          113          895 
TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB 
         855          622          918          850          351          216 
TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 
         182         1976          314          623          142          187 
TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 
        2878          140          558          310          536          423 
TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7872 TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 
         687          638          436            5            4          799 
TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 
         721         1157          142          392          817          993 
TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4740 
         642         1250          395          625         1960          811 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5360 
        1268         1988         1007         1045          173         1081 
TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6011 
        1977         1980         1966         1975          683          933 
TCGA-CN-6012 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6021 
         629          594          629           45          432         1970 
TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 
         202          224          318          611          394          735 
TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A49C 
         432           46          443          535          904          645 
TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A6V1 
         225          484          348          175          367          223 
TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 
         298         1466         1207          654         1660         1422 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 
        1393         1399          317          341          129         1253 
TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 
        1000         1057          985         1959         1959         1179 
TCGA-CQ-7063 TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 
        1750         1007         1309         1274          877         1950 
TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CE TCGA-CQ-A4CG 
        1353         1960         1963          893          785          391 
TCGA-CQ-A4CH TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 
         303         2562          358         1663         1152          799 
TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 
        1777         1521         1966         1050         1125         1971 
TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 
         514          362          311          354          234          379 
TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 
         350          479         1956         1435         1191         1440 
TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 
        1245         1960         1979          759          889           30 
TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 
         972         1968          796         1954          997         1430 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 
         913          946          908          898          930          216 
TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5432 
         156          181         1077          911         1472         1950 
TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5441 TCGA-CV-5443 TCGA-CV-5966 
        1438          584          546         2886         1958          519 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-6003 TCGA-CV-6433 
         406          701         2641         1478         1665          641 
TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 
        1899         1970         1948         3835         1948         1969 
TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7097 
        1966         1957         1969         1959         3837         1970 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7238 TCGA-CV-7242 
        1936         1959         1987         1979         1444         1095 
TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7424 
         797         1967         1974         1948         1955         1947 
TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 
        1937         1973         1972         1937         1984         1958 
TCGA-CV-7435 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 
        1959          851         1945         1960         1940         1946 
TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT 
        1722         1977         1970          906         1959          670 
TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 
         110          646          714          606          685         1950 
TCGA-CX-7085 TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 
         321          828          773          292          701           77 
TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB 
         491          154          106          128          539          376 
TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-DQ-5624 
         483          232          435          368          389         1778 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 
        1030          548         1965          775          622          299 
TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G 
         369          368          324         1131          658           15 
TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 
          92          585            3          384           14           13 
TCGA-F7-A623 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-HD-7229 
           6           58          133          414          403            2 
TCGA-HD-7753 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 
           5           55           44           24           25           11 
TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-IQ-7630 TCGA-IQ-7631 
          49           10          111           33          485          122 
TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61J TCGA-IQ-A61L TCGA-KU-A66S 
         441          588          360          440          351          224 
TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D 
         378          168           14           34          392           56 
TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5QA TCGA-P3-A5QE 
         111          112          254          240         1726         1559 
TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A64Z 
        1954          578         1917         1968          400          553 
TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ 
         357          245          218          228          225          387 
TCGA-QK-A6V9 TCGA-QK-A8ZB TCGA-QK-AA3K TCGA-UF-A718 TCGA-UF-A71B TCGA-UF-A7J9 
         567          135          168         1326         1319         1043 
TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JF TCGA-UF-A7JJ TCGA-UF-A7JS 
        1894          484         1497          214          413 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               25                 2 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             5480              3837 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              907               685 
[1] "25.0 - 5480.0 (907.0)" "2.0 - 3837.0 (685.0)" 
[1] "hr=" "1.3"
D2V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  1Q GAIN MUTATED         5       14        14        57         4         0
  1Q GAIN WILD-TYPE      21       61        60       178         8         1
D2V3, multiclass
           clus
vv          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  STAGE I                 5                21
  STAGE II               14                61
  STAGE III              14                60
  STAGE IVA              57               178
  STAGE IVB               4                 8
  STAGE IVC               0                 1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  1Q GAIN MUTATED       6  30  17  41
  1Q GAIN WILD-TYPE    41  97  77 121
D2V4, multiclass
       clus
vv      1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T0+T1               6                41
  T2                 30                97
  T3                 17                77
  T4                 41               121
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  1Q GAIN MUTATED    30  13  38   3
  1Q GAIN WILD-TYPE 140  50 114   5
D2V5, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  N0              30               140
  N1              13                50
  N2              38               114
  N3               3                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1  MX
  1Q GAIN MUTATED    28   0  13
  1Q GAIN WILD-TYPE 139   1  45
D2V6, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  M0              28               139
  M1               0                 1
  MX              13                45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V7, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    26  86
  1Q GAIN WILD-TYPE 106 270
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     26   86
  1Q GAIN WILD-TYPE  106  270
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE              26               106
  MALE                86               270
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  1Q GAIN MUTATED                                     105
  1Q GAIN WILD-TYPE                                   372
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  1Q GAIN MUTATED                                                             1
  1Q GAIN WILD-TYPE                                                           0
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  1Q GAIN MUTATED                                                     6
  1Q GAIN WILD-TYPE                                                   4
D2V8, multiclass
                                                             clus
vv                                                            1Q GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                   105
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       6
                                                             clus
vv                                                            1Q GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     372
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                 0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         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"
D2V9, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    22  90
  1Q GAIN WILD-TYPE  57 319
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     22   90
  1Q GAIN WILD-TYPE   57  319
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO               22                57
  YES              90               319
[1] 2 2
[1] FALSE
D2V10, continuous
D2V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1Q GAIN MUTATED                                  0     0
  1Q GAIN WILD-TYPE                                2    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1Q GAIN MUTATED                          19    88
  1Q GAIN WILD-TYPE                        25   327
D2V12, multiclass
                                  clus
vv                                 1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                     19                25
  WHITE                                         88               327
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V13, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED     7  96
  1Q GAIN WILD-TYPE  17 335
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      7   96
  1Q GAIN WILD-TYPE   17  335
                        clus
vv                       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   7                17
  NOT HISPANIC OR LATINO              96               335
[1] 2 2
[1] FALSE

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                 0   1
  2P GAIN MUTATED    55  14
  2P GAIN WILD-TYPE 246  99
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               69               345 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               14                99 
$`2P GAIN MUTATED`
TCGA-BA-4075 TCGA-BA-5555 TCGA-BA-A4IF TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-7864 
         283          520          895          623          142          687 
TCGA-BB-8596 TCGA-CN-4727 TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5359 TCGA-CN-5374 
        1955         1230         1988         1045         1980          290 
TCGA-CN-6010 TCGA-CN-6012 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 
         630          629         1110          224          318          611 
TCGA-CN-6994 TCGA-CN-A63T TCGA-CQ-5329 TCGA-CQ-5332 TCGA-CQ-7072 TCGA-CR-5247 
         735          225         1422          317         1950          358 
TCGA-CR-6477 TCGA-CR-7365 TCGA-CR-7372 TCGA-CR-7383 TCGA-CR-7398 TCGA-CR-7399 
         514         1191          759         1954          156          181 
TCGA-CV-5430 TCGA-CV-5440 TCGA-CV-6941 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7235 
        1955         1978         1959         3837         1959         1952 
TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 
        1095          954          797         1960         1976         1099 
TCGA-CV-7422 TCGA-CV-7435 TCGA-CV-A45Z TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 
        1957         1959         1940          237          828          773 
TCGA-D6-6823 TCGA-D6-8569 TCGA-D6-A4ZB TCGA-D6-A6EP TCGA-DQ-5629 TCGA-DQ-7589 
         701          128          376          424          516          575 
TCGA-DQ-7592 TCGA-F7-A620 TCGA-F7-A623 TCGA-HD-A633 TCGA-HD-A6HZ TCGA-HD-A6I0 
         299           13            6           49          111           33 
TCGA-IQ-A61E TCGA-IQ-A61H TCGA-MZ-A7D7 TCGA-QK-A8Z7 TCGA-QK-A8ZA TCGA-QK-AA3J 
         588          412          240          198          135          157 
TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JF 
        1278         1043         1497 

$`2P GAIN WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
         102          462          415         1983          276          248 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 
         722         1288         1762          725          623         1636 
TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 
        1747          190          644          451           63          384 
TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 
         113          236          855          622          918          850 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BB-4217 
         351          216          182         1976          314          187 
TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 
        2878          278          140          133          558          310 
TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 
         536          423          638         1153          428          436 
TCGA-BB-8601 TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 
         624            5            4          799          721         1157 
TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
         142         1151          392          817          993          642 
TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 
        1250          395          625         1960         1330          811 
TCGA-CN-4741 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 
        1268         1007          173         1081         1977         1980 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6011 TCGA-CN-6013 
        1966         1966         1975          683          933          628 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 
         594          629           45          432           98         1970 
TCGA-CN-6022 TCGA-CN-6992 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 
         202          394          432          429           46          443 
TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63U TCGA-CN-A63V 
         535          391          904          645          526          484 
TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 
         348          175          367          223          298         1466 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 
        1207          654         1660         1393         1399          341 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 
         129         1253         1000         1057          985         1959 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 
        1959         1179         1750         1560         1007          509 
TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
        1309         1274          877         1353         1960          707 
TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH 
        1963          893          998          785          391          303 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 
         950         2562         1663         1152          799         1777 
TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6478 
        1521         1966         1050         1125         1971         1969 
TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 
         362          311          345          354          234          379 
TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7367 TCGA-CR-7368 
         350          479         1956         1435         1440         1245 
TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 
        1960          105         1979          889           30          972 
TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 
        1968         1036          796          997         1430         1951 
TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 
         392          907          913          946          908          898 
TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5431 
         930          216         1077          911         1472          522 
TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5441 
        1950         3295         1438          584          546         2886 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 
        2327         1958         2437          519          406          701 
TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 
        2641         1478         1840          215         1315         1665 
TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 
         641         1899         1970         1948         1969         1952 
TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6960 
        3835         1948         1969         1966         1957         1969 
TCGA-CV-6961 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 
        1959         1970         1970         1936         1959         1939 
TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7238 TCGA-CV-7248 TCGA-CV-7406 
        1945         1987         1979         1444         1967         1974 
TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 
        1948         1955         1947         1937         1973         1972 
TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q 
        1937         1984         1958         1981          851         1945 
TCGA-CV-A45R TCGA-CV-A45Y TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A468 
        5480         1960         1946         1954         1722         1977 
TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU 
        1970         1075          906         1959          670          110 
TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 
         646          714          606          685         1950          317 
TCGA-CX-7085 TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 
         321          292           77          491          154          568 
TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EQ 
         106          539          483          232          435          368 
TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 
         389          338         1778         1081         1030          548 
TCGA-DQ-7588 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 
        1965          775          622          369          368          324 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I 
         340         1131          490          658           15           92 
TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-H7-7774 TCGA-H7-8501 
         585            3          384           14          407           58 
TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 
         133          414          403          206            2            5 
TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 
          25           37           55           44           24           25 
TCGA-HD-A4C1 TCGA-HD-A634 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 
          11           10         1057          485          122          441 
TCGA-IQ-A61G TCGA-IQ-A61J TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T 
         360          440          351          360          224          552 
TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D 
         378          168           14           34          392           56 
TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE 
         111          112          254          910         1726         1559 
TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-P3-A6T8 
        1120         1954          578         1917         1968          400 
TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II 
         553          357          245          218          228          225 
TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A8Z9 TCGA-QK-A8ZB TCGA-QK-AA3K TCGA-UF-A718 
         387          567          149          135          168         1326 
TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD 
        1663         1319         1252         1894          484          735 
TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JS 
         665          214          413 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                6                 2 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             3837              5480 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              687               707 
[1] "6.0 - 3837.0 (687.0)" "2.0 - 5480.0 (707.0)"
[1] "hr=" "1.4"
D3V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  2P GAIN MUTATED         5       15        15        46         3         0
  2P GAIN WILD-TYPE      21       60        59       189         9         1
D3V3, multiclass
           clus
vv          2P GAIN MUTATED 2P GAIN WILD-TYPE
  STAGE I                 5                21
  STAGE II               15                60
  STAGE III              15                59
  STAGE IVA              46               189
  STAGE IVB               3                 9
  STAGE IVC               0                 1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  2P GAIN MUTATED       8  22  21  34
  2P GAIN WILD-TYPE    39 105  73 128
D3V4, multiclass
       clus
vv      2P GAIN MUTATED 2P GAIN WILD-TYPE
  T0+T1               8                39
  T2                 22               105
  T3                 21                73
  T4                 34               128
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  2P GAIN MUTATED    37   8  31   2
  2P GAIN WILD-TYPE 133  55 121   6
D3V5, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  N0              37               133
  N1               8                55
  N2              31               121
  N3               2                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1  MX
  2P GAIN MUTATED    27   0  10
  2P GAIN WILD-TYPE 140   1  48
D3V6, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  M0              27               140
  M1               0                 1
  MX              10                48
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V7, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    15  76
  2P GAIN WILD-TYPE 117 280
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     15   76
  2P GAIN WILD-TYPE  117  280
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE              15               117
  MALE                76               280
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  2P GAIN MUTATED                                      88
  2P GAIN WILD-TYPE                                   389
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  2P GAIN MUTATED                                                             0
  2P GAIN WILD-TYPE                                                           1
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  2P GAIN MUTATED                                                     3
  2P GAIN WILD-TYPE                                                   7
D3V8, multiclass
                                                             clus
vv                                                            2P GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    88
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       3
                                                             clus
vv                                                            2P GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     389
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                 1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V9, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    15  76
  2P GAIN WILD-TYPE  64 333
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     15   76
  2P GAIN WILD-TYPE   64  333
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  NO               15                64
  YES              76               333
[1] 2 2
[1] FALSE
D3V10, continuous
D3V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2P GAIN MUTATED                                  1     0
  2P GAIN WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2P GAIN MUTATED                          11    78
  2P GAIN WILD-TYPE                        33   337
D3V12, multiclass
                                  clus
vv                                 2P GAIN MUTATED 2P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                     11                33
  WHITE                                         78               337
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V13, binary
                   cls
clus                  0   1
  2P GAIN MUTATED     4  80
  2P GAIN WILD-TYPE  20 351
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      4   80
  2P GAIN WILD-TYPE   20  351
                        clus
vv                       2P GAIN MUTATED 2P GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                20
  NOT HISPANIC OR LATINO              80               351
[1] 2 2
[1] FALSE

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                 0   1
  2Q GAIN MUTATED    41  17
  2Q GAIN WILD-TYPE 260  96
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               58               356 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               17                96 
$`2Q GAIN MUTATED`
TCGA-BA-4075 TCGA-BA-A4IF TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-7864 TCGA-BB-8596 
         283          895          623          142          687         1955 
TCGA-CN-4727 TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5359 TCGA-CN-5374 TCGA-CN-6012 
        1230         1988         1045         1980          290          629 
TCGA-CN-6024 TCGA-CN-6994 TCGA-CN-A63T TCGA-CQ-5329 TCGA-CQ-5332 TCGA-CQ-6224 
         224          735          225         1422          317          985 
TCGA-CQ-6228 TCGA-CQ-7072 TCGA-CR-5247 TCGA-CR-6477 TCGA-CR-7365 TCGA-CR-7383 
        1959         1950          358          514         1191         1954 
TCGA-CV-5430 TCGA-CV-5434 TCGA-CV-5440 TCGA-CV-6941 TCGA-CV-7091 TCGA-CV-7235 
        1955         3295         1978         1959         1959         1952 
TCGA-CV-7242 TCGA-CV-7245 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7422 
        1095          797         1960         1976         1099         1957 
TCGA-CV-7435 TCGA-CV-A45Z TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6823 TCGA-D6-8569 
        1959         1940          237          828          701          128 
TCGA-D6-A4ZB TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7592 TCGA-F7-A623 
         376          516         1965          575          299            6 
TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-IQ-A61E TCGA-IQ-A61H TCGA-MT-A67D TCGA-QK-A8ZA 
         111           33          588          412           56          135 
TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A7J9 TCGA-UF-A7JF 
        1663         1319         1043         1497 

$`2Q GAIN WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
         102          462          415         1983          276          248 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 
         722         1288         1762          520          725          623 
TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 
        1636         1747          190          644          451           63 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II 
         384          113          236          855          622          918 
TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DJ 
         850          351          216          182         1976          314 
TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 
         187         2878          278          140          133          558 
TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 
         310          536          423          638         1153          428 
TCGA-BB-7872 TCGA-BB-8601 TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 
         436          624            5            4          799          721 
TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 
        1157          142         1151          392          817          993 
TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 
         642         1250          395          625         1960         1330 
TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5363 
         811         1268         1007          173         1081         1977 
TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6010 
        1980         1966         1966         1975          683          630 
TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 
         933          628          594          629           45          432 
TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6988 TCGA-CN-6989 
          98         1970          202         1110          318          611 
TCGA-CN-6992 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A499 
         394          432          429           46          443          535 
TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W 
         391          904          645          526          484          348 
TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-5324 
         175          367          223          298         1466         1207 
TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 
         654         1660         1393         1399          341          129 
TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7063 
        1253         1000         1057         1959         1179         1750 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 
        1560         1007          509         1309         1274          877 
TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD 
        1353         1960          707         1963          893          998 
TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5248 
         785          391          303          950         2562         1663 
TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 
        1152          799         1777         1521         1966         1050 
TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 
        1125         1971         1969          362          311          345 
TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 
         354          234          379          350          479         1956 
TCGA-CR-7364 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 
        1435         1440         1245         1960          105         1979 
TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 
         759          889           30          972         1968         1036 
TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 
         796          997         1430         1951          392          907 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 
         913          946          908          898          930          216 
TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5431 
         156          181         1077          911         1472          522 
TCGA-CV-5432 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5441 TCGA-CV-5442 
        1950         1438          584          546         2886         2327 
TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 
        1958         2437          519          406          701         2641 
TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 
        1478         1840          215         1315         1665          641 
TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6942 
        1899         1970         1948         1969         1952         3835 
TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 
        1948         1969         1966         1957         1969         1959 
TCGA-CV-7090 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 
        3837         1970         1970         1936         1959         1939 
TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7238 TCGA-CV-7243 TCGA-CV-7248 
        1945         1987         1979         1444          954         1967 
TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7428 
        1974         1948         1955         1947         1937         1973 
TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7440 TCGA-CV-A45O 
        1972         1937         1984         1958         1981          851 
TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45Y TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A464 
        1945         5480         1960         1946         1954         1722 
TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT 
        1977         1970         1075          906         1959          670 
TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 
         110          646          714          606          685         1950 
TCGA-CX-7082 TCGA-CX-7085 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 
         317          321          773          292           77          491 
TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-D6-A6EK TCGA-D6-A6EM 
         154          568          106          539          483          232 
TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 
         435          424          368          389          338         1778 
TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7593 
        1081         1030          548          775          622          369 
TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 
         368          324          340         1131          490          658 
TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W 
          15           92          585            3          384           14 
TCGA-F7-A620 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 
          13          407           58          133          414          403 
TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 
         206            2            5           25           37           55 
TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 
          44           24           25           11           49           10 
TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61G TCGA-IQ-A61J 
        1057          485          122          441          360          440 
TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 
         351          360          224          552          378          168 
TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 
          14           34          392          111          112          254 
TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX 
         240          910         1726         1559         1120         1954 
TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 
         578         1917         1968          400          553          357 
TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 
         245          218          228          225          387          567 
TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-UF-A718 
         198          149          135          157          168         1326 
TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JH 
        1252         1278         1894          484          735          665 
TCGA-UF-A7JJ TCGA-UF-A7JS 
         214          413 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                6                 2 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             3295              5480 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            940.0             661.5 
[1] "6.0 - 3295.0 (940.0)" "2.0 - 5480.0 (661.5)"
[1] "hr=" "1.1"
D4V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  2Q GAIN MUTATED         2       13        11        37         1         0
  2Q GAIN WILD-TYPE      24       62        63       198        11         1
D4V3, multiclass
           clus
vv          2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  STAGE I                 2                24
  STAGE II               13                62
  STAGE III              11                63
  STAGE IVA              37               198
  STAGE IVB               1                11
  STAGE IVC               0                 1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  2Q GAIN MUTATED       6  20  13  26
  2Q GAIN WILD-TYPE    41 107  81 136
D4V4, multiclass
       clus
vv      2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  T0+T1               6                41
  T2                 20               107
  T3                 13                81
  T4                 26               136
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  2Q GAIN MUTATED    31   5  23   1
  2Q GAIN WILD-TYPE 139  58 129   7
D4V5, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  N0              31               139
  N1               5                58
  N2              23               129
  N3               1                 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"
                   vv
clus                 M0  M1  MX
  2Q GAIN MUTATED    21   0   9
  2Q GAIN WILD-TYPE 146   1  49
D4V6, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  M0              21               146
  M1               0                 1
  MX               9                49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V7, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    14  58
  2Q GAIN WILD-TYPE 118 298
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     14   58
  2Q GAIN WILD-TYPE  118  298
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE              14               118
  MALE                58               298
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  2Q GAIN MUTATED                                      72
  2Q GAIN WILD-TYPE                                   405
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  2Q GAIN MUTATED                                                             0
  2Q GAIN WILD-TYPE                                                           1
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  2Q GAIN MUTATED                                                     0
  2Q GAIN WILD-TYPE                                                  10
D4V8, multiclass
                                                             clus
vv                                                            2Q GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    72
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       0
                                                             clus
vv                                                            2Q GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     405
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                 1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V9, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    14  58
  2Q GAIN WILD-TYPE  65 351
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     14   58
  2Q GAIN WILD-TYPE   65  351
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  NO               14                65
  YES              58               351
[1] 2 2
[1] FALSE
D4V10, continuous
D4V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2Q GAIN MUTATED                                  1     0
  2Q GAIN WILD-TYPE                                1    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2Q GAIN MUTATED                           8    62
  2Q GAIN WILD-TYPE                        36   353
D4V12, multiclass
                                  clus
vv                                 2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 1
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      8                36
  WHITE                                         62               353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V13, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED     4  62
  2Q GAIN WILD-TYPE  20 369
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      4   62
  2Q GAIN WILD-TYPE   20  369
                        clus
vv                       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                20
  NOT HISPANIC OR LATINO              62               369
[1] 2 2
[1] FALSE

Clustering(5) Variable = 3P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                 0   1
  3P GAIN MUTATED    51  11
  3P GAIN WILD-TYPE 250 102
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               62               352 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               11               102 
$`3P GAIN MUTATED`
TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5153 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6868 
        1983          276         1762          623         1747          190 
TCGA-BA-6873 TCGA-BA-A4IF TCGA-BB-4223 TCGA-BB-4225 TCGA-CN-4723 TCGA-CN-4730 
         113          895         2878          140          721          817 
TCGA-CN-4731 TCGA-CN-6013 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6023 TCGA-CN-6988 
         993          628           98         1970         1110          318 
TCGA-CN-6994 TCGA-CN-A499 TCGA-CN-A49C TCGA-CN-A6V1 TCGA-CQ-5323 TCGA-CQ-6223 
         735          535          645          223         1466         1057 
TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6474 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 
        1777         1521         1971          354          234          379 
TCGA-CR-6492 TCGA-CR-7365 TCGA-CR-7368 TCGA-CR-7389 TCGA-CR-7397 TCGA-CV-5431 
         479         1191         1245          392          216          522 
TCGA-CV-5442 TCGA-CV-5977 TCGA-CV-6433 TCGA-CV-7097 TCGA-CV-7238 TCGA-CV-7243 
        2327         1840          641         1970         1444          954 
TCGA-CV-7261 TCGA-D6-A6EM TCGA-DQ-5624 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-8489 
        1099          232         1778          324          340          658 
TCGA-F7-A623 TCGA-HD-7917 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-A634 TCGA-IQ-A61E 
           6           37           44           24           10          588 
TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A6SX TCGA-P3-A6T8 TCGA-QK-A6IJ 
         112          254          240         1954          400          387 
TCGA-UF-A71D TCGA-UF-A7JA 
        1252         1894 

$`3P GAIN WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-5149 TCGA-BA-5151 
         102          462          283          415          248          722 
TCGA-BA-5152 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6869 TCGA-BA-6870 
        1288          520          725         1636          644          451 
TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II 
          63          384          236          855          622          918 
TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DJ 
         850          351          216          182         1976          314 
TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-4228 
         623          142          187          278          133          558 
TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 
         310          536          423          687          638         1153 
TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A47Z TCGA-C9-A480 
         428          436         1955          624            5            4 
TCGA-CN-4722 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 
         799         1157          142         1230         1151          392 
TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 
         642         1250          395          625         1960         1330 
TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 
         811         1268         1988         1007         1045          173 
TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 
        1980         1081         1977         1980         1966         1966 
TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 
        1975          683          290          630          933          629 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6022 TCGA-CN-6024 
         594          629           45          432          202          224 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 
         611          394          432          429           46          443 
TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W 
         391          904          225          526          484          348 
TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A6V3 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 
         175          367          298         1207          654         1660 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 
        1422         1393         1399          317          341          129 
TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 
        1253         1000          985         1959         1959         1179 
TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 
        1750         1560         1007          509         1309         1274 
TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CA 
         877         1950         1353         1960          707         1963 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI 
         893          998          785          391          303          950 
TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6471 
        2562          358         1663         1152          799         1966 
TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 
        1050         1125          514         1969          362          311 
TCGA-CR-6482 TCGA-CR-6491 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7367 TCGA-CR-7369 
         345          350         1956         1435         1440         1960 
TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 
         105         1979          759          889           30          972 
TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 
        1968         1036          796         1954          997         1430 
TCGA-CR-7388 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 
        1951          907          913          946          908          898 
TCGA-CR-7395 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 
         930          156          181         1077          911         1472 
TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 
        1955         1950         3295         1438          584          546 
TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 
        1978         2886         1958         2437          519          406 
TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 
         701         2641         1478          215         1315         1665 
TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6941 
        1899         1970         1948         1969         1952         1959 
TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6960 
        3835         1948         1969         1966         1957         1969 
TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7099 TCGA-CV-7100 
        1959         3837         1959         1970         1936         1959 
TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7242 
        1939         1945         1987         1979         1952         1095 
TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7406 TCGA-CV-7410 
         797         1967         1960         1976         1974         1948 
TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 
        1955         1957         1947         1937         1973         1972 
TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45O 
        1937         1984         1958         1959         1981          851 
TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 
        1945         5480         1960         1940         1946         1954 
TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO 
        1722         1977         1970         1075          906         1959 
TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 
         670          110          646          714          606          685 
TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 
        1950          317          321          237          828          773 
TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 
         292          701           77          491          154          568 
TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EO 
         106          128          539          376          483          435 
TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5625 TCGA-DQ-5629 
         424          368          389          338         1081          516 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 
        1030          548         1965          575          775          622 
TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-A50G 
         299          369          368         1131          490           15 
TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 
          92          585            3          384           14           13 
TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A 
         407           58          133          414          403          206 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-8224 TCGA-HD-8635 TCGA-HD-A4C1 
           2            5           25           55           25           11 
TCGA-HD-A633 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 
          49          111           33         1057          485          122 
TCGA-IQ-7632 TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61L TCGA-IQ-A61O 
         441          360          412          440          351          360 
TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X 
         224          552          378          168           14           34 
TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE 
         392           56          111          910         1726         1559 
TCGA-P3-A6SW TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-QK-A64Z TCGA-QK-A652 
        1120          578         1917         1968          553          357 
TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6V9 TCGA-QK-A8Z7 
         245          218          228          225          567          198 
TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-UF-A718 
         149          135          135          157          168         1326 
TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JC TCGA-UF-A7JD 
        1663         1319         1278         1043          484          735 
TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JS 
        1497          665          214          413 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                6                 2 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             2878              5480 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            634.5             718.0 
[1] "6.0 - 2878.0 (634.5)" "2.0 - 5480.0 (718.0)"
[1] "hr=" "1.4"
D5V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  3P GAIN MUTATED         3       12        11        35         1         1
  3P GAIN WILD-TYPE      23       63        63       200        11         0
D5V3, multiclass
           clus
vv          3P GAIN MUTATED 3P GAIN WILD-TYPE
  STAGE I                 3                23
  STAGE II               12                63
  STAGE III              11                63
  STAGE IVA              35               200
  STAGE IVB               1                11
  STAGE IVC               1                 0
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  3P GAIN MUTATED       7  24  10  23
  3P GAIN WILD-TYPE    40 103  84 139
D5V4, multiclass
       clus
vv      3P GAIN MUTATED 3P GAIN WILD-TYPE
  T0+T1               7                40
  T2                 24               103
  T3                 10                84
  T4                 23               139
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  3P GAIN MUTATED    21  14  24   1
  3P GAIN WILD-TYPE 149  49 128   7
D5V5, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  N0              21               149
  N1              14                49
  N2              24               128
  N3               1                 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"
                   vv
clus                 M0  M1  MX
  3P GAIN MUTATED    18   1  13
  3P GAIN WILD-TYPE 149   0  45
D5V6, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  M0              18               149
  M1               1                 0
  MX              13                45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V7, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    22  55
  3P GAIN WILD-TYPE 110 301
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     22   55
  3P GAIN WILD-TYPE  110  301
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE              22               110
  MALE                55               301
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  3P GAIN MUTATED                                      76
  3P GAIN WILD-TYPE                                   401
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  3P GAIN MUTATED                                                             0
  3P GAIN WILD-TYPE                                                           1
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  3P GAIN MUTATED                                                     1
  3P GAIN WILD-TYPE                                                   9
D5V8, multiclass
                                                             clus
vv                                                            3P GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    76
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       1
                                                             clus
vv                                                            3P GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     401
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                 1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V9, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    15  62
  3P GAIN WILD-TYPE  64 347
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     15   62
  3P GAIN WILD-TYPE   64  347
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  NO               15                64
  YES              62               347
[1] 2 2
[1] FALSE
D5V10, continuous
D5V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3P GAIN MUTATED                                  0     1
  3P GAIN WILD-TYPE                                2    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3P GAIN MUTATED                           6    67
  3P GAIN WILD-TYPE                        38   348
D5V12, multiclass
                                  clus
vv                                 3P GAIN MUTATED 3P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      6                38
  WHITE                                         67               348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V13, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     4  68
  3P GAIN WILD-TYPE  20 363
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      4   68
  3P GAIN WILD-TYPE   20  363
                        clus
vv                       3P GAIN MUTATED 3P GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                20
  NOT HISPANIC OR LATINO              68               363
[1] 2 2
[1] FALSE

Clustering(6) Variable = 3Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                 0   1
  3Q GAIN MUTATED   142  57
  3Q GAIN WILD-TYPE 159  56
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              199               215 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               57                56 
$`3Q GAIN MUTATED`
TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5153 TCGA-BA-5557 
        1983          276          248          722         1762          623 
TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 
        1747          190          451          384          113          236 
TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A8YP TCGA-BB-4223 TCGA-BB-4225 
         895          622          850          142         2878          140 
TCGA-BB-4227 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 
         133          423          687          428          436         1955 
TCGA-BB-8601 TCGA-C9-A47Z TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 
         624            5          721         1157          142         1230 
TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4736 TCGA-CN-4737 
        1151          392          817          993          395          625 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5358 
        1330          811         1268         1988         1045          173 
TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 
        1980         1081         1977         1980         1966         1966 
TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6019 
         683          290          629          628          594          432 
TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 
          98         1970         1110          224          318          611 
TCGA-CN-6994 TCGA-CN-6998 TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T 
         735           46          535          904          645          225 
TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-5329 TCGA-CQ-6223 TCGA-CQ-6228 
         223          298         1466         1422         1057         1959 
TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7067 TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4C6 
        1179         1560          509         1274         1950         1353 
TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CR-5243 TCGA-CR-5249 
         707         1963          785          391         2562         1152 
TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6474 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6484 
        1777         1521         1971         1969          362          354 
TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-7365 TCGA-CR-7368 
         234          379          350          479         1191         1245 
TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7377 TCGA-CR-7385 TCGA-CR-7386 
        1960         1979          759         1968          997         1430 
TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7397 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 
        1951          392          216          911         1472         1955 
TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5442 
         522         1950          584          546         1978         2327 
TCGA-CV-5444 TCGA-CV-5973 TCGA-CV-5977 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6935 
        2437         2641         1840         1665          641         1969 
TCGA-CV-6936 TCGA-CV-6945 TCGA-CV-6954 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7097 
        1952         1969         1957         3837         1959         1970 
TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 
        1939         1945         1987         1444         1095          954 
TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7406 
         797         1967         1960         1976         1099         1974 
TCGA-CV-7410 TCGA-CV-7424 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-A45R TCGA-CV-A45Z 
        1948         1947         1958         1959         5480         1940 
TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A6JZ TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-8569 
        1946         1954          714          237          828          128 
TCGA-D6-A4ZB TCGA-D6-A6EM TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5630 TCGA-DQ-5631 
         376          232          338         1778         1030          548 
TCGA-DQ-7589 TCGA-DQ-7592 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-8298 TCGA-F7-8489 
         575          299          324          340          490          658 
TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61V TCGA-F7-A623 TCGA-HD-7754 
          15           92          585          384            6           25 
TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-A634 TCGA-HL-7533 
          37           55           44           24           10         1057 
TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J TCGA-KU-A66T TCGA-MT-A67G 
         588          360          412          440          552          112 
TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A6SW TCGA-P3-A6SX 
         254          240          910         1726         1120         1954 
TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A652 TCGA-QK-A6IJ TCGA-QK-A8Z9 TCGA-UF-A719 
        1968          400          357          387          149         1663 
TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JD TCGA-UF-A7JF 
        1252         1278         1043         1894          735         1497 
TCGA-UF-A7JH 
         665 

$`3Q GAIN WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-5152 TCGA-BA-5555 
         102          462          283          415         1288          520 
TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6869 TCGA-BA-6871 TCGA-BA-A4IG TCGA-BA-A4II 
         725         1636          644           63          855          918 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A6DL 
         351          216          182         1976          314          623 
TCGA-BB-4217 TCGA-BB-4224 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7866 
         187          278          558          310          536          638 
TCGA-BB-7870 TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4738 
        1153            4          799          642         1250         1960 
TCGA-CN-5355 TCGA-CN-5370 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6017 TCGA-CN-6018 
        1007         1975          630          933          629           45 
TCGA-CN-6022 TCGA-CN-6992 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-A498 TCGA-CN-A49A 
         202          394          432          429          443          391 
TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 TCGA-CQ-5324 
         526          484          348          175          367         1207 
TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 
         654         1660         1393         1399          317          341 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-7063 
         129         1253         1000          985         1959         1750 
TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-A4C7 TCGA-CQ-A4CB TCGA-CQ-A4CD 
        1007         1309          877         1960          893          998 
TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5250 TCGA-CR-6471 
         303          950          358         1663          799         1966 
TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6477 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6493 
        1050         1125          514          311          345         1956 
TCGA-CR-7364 TCGA-CR-7367 TCGA-CR-7370 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 
        1435         1440          105          889           30          972 
TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 
        1036          796         1954          907          913          946 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 
         908          898          930          156          181         1077 
TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5441 TCGA-CV-5443 TCGA-CV-5966 TCGA-CV-5970 
        3295         1438         2886         1958          519          406 
TCGA-CV-5971 TCGA-CV-5976 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6436 TCGA-CV-6441 
         701         1478          215         1315         1899         1970 
TCGA-CV-6934 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6952 TCGA-CV-6960 
        1948         1959         3835         1948         1966         1969 
TCGA-CV-6961 TCGA-CV-7095 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7183 TCGA-CV-7235 
        1959         1970         1936         1959         1979         1952 
TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 
        1955         1957         1937         1973         1972         1937 
TCGA-CV-7433 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A45Y TCGA-CV-A464 
        1984         1981          851         1945         1960         1722 
TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT 
        1977         1970         1075          906         1959          670 
TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 
         110          646          606          685         1950          317 
TCGA-CX-7085 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 
         321          773          292          701           77          491 
TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-D6-A6EK TCGA-D6-A6EO 
         154          568          106          539          483          435 
TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-7588 
         424          368          389         1081          516         1965 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-F7-7848 TCGA-F7-A61S 
         775          622          369          368         1131            3 
TCGA-F7-A61W TCGA-F7-A620 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 
          14           13          407           58          133          414 
TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-8635 TCGA-HD-A4C1 
         403          206            2            5           25           11 
TCGA-HD-A633 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 
          49          111           33          485          122          441 
TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W 
         351          360          224          378          168           14 
TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-P3-A5QE TCGA-P3-A6T0 
          34          392           56          111         1559          578 
TCGA-P3-A6T2 TCGA-QK-A64Z TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II 
        1917          553          245          218          228          225 
TCGA-QK-A6V9 TCGA-QK-A8Z7 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K 
         567          198          135          135          157          168 
TCGA-UF-A718 TCGA-UF-A71B TCGA-UF-A7JC TCGA-UF-A7JJ TCGA-UF-A7JS 
        1326         1319          484          214          413 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                5                 2 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             5480              3835 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              817               623 
[1] "5.0 - 5480.0 (817.0)" "2.0 - 3835.0 (623.0)"
[1] "hr=" "1.3"
D6V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  3Q GAIN MUTATED        10       37        36       116         6         1
  3Q GAIN WILD-TYPE      16       38        38       119         6         0
D6V3, multiclass
           clus
vv          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  STAGE I                10                16
  STAGE II               37                38
  STAGE III              36                38
  STAGE IVA             116               119
  STAGE IVB               6                 6
  STAGE IVC               1                 0
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3 T4
  3Q GAIN MUTATED      20 64 46 79
  3Q GAIN WILD-TYPE    27 63 48 83
D6V4, multiclass
       clus
vv      3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  T0+T1              20                27
  T2                 64                63
  T3                 46                48
  T4                 79                83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  3Q GAIN MUTATED    70  35  82   6
  3Q GAIN WILD-TYPE 100  28  70   2
D6V5, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  N0              70               100
  N1              35                28
  N2              82                70
  N3               6                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1 MX
  3Q GAIN MUTATED   77  1 28
  3Q GAIN WILD-TYPE 90  0 30
D6V6, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  M0              77                90
  M1               1                 0
  MX              28                30
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V7, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    56 181
  3Q GAIN WILD-TYPE  76 175
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     56  181
  3Q GAIN WILD-TYPE   76  175
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE              56                76
  MALE               181               175
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  3Q GAIN MUTATED                                     232
  3Q GAIN WILD-TYPE                                   245
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  3Q GAIN MUTATED                                                             0
  3Q GAIN WILD-TYPE                                                           1
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  3Q GAIN MUTATED                                                     5
  3Q GAIN WILD-TYPE                                                   5
D6V8, multiclass
                                                             clus
vv                                                            3Q GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                   232
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       5
                                                             clus
vv                                                            3Q GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     245
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                 1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         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"
D6V9, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    48 189
  3Q GAIN WILD-TYPE  31 220
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     48  189
  3Q GAIN WILD-TYPE   31  220
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  NO               48                31
  YES             189               220
[1] 2 2
[1] FALSE
D6V10, continuous
D6V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3Q GAIN MUTATED                                  1     5
  3Q GAIN WILD-TYPE                                1     6
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3Q GAIN MUTATED                          21   200
  3Q GAIN WILD-TYPE                        23   215
D6V12, multiclass
                                  clus
vv                                 3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 1
  ASIAN                                          5                 6
  BLACK OR AFRICAN AMERICAN                     21                23
  WHITE                                        200               215
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V13, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    13 203
  3Q GAIN WILD-TYPE  11 228
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     13  203
  3Q GAIN WILD-TYPE   11  228
                        clus
vv                       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  HISPANIC OR LATINO                  13                11
  NOT HISPANIC OR LATINO             203               228
[1] 2 2
[1] FALSE

Clustering(7) Variable = 4P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                 0   1
  4P GAIN MUTATED    22   9
  4P GAIN WILD-TYPE 279 104
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               31               383 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                9               104 
$`4P GAIN MUTATED`
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BB-4225 TCGA-CN-4727 TCGA-CN-4737 
         384          113          236          140         1230          625 
TCGA-CN-4740 TCGA-CQ-6224 TCGA-CQ-7069 TCGA-CR-5247 TCGA-CR-7389 TCGA-CV-5430 
         811          985         1274          358          392         1955 
TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-6003 TCGA-CV-6945 TCGA-CV-6954 
        2641         1478         1840         1665         1969         1957 
TCGA-CV-7090 TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7424 TCGA-CV-7433 TCGA-DQ-5625 
        3837         1945         1987         1947         1984         1081 
TCGA-DQ-7592 TCGA-F7-A623 TCGA-IQ-A61L TCGA-MT-A67D TCGA-P3-A6T4 TCGA-QK-A6V9 
         299            6          351           56         1968          567 
TCGA-QK-A8Z9 
         149 

$`4P GAIN WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 
         102          462          283          415         1983          276 
TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 
         248          722         1288         1762          520          725 
TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 
         623         1636         1747          190          644          451 
TCGA-BA-6871 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 
          63          895          855          622          918          850 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A6DL 
         351          216          182         1976          314          623 
TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-4228 
         142          187         2878          278          133          558 
TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 
         310          536          423          687          638         1153 
TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A47Z TCGA-C9-A480 
         428          436         1955          624            5            4 
TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 
         799          721         1157          142         1151          392 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4738 
         817          993          642         1250          395         1960 
TCGA-CN-4739 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 
        1330         1268         1988         1007         1045          173 
TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 
        1980         1081         1977         1980         1966         1966 
TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 
        1975          683          290          630          933          629 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 
         628          594          629           45          432           98 
TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 
        1970          202         1110          224          318          611 
TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 
         394          735          432          429           46          443 
TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U 
         535          391          904          645          225          526 
TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A6V1 TCGA-CN-A6V3 
         484          348          175          367          223          298 
TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 
        1466         1207          654         1660         1422         1393 
TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 
        1399          317          341          129         1253         1000 
TCGA-CQ-6223 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 
        1057         1959         1959         1179         1750         1560 
TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 
        1007          509         1309          877         1950         1353 
TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE 
        1960          707         1963          893          998          785 
TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 
         391          303          950         2562         1663         1152 
TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 
         799         1777         1521         1966         1050         1125 
TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 
        1971          514         1969          362          311          345 
TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 
         354          234          379          350          479         1956 
TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 
        1435         1191         1440         1245         1960          105 
TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 
        1979          759          889           30          972         1968 
TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 
        1036          796         1954          997         1430         1951 
TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 
         907          913          946          908          898          930 
TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 
         216          156          181         1077          911         1472 
TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 
         522         1950         3295         1438          584          546 
TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 
        1978         2886         2327         1958         2437          519 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6436 
         406          701          215         1315          641         1899 
TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6942 
        1970         1948         1969         1952         1959         3835 
TCGA-CV-6943 TCGA-CV-6952 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7091 TCGA-CV-7095 
        1948         1966         1969         1959         1959         1970 
TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7183 TCGA-CV-7235 
        1970         1936         1959         1939         1979         1952 
TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 
        1444         1095          954          797         1967         1960 
TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7422 
        1976         1099         1974         1948         1955         1957 
TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7434 TCGA-CV-7435 
        1937         1973         1972         1937         1958         1959 
TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45Y TCGA-CV-A45Z 
        1981          851         1945         5480         1960         1940 
TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE 
        1946         1954         1722         1977         1970         1075 
TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ 
         906         1959          670          110          646          714 
TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 
         606          685         1950          317          321          237 
TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 
         828          773          292          701           77          491 
TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB 
         154          568          106          128          539          376 
TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES 
         483          232          435          424          368          389 
TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 
         338         1778          516         1030          548         1965 
TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 
         575          775          622          369          368          324 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I 
         340         1131          490          658           15           92 
TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-H7-7774 
         585            3          384           14           13          407 
TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 
          58          133          414          403          206            2 
TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 
           5           25           37           55           44           24 
TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 
          25           11           49           10          111           33 
TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G 
        1057          485          122          441          588          360 
TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 
         412          440          360          224          552          378 
TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G 
         168           14           34          392          111          112 
TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW 
         254          240          910         1726         1559         1120 
TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 
        1954          578         1917          400          553          357 
TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A8Z7 
         245          218          228          225          387          198 
TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-UF-A718 TCGA-UF-A719 
         135          135          157          168         1326         1663 
TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC 
        1319         1252         1278         1043         1894          484 
TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JS 
         735         1497          665          214          413 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                6                 2 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             3837              5480 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             1081               685 
[1] "6.0 - 3837.0 (1081.0)" "2.0 - 5480.0 (685.0)" 
[1] "hr=" "1.5"
D7V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  4P GAIN MUTATED         0        8         3        20         0         0
  4P GAIN WILD-TYPE      26       67        71       215        12         1
D7V3, multiclass
           clus
vv          4P GAIN MUTATED 4P GAIN WILD-TYPE
  STAGE I                 0                26
  STAGE II                8                67
  STAGE III               3                71
  STAGE IVA              20               215
  STAGE IVB               0                12
  STAGE IVC               0                 1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  4P GAIN MUTATED       1  12   4  14
  4P GAIN WILD-TYPE    46 115  90 148
D7V4, multiclass
       clus
vv      4P GAIN MUTATED 4P GAIN WILD-TYPE
  T0+T1               1                46
  T2                 12               115
  T3                  4                90
  T4                 14               148
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  4P GAIN MUTATED     8   4  13   0
  4P GAIN WILD-TYPE 162  59 139   8
D7V5, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  N0               8               162
  N1               4                59
  N2              13               139
  N3               0                 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"
                   vv
clus                 M0  M1  MX
  4P GAIN MUTATED     9   0   2
  4P GAIN WILD-TYPE 158   1  56
D7V6, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  M0               9               158
  M1               0                 1
  MX               2                56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V7, binary
                   cls
clus                  0   1
  4P GAIN MUTATED    10  29
  4P GAIN WILD-TYPE 122 327
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     10   29
  4P GAIN WILD-TYPE  122  327
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE              10               122
  MALE                29               327
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  4P GAIN MUTATED                                      39
  4P GAIN WILD-TYPE                                   438
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  4P GAIN MUTATED                                                             0
  4P GAIN WILD-TYPE                                                           1
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  4P GAIN MUTATED                                                     0
  4P GAIN WILD-TYPE                                                  10
D7V8, multiclass
                                                             clus
vv                                                            4P GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    39
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       0
                                                             clus
vv                                                            4P GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     438
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                 1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V9, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     8  31
  4P GAIN WILD-TYPE  71 378
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      8   31
  4P GAIN WILD-TYPE   71  378
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  NO                8                71
  YES              31               378
[1] 2 2
[1] FALSE
D7V10, continuous
D7V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4P GAIN MUTATED                                  1     1
  4P GAIN WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4P GAIN MUTATED                           6    30
  4P GAIN WILD-TYPE                        38   385
D7V12, multiclass
                                  clus
vv                                 4P GAIN MUTATED 4P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      6                38
  WHITE                                         30               385
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V13, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     4  31
  4P GAIN WILD-TYPE  20 400
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      4   31
  4P GAIN WILD-TYPE   20  400
                        clus
vv                       4P GAIN MUTATED 4P GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                20
  NOT HISPANIC OR LATINO              31               400
[1] 2 2
[1] FALSE

Clustering(8) Variable = 4Q GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                 0   1
  4Q GAIN MUTATED    19   9
  4Q GAIN WILD-TYPE 282 104
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               28               386 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                9               104 
$`4Q GAIN MUTATED`
TCGA-BA-6872 TCGA-BB-4225 TCGA-CN-4727 TCGA-CN-4740 TCGA-CN-5363 TCGA-CQ-7069 
         384          140         1230          811         1977         1274 
TCGA-CR-5247 TCGA-CR-6491 TCGA-CR-7389 TCGA-CV-5436 TCGA-CV-5977 TCGA-CV-6945 
         358          350          392          584         1840         1969 
TCGA-CV-7090 TCGA-CV-7102 TCGA-CV-7242 TCGA-CV-7245 TCGA-CV-7433 TCGA-D6-6826 
        3837         1945         1095          797         1984          154 
TCGA-DQ-5625 TCGA-F7-A623 TCGA-HD-7753 TCGA-IQ-A61L TCGA-MT-A67D TCGA-P3-A6SW 
        1081            6            5          351           56         1120 
TCGA-P3-A6T4 TCGA-QK-A6V9 TCGA-QK-A8Z9 TCGA-UF-A7J9 
        1968          567          149         1043 

$`4Q GAIN WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 
         102          462          283          415         1983          276 
TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 
         248          722         1288         1762          520          725 
TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 
         623         1636         1747          190          644          451 
TCGA-BA-6871 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH 
          63          113          236          895          855          622 
TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DG 
         918          850          351          216          182         1976 
TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 
         314          623          142          187         2878          278 
TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 
         133          558          310          536          423          687 
TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 
         638         1153          428          436         1955          624 
TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 
           5            4          799          721         1157          142 
TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 
        1151          392          817          993          642         1250 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4741 TCGA-CN-4742 
         395          625         1960         1330         1268         1988 
TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5365 
        1007         1045          173         1980         1081         1980 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 
        1966         1966         1975          683          290          630 
TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 
         933          629          628          594          629           45 
TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
         432           98         1970          202         1110          224 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 
         318          611          394          735          432          429 
TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C 
          46          443          535          391          904          645 
TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 
         225          526          484          348          175          367 
TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 
         223          298         1466         1207          654         1660 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 
        1422         1393         1399          317          341          129 
TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 
        1253         1000         1057          985         1959         1959 
TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 
        1179         1750         1560         1007          509         1309 
TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CA 
         877         1950         1353         1960          707         1963 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI 
         893          998          785          391          303          950 
TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 
        2562         1663         1152          799         1777         1521 
TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 
        1966         1050         1125         1971          514         1969 
TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 
         362          311          345          354          234          379 
TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 
         479         1956         1435         1191         1440         1245 
TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 
        1960          105         1979          759          889           30 
TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 
         972         1968         1036          796         1954          997 
TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
        1430         1951          907          913          946          908 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 
         898          930          216          156          181         1077 
TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 
         911         1472         1955          522         1950         3295 
TCGA-CV-5435 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 
        1438          546         1978         2886         2327         1958 
TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 
        2437          519          406          701         2641         1478 
TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 
         215         1315         1665          641         1899         1970 
TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 
        1948         1969         1952         1959         3835         1948 
TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7091 TCGA-CV-7095 
        1966         1957         1969         1959         1959         1970 
TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7180 TCGA-CV-7183 
        1970         1936         1959         1939         1987         1979 
TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7243 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7254 
        1952         1444          954         1967         1960         1976 
TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 
        1099         1974         1948         1955         1957         1947 
TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7434 TCGA-CV-7435 
        1937         1973         1972         1937         1958         1959 
TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45Y TCGA-CV-A45Z 
        1981          851         1945         5480         1960         1940 
TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE 
        1946         1954         1722         1977         1970         1075 
TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ 
         906         1959          670          110          646          714 
TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 
         606          685         1950          317          321          237 
TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 
         828          773          292          701           77          491 
TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK 
         568          106          128          539          376          483 
TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q 
         232          435          424          368          389          338 
TCGA-DQ-5624 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 
        1778          516         1030          548         1965          575 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 
         775          622          299          369          368          324 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I 
         340         1131          490          658           15           92 
TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-H7-7774 
         585            3          384           14           13          407 
TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 
          58          133          414          403          206            2 
TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 
          25           37           55           44           24           25 
TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 
          11           49           10          111           33         1057 
TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H 
         485          122          441          588          360          412 
TCGA-IQ-A61J TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 
         440          360          224          552          378          168 
TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 
          14           34          392          111          112          254 
TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SX TCGA-P3-A6T0 
         240          910         1726         1559         1954          578 
TCGA-P3-A6T2 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG 
        1917          400          553          357          245          218 
TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A8Z7 TCGA-QK-A8ZA TCGA-QK-A8ZB 
         228          225          387          198          135          135 
TCGA-QK-AA3J TCGA-QK-AA3K TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71D 
         157          168         1326         1663         1319         1252 
TCGA-UF-A71E TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH 
        1278         1894          484          735         1497          665 
TCGA-UF-A7JJ TCGA-UF-A7JS 
         214          413 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                5                 2 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
             3837              5480 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
              804               694 
[1] "5.0 - 3837.0 (804.0)" "2.0 - 5480.0 (694.0)"
[1] "hr=" "1.1"
D8V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  4Q GAIN MUTATED         1        8         0        18         2         0
  4Q GAIN WILD-TYPE      25       67        74       217        10         1
D8V3, multiclass
           clus
vv          4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  STAGE I                 1                25
  STAGE II                8                67
  STAGE III               0                74
  STAGE IVA              18               217
  STAGE IVB               2                10
  STAGE IVC               0                 1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  4Q GAIN MUTATED       2   9   4  14
  4Q GAIN WILD-TYPE    45 118  90 148
D8V4, multiclass
       clus
vv      4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  T0+T1               2                45
  T2                  9               118
  T3                  4                90
  T4                 14               148
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  4Q GAIN MUTATED    10   1  12   2
  4Q GAIN WILD-TYPE 160  62 140   6
D8V5, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  N0              10               160
  N1               1                62
  N2              12               140
  N3               2                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1  MX
  4Q GAIN MUTATED    11   0   2
  4Q GAIN WILD-TYPE 156   1  56
D8V6, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  M0              11               156
  M1               0                 1
  MX               2                56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V7, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     8  27
  4Q GAIN WILD-TYPE 124 329
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      8   27
  4Q GAIN WILD-TYPE  124  329
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE               8               124
  MALE                27               329
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  4Q GAIN MUTATED                                      34
  4Q GAIN WILD-TYPE                                   443
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  4Q GAIN MUTATED                                                             0
  4Q GAIN WILD-TYPE                                                           1
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  4Q GAIN MUTATED                                                     1
  4Q GAIN WILD-TYPE                                                   9
D8V8, multiclass
                                                             clus
vv                                                            4Q GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    34
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       1
                                                             clus
vv                                                            4Q GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     443
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                 1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V9, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     3  32
  4Q GAIN WILD-TYPE  76 377
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      3   32
  4Q GAIN WILD-TYPE   76  377
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  NO                3                76
  YES              32               377
[1] 2 2
[1] FALSE
D8V10, continuous
D8V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4Q GAIN MUTATED                                  0     0
  4Q GAIN WILD-TYPE                                2    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4Q GAIN MUTATED                           7    27
  4Q GAIN WILD-TYPE                        37   388
D8V12, multiclass
                                  clus
vv                                 4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      7                37
  WHITE                                         27               388
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V13, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     4  27
  4Q GAIN WILD-TYPE  20 404
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      4   27
  4Q GAIN WILD-TYPE   20  404
                        clus
vv                       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                20
  NOT HISPANIC OR LATINO              27               404
[1] 2 2
[1] FALSE

Clustering(9) Variable = 5P GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                 0   1
  5P GAIN MUTATED   118  42
  5P GAIN WILD-TYPE 183  71
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              160               254 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               42                71 
$`5P GAIN MUTATED`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4078 TCGA-BA-5555 TCGA-BA-5556 
         102          462          283          276          520          725 
TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 
        1636         1747          190          644          451          384 
TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A6D8 TCGA-BA-A6DB 
         113          236          895          855          850          216 
TCGA-BA-A6DE TCGA-BA-A6DL TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4227 TCGA-BB-4228 
         182          623          187         2878          133          558 
TCGA-BB-7861 TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A47Z 
         310          687         1153         1955          624            5 
TCGA-CN-4723 TCGA-CN-4727 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4736 
         721         1230          392          817          993          395 
TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4742 TCGA-CN-5359 TCGA-CN-5363 
         625         1960         1330         1988         1980         1977 
TCGA-CN-5366 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6023 
        1966          630          933          432           98         1110 
TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6997 TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63W 
         394          735          429          443          904          348 
TCGA-CN-A6V3 TCGA-CQ-5330 TCGA-CQ-6221 TCGA-CQ-6224 TCGA-CQ-7064 TCGA-CQ-7067 
         298         1393         1000          985         1560          509 
TCGA-CQ-7072 TCGA-CQ-A4CA TCGA-CQ-A4CD TCGA-CR-5243 TCGA-CR-6467 TCGA-CR-6471 
        1950         1963          998         2562         1777         1966 
TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6484 TCGA-CR-6488 TCGA-CR-6492 
        1125         1971          514          354          379          479 
TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7379 TCGA-CR-7383 
        1191         1440         1245         1960         1036         1954 
TCGA-CR-7389 TCGA-CR-7392 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7404 TCGA-CV-5431 
         392          946          156          181         1472          522 
TCGA-CV-5435 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5444 TCGA-CV-5966 
        1438          546         1978         2327         2437          519 
TCGA-CV-5970 TCGA-CV-5978 TCGA-CV-6441 TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6945 
         406          215         1970         1952         1959         1969 
TCGA-CV-6954 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7101 
        1957         1959         3837         1959         1970         1939 
TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7235 TCGA-CV-7245 TCGA-CV-7424 TCGA-CV-A45R 
        1945         1987         1952          797         1947         5480 
TCGA-CV-A45Z TCGA-CV-A6JE TCGA-CX-7086 TCGA-D6-8568 TCGA-D6-8569 TCGA-DQ-5629 
        1940         1075          237          106          128          516 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7592 TCGA-DQ-7596 
        1030          548          575          775          299          340 
TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A620 TCGA-H7-8502 TCGA-H7-A76A TCGA-HD-7753 
         585            3           13          133          206            5 
TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8635 TCGA-HD-A6HZ TCGA-HL-7533 TCGA-IQ-7630 
          37           55           25          111         1057          485 
TCGA-IQ-A61E TCGA-IQ-A61J TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 
         588          440          360          224          552          378 
TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67D TCGA-MZ-A7D7 TCGA-P3-A5QA TCGA-P3-A6SW 
          14           34           56          240         1726         1120 
TCGA-P3-A6SX TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 
        1954         1917         1968          400          553          357 
TCGA-QK-A6IG TCGA-QK-A6IJ TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-AA3K TCGA-UF-A71B 
         218          387          149          135          168         1319 
TCGA-UF-A71D TCGA-UF-A7JA TCGA-UF-A7JF TCGA-UF-A7JS 
        1252         1894         1497          413 

$`5P GAIN WILD-TYPE`
TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 
         415         1983          248          722         1288         1762 
TCGA-BA-5557 TCGA-BA-6871 TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6DA TCGA-BA-A6DG 
         623           63          622          918          351         1976 
TCGA-BA-A6DJ TCGA-BA-A8YP TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-7862 TCGA-BB-7863 
         314          142          278          140          536          423 
TCGA-BB-7866 TCGA-BB-7871 TCGA-BB-7872 TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4725 
         638          428          436            4          799         1157 
TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4740 TCGA-CN-4741 
         142         1151          642         1250          811         1268 
TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5365 TCGA-CN-5367 
        1007         1045          173         1081         1980         1966 
TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 
        1975          683          290          629          628          594 
TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6988 
         629           45         1970          202          224          318 
TCGA-CN-6989 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49C 
         611          432           46          535          391          645 
TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A6V1 
         225          526          484          175          367          223 
TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5331 
        1466         1207          654         1660         1422         1399 
TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6223 TCGA-CQ-6227 
         317          341          129         1253         1057         1959 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7069 
        1959         1179         1750         1007         1309         1274 
TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CE 
         877         1353         1960          707          893          785 
TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 
         391          303          950          358         1663         1152 
TCGA-CR-5250 TCGA-CR-6470 TCGA-CR-6472 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 
         799         1521         1050         1969          362          311 
TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6491 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7370 
         345          234          350         1956         1435          105 
TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 
        1979          759          889           30          972         1968 
TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7390 TCGA-CR-7391 
         796          997         1430         1951          907          913 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7401 TCGA-CR-7402 
         908          898          930          216         1077          911 
TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5436 TCGA-CV-5441 TCGA-CV-5443 
        1955         1950         3295          584         2886         1958 
TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5979 TCGA-CV-6003 
         701         2641         1478         1840         1315         1665 
TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6942 TCGA-CV-6943 
         641         1899         1948         1969         3835         1948 
TCGA-CV-6952 TCGA-CV-6960 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7183 
        1966         1969         1970         1936         1959         1979 
TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7254 
        1444         1095          954         1967         1960         1976 
TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7427 
        1099         1974         1948         1955         1957         1937 
TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 
        1973         1972         1937         1984         1958         1959 
TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A45Y TCGA-CV-A460 TCGA-CV-A461 
        1981          851         1945         1960         1946         1954 
TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT 
        1722         1977         1970          906         1959          670 
TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 
         110          646          714          606          685         1950 
TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 
         317          321          828          773          292          701 
TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-A4Z9 TCGA-D6-A4ZB 
          77          491          154          568          539          376 
TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES 
         483          232          435          424          368          389 
TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-7588 TCGA-DQ-7591 TCGA-DQ-7593 
         338         1778         1081         1965          622          369 
TCGA-DQ-7594 TCGA-DQ-7595 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G 
         368          324         1131          490          658           15 
TCGA-F7-A50I TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8501 
          92          384           14            6          407           58 
TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-8314 TCGA-HD-8634 
         414          403            2           25           44           24 
TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-IQ-7631 TCGA-IQ-7632 
          11           49           10           33          122          441 
TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61L TCGA-KU-A6H8 TCGA-MT-A67A TCGA-MT-A67F 
         360          412          351          168          392          111 
TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A6T0 TCGA-QK-A6IF 
         112          254          910         1559          578          245 
TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6V9 TCGA-QK-A8Z7 TCGA-QK-A8ZB TCGA-QK-AA3J 
         228          225          567          198          135          157 
TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JC TCGA-UF-A7JD 
        1326         1663         1278         1043          484          735 
TCGA-UF-A7JH TCGA-UF-A7JJ 
         665          214 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                3                 2 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             5480              3835 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            627.5             718.0 
[1] "3.0 - 5480.0 (627.5)" "2.0 - 3835.0 (718.0)"
[1] "hr=" "1.2"
D9V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  5P GAIN MUTATED         7       21        33        92         5         1
  5P GAIN WILD-TYPE      19       54        41       143         7         0
D9V3, multiclass
           clus
vv          5P GAIN MUTATED 5P GAIN WILD-TYPE
  STAGE I                 7                19
  STAGE II               21                54
  STAGE III              33                41
  STAGE IVA              92               143
  STAGE IVB               5                 7
  STAGE IVC               1                 0
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3 T4
  5P GAIN MUTATED      16 47 37 63
  5P GAIN WILD-TYPE    31 80 57 99
D9V4, multiclass
       clus
vv      5P GAIN MUTATED 5P GAIN WILD-TYPE
  T0+T1              16                31
  T2                 47                80
  T3                 37                57
  T4                 63                99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  5P GAIN MUTATED    51  30  63   4
  5P GAIN WILD-TYPE 119  33  89   4
D9V5, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  N0              51               119
  N1              30                33
  N2              63                89
  N3               4                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1  MX
  5P GAIN MUTATED    60   1  30
  5P GAIN WILD-TYPE 107   0  28
D9V6, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  M0              60               107
  M1               1                 0
  MX              30                28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V7, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    44 143
  5P GAIN WILD-TYPE  88 213
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     44  143
  5P GAIN WILD-TYPE   88  213
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE              44                88
  MALE               143               213
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  5P GAIN MUTATED                                     184
  5P GAIN WILD-TYPE                                   293
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  5P GAIN MUTATED                                                             1
  5P GAIN WILD-TYPE                                                           0
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  5P GAIN MUTATED                                                     2
  5P GAIN WILD-TYPE                                                   8
D9V8, multiclass
                                                             clus
vv                                                            5P GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                   184
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       2
                                                             clus
vv                                                            5P GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     293
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                 0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V9, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    40 147
  5P GAIN WILD-TYPE  39 262
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     40  147
  5P GAIN WILD-TYPE   39  262
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  NO               40                39
  YES             147               262
[1] 2 2
[1] FALSE
D9V10, continuous
D9V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5P GAIN MUTATED                                  1     3
  5P GAIN WILD-TYPE                                1     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5P GAIN MUTATED                          22   155
  5P GAIN WILD-TYPE                        22   260
D9V12, multiclass
                                  clus
vv                                 5P GAIN MUTATED 5P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 1
  ASIAN                                          3                 8
  BLACK OR AFRICAN AMERICAN                     22                22
  WHITE                                        155               260
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V13, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    13 163
  5P GAIN WILD-TYPE  11 268
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     13  163
  5P GAIN WILD-TYPE   11  268
                        clus
vv                       5P GAIN MUTATED 5P GAIN WILD-TYPE
  HISPANIC OR LATINO                  13                11
  NOT HISPANIC OR LATINO             163               268
[1] 2 2
[1] FALSE

Clustering(10) Variable = 5Q GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                 0   1
  5Q GAIN MUTATED    40  15
  5Q GAIN WILD-TYPE 261  98
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               55               359 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               15                98 
$`5Q GAIN MUTATED`
TCGA-BA-4074 TCGA-BA-5149 TCGA-BA-5556 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-A4IF 
         462          248          725          644          451          895 
TCGA-BA-A6DL TCGA-BB-4223 TCGA-BB-7861 TCGA-BB-7864 TCGA-CN-4738 TCGA-CN-5363 
         623         2878          310          687         1960         1977 
TCGA-CN-6011 TCGA-CN-6023 TCGA-CN-6997 TCGA-CN-A49B TCGA-CN-A6V3 TCGA-CQ-6224 
         933         1110          429          904          298          985 
TCGA-CQ-7067 TCGA-CR-5243 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6484 TCGA-CR-7389 
         509         2562         1966         1125          354          392 
TCGA-CR-7399 TCGA-CV-5431 TCGA-CV-5439 TCGA-CV-5442 TCGA-CV-5444 TCGA-CV-6441 
         181          522          546         2327         2437         1970 
TCGA-CV-6936 TCGA-CV-6945 TCGA-CV-6954 TCGA-CV-7102 TCGA-CV-7235 TCGA-CV-7245 
        1952         1969         1957         1945         1952          797 
TCGA-D6-8569 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-7590 TCGA-F7-A50J TCGA-F7-A61S 
         128          516         1030          775          585            3 
TCGA-HD-8635 TCGA-HD-A6HZ TCGA-IQ-A61O TCGA-MT-A51W TCGA-MZ-A7D7 TCGA-P3-A5QA 
          25          111          360           14          240         1726 
TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A6IG TCGA-QK-A8ZA TCGA-QK-AA3K 
        1917         1968          400          218          135          168 
TCGA-UF-A7JS 
         413 

$`5Q GAIN WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5151 
         102          283          415         1983          276          722 
TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 
        1288         1762          520          623         1636         1747 
TCGA-BA-6868 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IG 
         190           63          384          113          236          855 
TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE 
         622          918          850          351          216          182 
TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4224 TCGA-BB-4225 
        1976          314          142          187          278          140 
TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7866 TCGA-BB-7870 
         133          558          536          423          638         1153 
TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A47Z TCGA-C9-A480 
         428          436         1955          624            5            4 
TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 
         799          721         1157          142         1230         1151 
TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 
         392          817          993          642         1250          395 
TCGA-CN-4737 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 
         625         1330          811         1268         1988         1007 
TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5365 TCGA-CN-5366 
        1045          173         1980         1081         1980         1966 
TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6012 
        1966         1975          683          290          630          629 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 
         628          594          629           45          432           98 
TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 
        1970          202          224          318          611          394 
TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A 
         735          432           46          443          535          391 
TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y 
         645          225          526          484          348          175 
TCGA-CN-A641 TCGA-CN-A6V1 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 
         367          223         1466         1207          654         1660 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 
        1422         1393         1399          317          341          129 
TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 
        1253         1000         1057         1959         1959         1179 
TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 
        1750         1560         1007         1309         1274          877 
TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB 
        1950         1353         1960          707         1963          893 
TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5247 
         998          785          391          303          950          358 
TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6472 
        1663         1152          799         1777         1521         1050 
TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 
        1971          514         1969          362          311          345 
TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 
         234          379          350          479         1956         1435 
TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 
        1191         1440         1245         1960          105         1979 
TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 
         759          889           30          972         1968         1036 
TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7390 
         796         1954          997         1430         1951          907 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 
         913          946          908          898          930          216 
TCGA-CR-7398 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5432 
         156         1077          911         1472         1955         1950 
TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5443 
        3295         1438          584         1978         2886         1958 
TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 
         519          406          701         2641         1478         1840 
TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6934 
         215         1315         1665          641         1899         1948 
TCGA-CV-6935 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6952 TCGA-CV-6960 
        1969         1959         3835         1948         1966         1969 
TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 
        1959         3837         1959         1970         1970         1936 
TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7238 TCGA-CV-7242 
        1959         1939         1987         1979         1444         1095 
TCGA-CV-7243 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7406 
         954         1967         1960         1976         1099         1974 
TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7428 
        1948         1955         1957         1947         1937         1973 
TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7440 
        1972         1937         1984         1958         1959         1981 
TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 
         851         1945         5480         1960         1940         1946 
TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN 
        1954         1722         1977         1970         1075          906 
TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 
        1959          670          110          646          714          606 
TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 
         685         1950          317          321          237          828 
TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 
         773          292          701           77          491          154 
TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM 
         568          106          539          376          483          232 
TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 
         435          424          368          389          338         1778 
TCGA-DQ-5625 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7591 TCGA-DQ-7592 
        1081          548         1965          575          622          299 
TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 
         369          368          324          340         1131          490 
TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 
         658           15           92          384           14           13 
TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 
           6          407           58          133          414          403 
TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 
         206            2            5           25           37           55 
TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6I0 
          44           24           11           49           10           33 
TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G 
        1057          485          122          441          588          360 
TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61L TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 
         412          440          351          224          552          378 
TCGA-KU-A6H8 TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G 
         168           34          392           56          111          112 
TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 
         254          910         1559         1120         1954          578 
TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ 
         553          357          245          228          225          387 
TCGA-QK-A6V9 TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-UF-A718 
         567          198          149          135          157         1326 
TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA 
        1663         1319         1252         1278         1043         1894 
TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ 
         484          735         1497          665          214 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                3                 2 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             2878              5480 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
              644               707 
[1] "3.0 - 2878.0 (644.0)" "2.0 - 5480.0 (707.0)"
[1] "hr=" "1.3"
D10V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  5Q GAIN MUTATED         3        3        10        36         1         0
  5Q GAIN WILD-TYPE      23       72        64       199        11         1
D10V3, multiclass
           clus
vv          5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  STAGE I                 3                23
  STAGE II                3                72
  STAGE III              10                64
  STAGE IVA              36               199
  STAGE IVB               1                11
  STAGE IVC               0                 1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  5Q GAIN MUTATED       6  12  17  19
  5Q GAIN WILD-TYPE    41 115  77 143
D10V4, multiclass
       clus
vv      5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T0+T1               6                41
  T2                 12               115
  T3                 17                77
  T4                 19               143
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  5Q GAIN MUTATED    15   9  26   1
  5Q GAIN WILD-TYPE 155  54 126   7
D10V5, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  N0              15               155
  N1               9                54
  N2              26               126
  N3               1                 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"
                   vv
clus                 M0  M1  MX
  5Q GAIN MUTATED    18   0  13
  5Q GAIN WILD-TYPE 149   1  45
D10V6, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  M0              18               149
  M1               0                 1
  MX              13                45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V7, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    13  51
  5Q GAIN WILD-TYPE 119 305
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     13   51
  5Q GAIN WILD-TYPE  119  305
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE              13               119
  MALE                51               305
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  5Q GAIN MUTATED                                      63
  5Q GAIN WILD-TYPE                                   414
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  5Q GAIN MUTATED                                                             1
  5Q GAIN WILD-TYPE                                                           0
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  5Q GAIN MUTATED                                                     0
  5Q GAIN WILD-TYPE                                                  10
D10V8, multiclass
                                                             clus
vv                                                            5Q GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    63
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       0
                                                             clus
vv                                                            5Q GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     414
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                 0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V9, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    15  49
  5Q GAIN WILD-TYPE  64 360
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     15   49
  5Q GAIN WILD-TYPE   64  360
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  NO               15                64
  YES              49               360
[1] 2 2
[1] FALSE
D10V10, continuous
D10V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5Q GAIN MUTATED                                  0     1
  5Q GAIN WILD-TYPE                                2    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5Q GAIN MUTATED                           8    53
  5Q GAIN WILD-TYPE                        36   362
D10V12, multiclass
                                  clus
vv                                 5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      8                36
  WHITE                                         53               362
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V13, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     7  54
  5Q GAIN WILD-TYPE  17 377
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      7   54
  5Q GAIN WILD-TYPE   17  377
                        clus
vv                       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   7                17
  NOT HISPANIC OR LATINO              54               377
[1] 2 2
[1] FALSE

Clustering(11) Variable = 6P GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                 0   1
  6P GAIN MUTATED    52  12
  6P GAIN WILD-TYPE 249 101
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               64               350 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               12               101 
$`6P GAIN MUTATED`
TCGA-BA-4075 TCGA-BA-5555 TCGA-BA-6870 TCGA-BA-6873 TCGA-BA-A4II TCGA-BB-4224 
         283          520          451          113          918          278 
TCGA-BB-7870 TCGA-C9-A47Z TCGA-CN-4723 TCGA-CN-5356 TCGA-CN-5363 TCGA-CN-5367 
        1153            5          721         1045         1977         1966 
TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6989 TCGA-CN-A49A TCGA-CN-A63U 
          98          202         1110          611          391          526 
TCGA-CN-A63W TCGA-CN-A641 TCGA-CQ-5329 TCGA-CQ-5331 TCGA-CQ-5334 TCGA-CQ-7067 
         348          367         1422         1399          129          509 
TCGA-CQ-A4C7 TCGA-CQ-A4CA TCGA-CQ-A4CE TCGA-CR-5247 TCGA-CR-6487 TCGA-CR-7368 
        1960         1963          785          358          234         1245 
TCGA-CR-7389 TCGA-CR-7402 TCGA-CV-5430 TCGA-CV-5442 TCGA-CV-5977 TCGA-CV-6003 
         392          911         1955         2327         1840         1665 
TCGA-CV-6954 TCGA-CV-7235 TCGA-CV-7243 TCGA-CV-7250 TCGA-CV-7440 TCGA-CV-A6JE 
        1957         1952          954         1960         1981         1075 
TCGA-CV-A6JU TCGA-D6-A6EP TCGA-DQ-5625 TCGA-F7-A50I TCGA-H7-8502 TCGA-HD-7753 
         110          424         1081           92          133            5 
TCGA-HD-7917 TCGA-HD-A6I0 TCGA-IQ-A61E TCGA-IQ-A61L TCGA-KU-A66T TCGA-MT-A51W 
          37           33          588          351          552           14 
TCGA-MT-A67D TCGA-P3-A6SW TCGA-P3-A6T4 TCGA-QK-A6IG TCGA-QK-A8Z7 TCGA-QK-A8Z9 
          56         1120         1968          218          198          149 
TCGA-QK-A8ZA TCGA-UF-A719 TCGA-UF-A7JD TCGA-UF-A7JH 
         135         1663          735          665 

$`6P GAIN WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
         102          462          415         1983          276          248 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 
         722         1288         1762          725          623         1636 
TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-7269 
        1747          190          644           63          384          236 
TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB 
         895          855          622          850          351          216 
TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 
         182         1976          314          623          142          187 
TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 
        2878          140          133          558          310          536 
TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 
         423          687          638          428          436         1955 
TCGA-BB-8601 TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 
         624            4          799         1157          142         1230 
TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 
        1151          392          817          993          642         1250 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 
         395          625         1960         1330          811         1268 
TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5365 
        1988         1007          173         1980         1081         1980 
TCGA-CN-5366 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 
        1966         1975          683          290          630          933 
TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 
         629          628          594          629           45          432 
TCGA-CN-6021 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 
        1970          224          318          394          735          432 
TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A49C 
         429           46          443          535          904          645 
TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 
         225          484          175          223          298         1466 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5330 TCGA-CQ-5332 TCGA-CQ-5333 
        1207          654         1660         1393          317          341 
TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 
        1253         1000         1057          985         1959         1959 
TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7069 
        1179         1750         1560         1007         1309         1274 
TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD 
         877         1950         1353          707          893          998 
TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 
         391          303          950         2562         1663         1152 
TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 
         799         1777         1521         1966         1050         1125 
TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 
        1971          514         1969          362          311          345 
TCGA-CR-6484 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 
         354          379          350          479         1956         1435 
TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 
        1191         1440         1960          105         1979          759 
TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 
         889           30          972         1968         1036          796 
TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7390 TCGA-CR-7391 
        1954          997         1430         1951          907          913 
TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 
         946          908          898          930          216          156 
TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 
         181         1077         1472          522         1950         3295 
TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5443 
        1438          584          546         1978         2886         1958 
TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 
        2437          519          406          701         2641         1478 
TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 
         215         1315          641         1899         1970         1948 
TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 
        1969         1952         1959         3835         1948         1969 
TCGA-CV-6952 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 
        1966         1969         1959         3837         1959         1970 
TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7180 
        1970         1936         1959         1939         1945         1987 
TCGA-CV-7183 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7254 
        1979         1444         1095          797         1967         1976 
TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 
        1099         1974         1948         1955         1957         1947 
TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 
        1937         1973         1972         1937         1984         1958 
TCGA-CV-7435 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45Y TCGA-CV-A45Z 
        1959          851         1945         5480         1960         1940 
TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JN 
        1946         1954         1722         1977         1970          906 
TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 
        1959          670          646          714          606          685 
TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 
        1950          317          321          237          828          773 
TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 
         292          701           77          491          154          568 
TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM 
         106          128          539          376          483          232 
TCGA-D6-A6EO TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5629 
         435          368          389          338         1778          516 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 
        1030          548         1965          575          775          622 
TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 
         299          369          368          324          340         1131 
TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V 
         490          658           15          585            3          384 
TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-A6C4 
          14           13            6          407           58          414 
TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-8224 TCGA-HD-8314 
         403          206            2           25           55           44 
TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ 
          24           25           11           49           10          111 
TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61G TCGA-IQ-A61H 
        1057          485          122          441          360          412 
TCGA-IQ-A61J TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51X 
         440          360          224          378          168           34 
TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 
         392          111          112          254          240          910 
TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T8 
        1726         1559         1954          578         1917          400 
TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ 
         553          357          245          228          225          387 
TCGA-QK-A6V9 TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-UF-A718 TCGA-UF-A71B 
         567          135          157          168         1326         1319 
TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JF 
        1252         1278         1043         1894          484         1497 
TCGA-UF-A7JJ TCGA-UF-A7JS 
         214          413 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                5                 2 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             2327              5480 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              570               718 
[1] "5.0 - 2327.0 (570.0)" "2.0 - 5480.0 (718.0)"
[1] "hr=" "1.2"
D11V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  6P GAIN MUTATED         4       12        13        34         4         0
  6P GAIN WILD-TYPE      22       63        61       201         8         1
D11V3, multiclass
           clus
vv          6P GAIN MUTATED 6P GAIN WILD-TYPE
  STAGE I                 4                22
  STAGE II               12                63
  STAGE III              13                61
  STAGE IVA              34               201
  STAGE IVB               4                 8
  STAGE IVC               0                 1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  6P GAIN MUTATED       4  21  16  27
  6P GAIN WILD-TYPE    43 106  78 135
D11V4, multiclass
       clus
vv      6P GAIN MUTATED 6P GAIN WILD-TYPE
  T0+T1               4                43
  T2                 21               106
  T3                 16                78
  T4                 27               135
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  6P GAIN MUTATED    29  11  22   2
  6P GAIN WILD-TYPE 141  52 130   6
D11V5, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  N0              29               141
  N1              11                52
  N2              22               130
  N3               2                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1  MX
  6P GAIN MUTATED    26   0  12
  6P GAIN WILD-TYPE 141   1  46
D11V6, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  M0              26               141
  M1               0                 1
  MX              12                46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V7, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    18  58
  6P GAIN WILD-TYPE 114 298
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     18   58
  6P GAIN WILD-TYPE  114  298
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE              18               114
  MALE                58               298
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  6P GAIN MUTATED                                      74
  6P GAIN WILD-TYPE                                   403
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  6P GAIN MUTATED                                                             0
  6P GAIN WILD-TYPE                                                           1
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  6P GAIN MUTATED                                                     2
  6P GAIN WILD-TYPE                                                   8
D11V8, multiclass
                                                             clus
vv                                                            6P GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    74
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       2
                                                             clus
vv                                                            6P GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     403
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                 1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V9, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     6  70
  6P GAIN WILD-TYPE  73 339
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      6   70
  6P GAIN WILD-TYPE   73  339
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  NO                6                73
  YES              70               339
[1] 2 2
[1] FALSE
D11V10, continuous
D11V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6P GAIN MUTATED                                  0     1
  6P GAIN WILD-TYPE                                2    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6P GAIN MUTATED                          14    56
  6P GAIN WILD-TYPE                        30   359
D11V12, multiclass
                                  clus
vv                                 6P GAIN MUTATED 6P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                     14                30
  WHITE                                         56               359
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V13, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     4  65
  6P GAIN WILD-TYPE  20 366
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      4   65
  6P GAIN WILD-TYPE   20  366
                        clus
vv                       6P GAIN MUTATED 6P GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                20
  NOT HISPANIC OR LATINO              65               366
[1] 2 2
[1] FALSE

Clustering(12) Variable = 6Q GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                 0   1
  6Q GAIN MUTATED    38   8
  6Q GAIN WILD-TYPE 263 105
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               46               368 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                8               105 
$`6Q GAIN MUTATED`
TCGA-BA-4075 TCGA-BA-6873 TCGA-BA-A4II TCGA-BB-7870 TCGA-C9-A47Z TCGA-CN-4723 
         283          113          918         1153            5          721 
TCGA-CN-5356 TCGA-CN-5363 TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-A49A TCGA-CN-A63U 
        1045         1977           98          202          391          526 
TCGA-CN-A63W TCGA-CQ-5331 TCGA-CQ-5334 TCGA-CQ-7067 TCGA-CQ-A4CA TCGA-CQ-A4CE 
         348         1399          129          509         1963          785 
TCGA-CR-5247 TCGA-CR-7389 TCGA-CV-5430 TCGA-CV-5442 TCGA-CV-5973 TCGA-CV-5977 
         358          392         1955         2327         2641         1840 
TCGA-CV-6003 TCGA-CV-7434 TCGA-CV-7440 TCGA-CV-A45R TCGA-CX-7219 TCGA-D6-A6EP 
        1665         1958         1981         5480          828          424 
TCGA-DQ-5625 TCGA-F7-A50I TCGA-HD-7753 TCGA-HD-7917 TCGA-HD-A6I0 TCGA-IQ-A61E 
        1081           92            5           37           33          588 
TCGA-IQ-A61L TCGA-KU-A66T TCGA-MT-A51W TCGA-MT-A67D TCGA-P3-A6T4 TCGA-QK-A6IG 
         351          552           14           56         1968          218 
TCGA-QK-A8Z7 TCGA-QK-A8ZA TCGA-UF-A719 TCGA-UF-A71E 
         198          135         1663         1278 

$`6Q GAIN WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
         102          462          415         1983          276          248 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 
         722         1288         1762          520          725          623 
TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 
        1636         1747          190          644          451           63 
TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A6D8 
         384          236          895          855          622          850 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A6DL 
         351          216          182         1976          314          623 
TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 
         142          187         2878          278          140          133 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 
         558          310          536          423          687          638 
TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A480 TCGA-CN-4722 
         428          436         1955          624            4          799 
TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 
        1157          142         1230         1151          392          817 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 
         993          642         1250          395          625         1960 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 
        1330          811         1268         1988         1007          173 
TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 
        1980         1081         1980         1966         1966         1975 
TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 
         683          290          630          933          629          628 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6021 TCGA-CN-6023 
         594          629           45          432         1970         1110 
TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 
         224          318          611          394          735          432 
TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A49C 
         429           46          443          535          904          645 
TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A6V1 TCGA-CN-A6V3 
         225          484          175          367          223          298 
TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 
        1466         1207          654         1660         1422         1393 
TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 
         317          341         1253         1000         1057          985 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 
        1959         1959         1179         1750         1560         1007 
TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 
        1309         1274          877         1950         1353         1960 
TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI 
         707          893          998          391          303          950 
TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 
        2562         1663         1152          799         1777         1521 
TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 
        1966         1050         1125         1971          514         1969 
TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 
         362          311          345          354          234          379 
TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 
         350          479         1956         1435         1191         1440 
TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 
        1245         1960          105         1979          759          889 
TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 
          30          972         1968         1036          796         1954 
TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 
         997         1430         1951          907          913          946 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 
         908          898          930          216          156          181 
TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 
        1077          911         1472          522         1950         3295 
TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5443 
        1438          584          546         1978         2886         1958 
TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5976 TCGA-CV-5978 
        2437          519          406          701         1478          215 
TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 
        1315          641         1899         1970         1948         1969 
TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6952 
        1952         1959         3835         1948         1969         1966 
TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 
        1957         1969         1959         3837         1959         1970 
TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7180 
        1970         1936         1959         1939         1945         1987 
TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 
        1979         1952         1444         1095          954          797 
TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 
        1967         1960         1976         1099         1974         1948 
TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 
        1955         1957         1947         1937         1973         1972 
TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7435 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A45Y 
        1937         1984         1959          851         1945         1960 
TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD 
        1940         1946         1954         1722         1977         1970 
TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY 
        1075          906         1959          670          110          646 
TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 
         714          606          685         1950          317          321 
TCGA-CX-7086 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 
         237          773          292          701           77          491 
TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB 
         154          568          106          128          539          376 
TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q 
         483          232          435          368          389          338 
TCGA-DQ-5624 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 
        1778          516         1030          548         1965          575 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 
         775          622          299          369          368          324 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50J 
         340         1131          490          658           15          585 
TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-7774 
           3          384           14           13            6          407 
TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 
          58          133          414          403          206            2 
TCGA-HD-7754 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 
          25           55           44           24           25           11 
TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 
          49           10          111         1057          485          122 
TCGA-IQ-7632 TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61O TCGA-KU-A66S 
         441          360          412          440          360          224 
TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G 
         378          168           34          392          111          112 
TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW 
         254          240          910         1726         1559         1120 
TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 
        1954          578         1917          400          553          357 
TCGA-QK-A6IF TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A8Z9 
         245          228          225          387          567          149 
TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-UF-A718 TCGA-UF-A71B TCGA-UF-A71D 
         135          157          168         1326         1319         1252 
TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH 
        1043         1894          484          735         1497          665 
TCGA-UF-A7JJ TCGA-UF-A7JS 
         214          413 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                5                 2 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
             5480              3837 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            539.0             710.5 
[1] "5.0 - 5480.0 (539.0)" "2.0 - 3837.0 (710.5)"
[1] "hr=" "2"  
D12V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  6Q GAIN MUTATED         3        8        14        24         3         0
  6Q GAIN WILD-TYPE      23       67        60       211         9         1
D12V3, multiclass
           clus
vv          6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  STAGE I                 3                23
  STAGE II                8                67
  STAGE III              14                60
  STAGE IVA              24               211
  STAGE IVB               3                 9
  STAGE IVC               0                 1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  6Q GAIN MUTATED       3  16  12  22
  6Q GAIN WILD-TYPE    44 111  82 140
D12V4, multiclass
       clus
vv      6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  T0+T1               3                44
  T2                 16               111
  T3                 12                82
  T4                 22               140
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  6Q GAIN MUTATED    25  11  13   1
  6Q GAIN WILD-TYPE 145  52 139   7
D12V5, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  N0              25               145
  N1              11                52
  N2              13               139
  N3               1                 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"
                   vv
clus                 M0  M1  MX
  6Q GAIN MUTATED    18   0   9
  6Q GAIN WILD-TYPE 149   1  49
D12V6, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  M0              18               149
  M1               0                 1
  MX               9                49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V7, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    14  44
  6Q GAIN WILD-TYPE 118 312
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     14   44
  6Q GAIN WILD-TYPE  118  312
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE              14               118
  MALE                44               312
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  6Q GAIN MUTATED                                      56
  6Q GAIN WILD-TYPE                                   421
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  6Q GAIN MUTATED                                                             0
  6Q GAIN WILD-TYPE                                                           1
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  6Q GAIN MUTATED                                                     2
  6Q GAIN WILD-TYPE                                                   8
D12V8, multiclass
                                                             clus
vv                                                            6Q GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    56
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       2
                                                             clus
vv                                                            6Q GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     421
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                 1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V9, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     3  55
  6Q GAIN WILD-TYPE  76 354
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      3   55
  6Q GAIN WILD-TYPE   76  354
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  NO                3                76
  YES              55               354
[1] 2 2
[1] FALSE
D12V10, continuous
D12V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6Q GAIN MUTATED                                  0     1
  6Q GAIN WILD-TYPE                                2    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6Q GAIN MUTATED                           9    44
  6Q GAIN WILD-TYPE                        35   371
D12V12, multiclass
                                  clus
vv                                 6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      9                35
  WHITE                                         44               371
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V13, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     7  46
  6Q GAIN WILD-TYPE  17 385
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      7   46
  6Q GAIN WILD-TYPE   17  385
                        clus
vv                       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   7                17
  NOT HISPANIC OR LATINO              46               385
[1] 2 2
[1] FALSE

Clustering(13) Variable = 7P GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                 0   1
  7P GAIN MUTATED    94  44
  7P GAIN WILD-TYPE 207  69
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              138               276 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               44                69 
$`7P GAIN MUTATED`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-5149 TCGA-BA-5555 TCGA-BA-6870 
         462          283          415          248          520          451 
TCGA-BA-A6DL TCGA-BB-4224 TCGA-BB-7863 TCGA-BB-7870 TCGA-BB-8596 TCGA-BB-8601 
         623          278          423         1153         1955          624 
TCGA-C9-A47Z TCGA-CN-4722 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4737 
           5          799          392          817          993          625 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5363 
        1960         1330         1045          173         1980         1977 
TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 
        1980         1966         1966          933          629          628 
TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 
          98          202         1110          224          318          611 
TCGA-CN-6997 TCGA-CN-A49A TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A641 TCGA-CQ-5329 
         429          391          225          484          367         1422 
TCGA-CQ-5334 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4C7 
         129          509         1309         1274         1950         1960 
TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CH TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 
         707         1963          303         1971          514         1969 
TCGA-CR-6484 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7370 TCGA-CR-7377 
         354         1435         1191         1440          105         1968 
TCGA-CR-7382 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7398 TCGA-CV-5430 TCGA-CV-5431 
         796          392          907          156         1955          522 
TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5444 
        1950         3295          546         1978         2327         2437 
TCGA-CV-5978 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6945 TCGA-CV-6954 TCGA-CV-7090 
         215         1969         1952         1969         1957         3837 
TCGA-CV-7091 TCGA-CV-7101 TCGA-CV-7180 TCGA-CV-7235 TCGA-CV-7243 TCGA-CV-7245 
        1959         1939         1987         1952          954          797 
TCGA-CV-7248 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7435 
        1967         1976         1099         1957         1947         1959 
TCGA-CV-7440 TCGA-CV-A45Z TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JZ TCGA-CX-7086 
        1981         1940         1959          670          714          237 
TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6823 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8569 
         828          773          701          154          568          128 
TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EP TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5631 
         483          232          424         1081          516          548 
TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7592 TCGA-F7-8298 TCGA-F7-A50I TCGA-F7-A61S 
        1965          575          299          490           92            3 
TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7917 TCGA-HD-8634 TCGA-HD-A633 
         403            2            5           37           24           49 
TCGA-IQ-7631 TCGA-IQ-A61H TCGA-IQ-A61O TCGA-KU-A66T TCGA-MT-A51W TCGA-MT-A51X 
         122          412          360          552           14           34 
TCGA-MT-A67A TCGA-MT-A67G TCGA-MZ-A7D7 TCGA-P3-A6SX TCGA-P3-A6T4 TCGA-P3-A6T8 
         392          112          240         1954         1968          400 
TCGA-QK-A6IG TCGA-QK-A6II TCGA-QK-A8Z7 TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA 
         218          225          198         1278         1043         1894 

$`7P GAIN WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 
         102         1983          276          722         1288         1762 
TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 
         725          623         1636         1747          190          644 
TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG 
          63          384          113          236          895          855 
TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE 
         622          918          850          351          216          182 
TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4225 
        1976          314          142          187         2878          140 
TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7864 TCGA-BB-7866 
         133          558          310          536          687          638 
TCGA-BB-7871 TCGA-BB-7872 TCGA-C9-A480 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 
         428          436            4          721         1157          142 
TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4740 
        1230         1151          642         1250          395          811 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5360 TCGA-CN-5370 TCGA-CN-5373 
        1268         1988         1007         1081         1975          683 
TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 
         290          630          594          629           45          432 
TCGA-CN-6021 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A498 
        1970          394          735          432           46          443 
TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A63Y 
         535          904          645          526          348          175 
TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 
         223          298         1466         1207          654         1660 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-6218 TCGA-CQ-6221 
        1393         1399          317          341         1253         1000 
TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 
        1057          985         1959         1959         1179         1750 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4CB TCGA-CQ-A4CD 
        1560         1007          877         1353          893          998 
TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 
         785          391          950         2562          358         1663 
TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 
        1152          799         1777         1521         1966         1050 
TCGA-CR-6473 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6488 
        1125          362          311          345          234          379 
TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7371 
         350          479         1956         1245         1960         1979 
TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7379 TCGA-CR-7383 
         759          889           30          972         1036         1954 
TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
         997         1430         1951          913          946          908 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 
         898          930          216          181         1077          911 
TCGA-CR-7404 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5441 TCGA-CV-5443 TCGA-CV-5966 
        1472         1438          584         2886         1958          519 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5979 
         406          701         2641         1478         1840         1315 
TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6941 
        1665          641         1899         1970         1948         1959 
TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6952 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7095 
        3835         1948         1966         1969         1959         1970 
TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7183 TCGA-CV-7238 
        1970         1936         1959         1945         1979         1444 
TCGA-CV-7242 TCGA-CV-7250 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7427 
        1095         1960         1974         1948         1955         1937 
TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-A45O 
        1973         1972         1937         1984         1958          851 
TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45Y TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A464 
        1945         5480         1960         1946         1954         1722 
TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JU TCGA-CV-A6JY 
        1977         1970         1075          906          110          646 
TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-D6-6517 
         606          685         1950          317          321          292 
TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EO 
          77          491          106          539          376          435 
TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5630 TCGA-DQ-7590 
         368          389          338         1778         1030          775 
TCGA-DQ-7591 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 
         622          369          368          324          340         1131 
TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50J TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 
         658           15          585          384           14           13 
TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A76A 
           6          407           58          133          414          206 
TCGA-HD-7754 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A634 
          25           55           44           25           11           10 
TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7632 TCGA-IQ-A61E 
         111           33         1057          485          441          588 
TCGA-IQ-A61G TCGA-IQ-A61J TCGA-IQ-A61L TCGA-KU-A66S TCGA-KU-A6H7 TCGA-KU-A6H8 
         360          440          351          224          378          168 
TCGA-MT-A67D TCGA-MT-A67F TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE 
          56          111          254          910         1726         1559 
TCGA-P3-A6SW TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF 
        1120          578         1917          553          357          245 
TCGA-QK-A6IH TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB 
         228          387          567          149          135          135 
TCGA-QK-AA3J TCGA-QK-AA3K TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71D 
         157          168         1326         1663         1319         1252 
TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JS 
         484          735         1497          665          214          413 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                2                 4 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             3837              5480 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            628.5             723.5 
[1] "2.0 - 3837.0 (628.5)" "4.0 - 5480.0 (723.5)"
[1] "hr=" "1"  
D13V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  7P GAIN MUTATED         9       30        25        87         6         0
  7P GAIN WILD-TYPE      17       45        49       148         6         1
D13V3, multiclass
           clus
vv          7P GAIN MUTATED 7P GAIN WILD-TYPE
  STAGE I                 9                17
  STAGE II               30                45
  STAGE III              25                49
  STAGE IVA              87               148
  STAGE IVB               6                 6
  STAGE IVC               0                 1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  7P GAIN MUTATED      13  47  36  62
  7P GAIN WILD-TYPE    34  80  58 100
D13V4, multiclass
       clus
vv      7P GAIN MUTATED 7P GAIN WILD-TYPE
  T0+T1              13                34
  T2                 47                80
  T3                 36                58
  T4                 62               100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  7P GAIN MUTATED    61  21  55   4
  7P GAIN WILD-TYPE 109  42  97   4
D13V5, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  N0              61               109
  N1              21                42
  N2              55                97
  N3               4                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1  MX
  7P GAIN MUTATED    54   0  20
  7P GAIN WILD-TYPE 113   1  38
D13V6, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  M0              54               113
  M1               0                 1
  MX              20                38
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V7, binary
                   cls
clus                  0   1
  7P GAIN MUTATED    44 128
  7P GAIN WILD-TYPE  88 228
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     44  128
  7P GAIN WILD-TYPE   88  228
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE              44                88
  MALE               128               228
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  7P GAIN MUTATED                                     169
  7P GAIN WILD-TYPE                                   308
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  7P GAIN MUTATED                                                             1
  7P GAIN WILD-TYPE                                                           0
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  7P GAIN MUTATED                                                     2
  7P GAIN WILD-TYPE                                                   8
D13V8, multiclass
                                                             clus
vv                                                            7P GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                   169
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       2
                                                             clus
vv                                                            7P GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     308
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                 0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V9, binary
                   cls
clus                  0   1
  7P GAIN MUTATED    31 141
  7P GAIN WILD-TYPE  48 268
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     31  141
  7P GAIN WILD-TYPE   48  268
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  NO               31                48
  YES             141               268
[1] 2 2
[1] FALSE
D13V10, continuous
D13V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7P GAIN MUTATED                                  1     4
  7P GAIN WILD-TYPE                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7P GAIN MUTATED                          19   145
  7P GAIN WILD-TYPE                        25   270
D13V12, multiclass
                                  clus
vv                                 7P GAIN MUTATED 7P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 1
  ASIAN                                          4                 7
  BLACK OR AFRICAN AMERICAN                     19                25
  WHITE                                        145               270
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V13, binary
                   cls
clus                  0   1
  7P GAIN MUTATED     8 155
  7P GAIN WILD-TYPE  16 276
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      8  155
  7P GAIN WILD-TYPE   16  276
                        clus
vv                       7P GAIN MUTATED 7P GAIN WILD-TYPE
  HISPANIC OR LATINO                   8                16
  NOT HISPANIC OR LATINO             155               276
[1] 2 2
[1] FALSE

Clustering(14) Variable = 7Q GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                 0   1
  7Q GAIN MUTATED    69  31
  7Q GAIN WILD-TYPE 232  82
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              100               314 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               31                82 
$`7Q GAIN MUTATED`
TCGA-BA-6870 TCGA-BB-7863 TCGA-BB-7870 TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A47Z 
         451          423         1153         1955          624            5 
TCGA-CN-4722 TCGA-CN-4727 TCGA-CN-4729 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-5356 
         799         1230          392         1960         1330         1045 
TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5367 TCGA-CN-6012 
         173         1081         1977         1980         1966          629 
TCGA-CN-6013 TCGA-CN-6020 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 
         628           98         1110          224          318          611 
TCGA-CN-6997 TCGA-CN-A49A TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A641 TCGA-CQ-7067 
         429          391          225          484          367          509 
TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CR-6478 
        1274         1950         1960          707         1963         1969 
TCGA-CR-7365 TCGA-CR-7370 TCGA-CR-7389 TCGA-CR-7390 TCGA-CV-5430 TCGA-CV-5431 
        1191          105          392          907         1955          522 
TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5442 
        1950         3295         1438          546         1978         2327 
TCGA-CV-5978 TCGA-CV-6935 TCGA-CV-6941 TCGA-CV-6945 TCGA-CV-7090 TCGA-CV-7091 
         215         1969         1959         1969         3837         1959 
TCGA-CV-7101 TCGA-CV-7235 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7254 TCGA-CV-7261 
        1939         1952          797         1967         1976         1099 
TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7435 TCGA-CV-A45Z TCGA-CV-A6JZ TCGA-CX-7086 
        1957         1947         1959         1940          714          237 
TCGA-D6-6516 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8569 TCGA-D6-A6EK TCGA-D6-A6EM 
         773          154          568          128          483          232 
TCGA-D6-A6EP TCGA-D6-A74Q TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5631 TCGA-DQ-7588 
         424          338         1081          516          548         1965 
TCGA-DQ-7589 TCGA-DQ-7592 TCGA-F7-8298 TCGA-F7-A50I TCGA-F7-A61S TCGA-HD-7753 
         575          299          490           92            3            5 
TCGA-HD-7917 TCGA-IQ-7631 TCGA-IQ-A61H TCGA-IQ-A61O TCGA-MT-A51W TCGA-MT-A67A 
          37          122          412          360           14          392 
TCGA-MT-A67G TCGA-MZ-A7D7 TCGA-P3-A6SX TCGA-P3-A6T4 TCGA-QK-A6II TCGA-QK-A8Z7 
         112          240         1954         1968          225          198 
TCGA-QK-AA3J TCGA-UF-A719 TCGA-UF-A7J9 TCGA-UF-A7JA 
         157         1663         1043         1894 

$`7Q GAIN WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 
         102          462          283          415         1983          276 
TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 
         248          722         1288         1762          520          725 
TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6871 
         623         1636         1747          190          644           63 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH 
         384          113          236          895          855          622 
TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DG 
         918          850          351          216          182         1976 
TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 
         314          623          142          187         2878          278 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7864 
         140          133          558          310          536          687 
TCGA-BB-7866 TCGA-BB-7871 TCGA-BB-7872 TCGA-C9-A480 TCGA-CN-4723 TCGA-CN-4725 
         638          428          436            4          721         1157 
TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 
         142         1151          817          993          642         1250 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 
         395          625          811         1268         1988         1007 
TCGA-CN-5359 TCGA-CN-5366 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 
        1980         1966         1975          683          290          630 
TCGA-CN-6011 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6021 
         933          594          629           45          432         1970 
TCGA-CN-6022 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A498 
         202          394          735          432           46          443 
TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A63Y 
         535          904          645          526          348          175 
TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 
         223          298         1466         1207          654         1660 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 
        1422         1393         1399          317          341          129 
TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 
        1253         1000         1057          985         1959         1959 
TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7071 
        1179         1750         1560         1007         1309          877 
TCGA-CQ-A4C6 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH 
        1353          893          998          785          391          303 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 
         950         2562          358         1663         1152          799 
TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 
        1777         1521         1966         1050         1125         1971 
TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 
         514          362          311          345          354          234 
TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7367 
         379          350          479         1956         1435         1440 
TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 
        1245         1960         1979          759          889           30 
TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 
         972         1968         1036          796         1954          997 
TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 
        1430         1951          913          946          908          898 
TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 
         930          216          156          181         1077          911 
TCGA-CR-7404 TCGA-CV-5436 TCGA-CV-5441 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 
        1472          584         2886         1958         2437          519 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5979 
         406          701         2641         1478         1840         1315 
TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6936 
        1665          641         1899         1970         1948         1952 
TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 
        3835         1948         1966         1957         1969         1959 
TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7180 
        1970         1970         1936         1959         1945         1987 
TCGA-CV-7183 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7250 TCGA-CV-7406 
        1979         1444         1095          954         1960         1974 
TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 
        1948         1955         1937         1973         1972         1937 
TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A45R 
        1984         1958         1981          851         1945         5480 
TCGA-CV-A45Y TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD 
        1960         1946         1954         1722         1977         1970 
TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY 
        1075          906         1959          670          110          646 
TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7219 
         606          685         1950          317          321          828 
TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-8568 TCGA-D6-A4Z9 
         292          701           77          491          106          539 
TCGA-D6-A4ZB TCGA-D6-A6EO TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-DQ-5624 TCGA-DQ-5630 
         376          435          368          389         1778         1030 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
         775          622          369          368          324          340 
TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50J TCGA-F7-A61V TCGA-F7-A61W 
        1131          658           15          585          384           14 
TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 
          13            6          407           58          133          414 
TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-8224 TCGA-HD-8314 
         403          206            2           25           55           44 
TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ 
          24           25           11           49           10          111 
TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G 
          33         1057          485          441          588          360 
TCGA-IQ-A61J TCGA-IQ-A61L TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 
         440          351          224          552          378          168 
TCGA-MT-A51X TCGA-MT-A67D TCGA-MT-A67F TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QA 
          34           56          111          254          910         1726 
TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T8 TCGA-QK-A64Z 
        1559         1120          578         1917          400          553 
TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6IJ TCGA-QK-A6V9 
         357          245          218          228          387          567 
TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3K TCGA-UF-A718 TCGA-UF-A71B 
         149          135          135          168         1326         1319 
TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH 
        1252         1278          484          735         1497          665 
TCGA-UF-A7JJ TCGA-UF-A7JS 
         214          413 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                3                 2 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             3837              5480 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              668               701 
[1] "3.0 - 3837.0 (668.0)" "2.0 - 5480.0 (701.0)"
[1] "hr=" "1"  
D14V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  7Q GAIN MUTATED         9       21        18        59         4         0
  7Q GAIN WILD-TYPE      17       54        56       176         8         1
D14V3, multiclass
           clus
vv          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  STAGE I                 9                17
  STAGE II               21                54
  STAGE III              18                56
  STAGE IVA              59               176
  STAGE IVB               4                 8
  STAGE IVC               0                 1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  7Q GAIN MUTATED      11  29  26  45
  7Q GAIN WILD-TYPE    36  98  68 117
D14V4, multiclass
       clus
vv      7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T0+T1              11                36
  T2                 29                98
  T3                 26                68
  T4                 45               117
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  7Q GAIN MUTATED    47  14  35   3
  7Q GAIN WILD-TYPE 123  49 117   5
D14V5, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  N0              47               123
  N1              14                49
  N2              35               117
  N3               3                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1  MX
  7Q GAIN MUTATED    37   0  15
  7Q GAIN WILD-TYPE 130   1  43
D14V6, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  M0              37               130
  M1               0                 1
  MX              15                43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V7, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED    32  91
  7Q GAIN WILD-TYPE 100 265
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     32   91
  7Q GAIN WILD-TYPE  100  265
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE              32               100
  MALE                91               265
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  7Q GAIN MUTATED                                     120
  7Q GAIN WILD-TYPE                                   357
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  7Q GAIN MUTATED                                                             1
  7Q GAIN WILD-TYPE                                                           0
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  7Q GAIN MUTATED                                                     2
  7Q GAIN WILD-TYPE                                                   8
D14V8, multiclass
                                                             clus
vv                                                            7Q GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                   120
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       2
                                                             clus
vv                                                            7Q GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     357
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                 0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V9, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED    23 100
  7Q GAIN WILD-TYPE  56 309
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     23  100
  7Q GAIN WILD-TYPE   56  309
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NO               23                56
  YES             100               309
[1] 2 2
[1] FALSE
D14V10, continuous
D14V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7Q GAIN MUTATED                                  1     2
  7Q GAIN WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7Q GAIN MUTATED                          14   102
  7Q GAIN WILD-TYPE                        30   313
D14V12, multiclass
                                  clus
vv                                 7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 1
  ASIAN                                          2                 9
  BLACK OR AFRICAN AMERICAN                     14                30
  WHITE                                        102               313
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V13, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED     8 106
  7Q GAIN WILD-TYPE  16 325
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      8  106
  7Q GAIN WILD-TYPE   16  325
                        clus
vv                       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   8                16
  NOT HISPANIC OR LATINO             106               325
[1] 2 2
[1] FALSE

Clustering(15) Variable = 8P GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                 0   1
  8P GAIN MUTATED    96  35
  8P GAIN WILD-TYPE 205  78
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              131               283 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               35                78 
$`8P GAIN MUTATED`
TCGA-4P-AA8J TCGA-BA-4075 TCGA-BA-5555 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6868 
         102          283          520          623         1747          190 
TCGA-BA-6871 TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6DG TCGA-BA-A6DL 
          63          855          622          918         1976          623 
TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-7861 
         142          187         2878          278          140          310 
TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-CN-4722 
         687         1153          436         1955          624          799 
TCGA-CN-4723 TCGA-CN-4729 TCGA-CN-4731 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 
         721          392          993         1960         1330          811 
TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5359 TCGA-CN-5366 TCGA-CN-6010 TCGA-CN-6012 
        1007         1045         1980         1966          630          629 
TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6994 TCGA-CN-6998 TCGA-CN-A499 TCGA-CN-A63T 
         202          224          735           46          535          225 
TCGA-CN-A63U TCGA-CN-A63V TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5330 TCGA-CQ-6224 
         526          484         1207          654         1393          985 
TCGA-CQ-7068 TCGA-CQ-A4C9 TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CI TCGA-CR-5243 
        1309          707          785          391          950         2562 
TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6482 TCGA-CR-6487 
        1777         1521          514         1969          345          234 
TCGA-CR-6493 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7370 TCGA-CR-7376 TCGA-CR-7379 
        1956         1191         1440          105          972         1036 
TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7389 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5435 
         796         1954          392         1955          522         1438 
TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5444 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-6003 
        1978         2327         2437         1478         1840         1665 
TCGA-CV-6433 TCGA-CV-6934 TCGA-CV-6936 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-7091 
         641         1948         1952         1948         1969         1959 
TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7180 TCGA-CV-7243 TCGA-CV-7254 TCGA-CV-7424 
        1970         1970         1987          954         1976         1947 
TCGA-CV-7428 TCGA-CV-A45R TCGA-CV-A45Z TCGA-CV-A461 TCGA-CV-A468 TCGA-CV-A6JE 
        1973         5480         1940         1954         1977         1075 
TCGA-CV-A6K0 TCGA-CX-7086 TCGA-D6-6516 TCGA-D6-6823 TCGA-D6-8568 TCGA-D6-A6EK 
         606          237          773          701          106          483 
TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-DQ-5629 TCGA-DQ-7588 TCGA-F7-7848 
         435          424          368          516         1965         1131 
TCGA-F7-8489 TCGA-F7-A61S TCGA-H7-A6C4 TCGA-H7-A76A TCGA-HD-7917 TCGA-HD-8314 
         658            3          414          206           37           44 
TCGA-HD-A634 TCGA-IQ-A61O TCGA-KU-A66S TCGA-MT-A51W TCGA-MT-A67D TCGA-MT-A67G 
          10          360          224           14           56          112 
TCGA-MZ-A7D7 TCGA-P3-A5QE TCGA-QK-A6IG TCGA-QK-A6IJ TCGA-UF-A719 TCGA-UF-A7JA 
         240         1559          218          387         1663         1894 
TCGA-UF-A7JC TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JS 
         484         1497          665          214          413 

$`8P GAIN WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 
         462          415         1983          276          248          722 
TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6869 TCGA-BA-6870 
        1288         1762          725         1636          644          451 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A6D8 TCGA-BA-A6DA 
         384          113          236          895          850          351 
TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DJ TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7862 
         216          182          314          133          558          536 
TCGA-BB-7863 TCGA-BB-7866 TCGA-BB-7871 TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4725 
         423          638          428            5            4         1157 
TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4730 TCGA-CN-4733 TCGA-CN-4735 
         142         1230         1151          817          642         1250 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5358 TCGA-CN-5360 
         395          625         1268         1988          173         1081 
TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 
        1977         1980         1966         1975          683          290 
TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 
         933          628          594          629           45          432 
TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6023 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 
          98         1970         1110          318          611          394 
TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-A498 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C 
         432          429          443          391          904          645 
TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 
         348          175          367          223          298         1466 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 
        1660         1422         1399          317          341          129 
TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 
        1253         1000         1057         1959         1959         1179 
TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7069 TCGA-CQ-7071 
        1750         1560         1007          509         1274          877 
TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD 
        1950         1353         1960         1963          893          998 
TCGA-CQ-A4CH TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6471 
         303          358         1663         1152          799         1966 
TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6484 
        1050         1125         1971          362          311          354 
TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-7364 TCGA-CR-7368 TCGA-CR-7369 
         379          350          479         1435         1245         1960 
TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7377 TCGA-CR-7385 
        1979          759          889           30         1968          997 
TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
        1430         1951          907          913          946          908 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 
         898          930          216          156          181         1077 
TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5436 TCGA-CV-5439 
         911         1472         1950         3295          584          546 
TCGA-CV-5441 TCGA-CV-5443 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 
        2886         1958          519          406          701         2641 
TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6935 TCGA-CV-6941 
         215         1315         1899         1970         1969         1959 
TCGA-CV-6942 TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 
        3835         1966         1957         1969         1959         3837 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7183 TCGA-CV-7235 
        1936         1959         1939         1945         1979         1952 
TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7261 
        1444         1095          797         1967         1960         1099 
TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7427 TCGA-CV-7430 
        1974         1948         1955         1957         1937         1972 
TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45O 
        1937         1984         1958         1959         1981          851 
TCGA-CV-A45Q TCGA-CV-A45Y TCGA-CV-A460 TCGA-CV-A464 TCGA-CV-A6JD TCGA-CV-A6JN 
        1945         1960         1946         1722         1970          906 
TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K1 
        1959          670          110          646          714          685 
TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7219 TCGA-D6-6517 TCGA-D6-6824 
        1950          317          321          828          292           77 
TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB 
         491          154          568          128          539          376 
TCGA-D6-A6EM TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 
         232          389          338         1778         1081         1030 
TCGA-DQ-5631 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 
         548          575          775          622          299          369 
TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-8298 TCGA-F7-A50G TCGA-F7-A50I 
         368          324          340          490           15           92 
TCGA-F7-A50J TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-7774 
         585          384           14           13            6          407 
TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 
          58          133          403            2            5           25 
TCGA-HD-8224 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A6HZ 
          55           24           25           11           49          111 
TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E 
          33         1057          485          122          441          588 
TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61L TCGA-KU-A66T TCGA-KU-A6H7 
         360          412          440          351          552          378 
TCGA-KU-A6H8 TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67F TCGA-MZ-A6I9 TCGA-P3-A5Q5 
         168           34          392          111          254          910 
TCGA-P3-A5QA TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T4 
        1726         1120         1954          578         1917         1968 
TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IH TCGA-QK-A6II 
         400          553          357          245          228          225 
TCGA-QK-A6V9 TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J 
         567          198          149          135          135          157 
TCGA-QK-AA3K TCGA-UF-A718 TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 
         168         1326         1319         1252         1278         1043 
TCGA-UF-A7JD 
         735 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                3                 2 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             5480              3837 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              735               670 
[1] "3.0 - 5480.0 (735.0)" "2.0 - 3837.0 (670.0)"
[1] "hr=" "1.3"
D15V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  8P GAIN MUTATED         8       23        25        68         3         0
  8P GAIN WILD-TYPE      18       52        49       167         9         1
D15V3, multiclass
           clus
vv          8P GAIN MUTATED 8P GAIN WILD-TYPE
  STAGE I                 8                18
  STAGE II               23                52
  STAGE III              25                49
  STAGE IVA              68               167
  STAGE IVB               3                 9
  STAGE IVC               0                 1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  8P GAIN MUTATED      17  44  25  43
  8P GAIN WILD-TYPE    30  83  69 119
D15V4, multiclass
       clus
vv      8P GAIN MUTATED 8P GAIN WILD-TYPE
  T0+T1              17                30
  T2                 44                83
  T3                 25                69
  T4                 43               119
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  8P GAIN MUTATED    47  25  45   3
  8P GAIN WILD-TYPE 123  38 107   5
D15V5, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  N0              47               123
  N1              25                38
  N2              45               107
  N3               3                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1  MX
  8P GAIN MUTATED    52   0  18
  8P GAIN WILD-TYPE 115   1  40
D15V6, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  M0              52               115
  M1               0                 1
  MX              18                40
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V7, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    28 118
  8P GAIN WILD-TYPE 104 238
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     28  118
  8P GAIN WILD-TYPE  104  238
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE              28               104
  MALE               118               238
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  8P GAIN MUTATED                                     140
  8P GAIN WILD-TYPE                                   337
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  8P GAIN MUTATED                                                             1
  8P GAIN WILD-TYPE                                                           0
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  8P GAIN MUTATED                                                     5
  8P GAIN WILD-TYPE                                                   5
D15V8, multiclass
                                                             clus
vv                                                            8P GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                   140
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       5
                                                             clus
vv                                                            8P GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     337
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                 0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         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"
D15V9, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    25 121
  8P GAIN WILD-TYPE  54 288
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     25  121
  8P GAIN WILD-TYPE   54  288
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  NO               25                54
  YES             121               288
[1] 2 2
[1] FALSE
D15V10, continuous
D15V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8P GAIN MUTATED                                  0     2
  8P GAIN WILD-TYPE                                2     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8P GAIN MUTATED                          17   120
  8P GAIN WILD-TYPE                        27   295
D15V12, multiclass
                                  clus
vv                                 8P GAIN MUTATED 8P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          2                 9
  BLACK OR AFRICAN AMERICAN                     17                27
  WHITE                                        120               295
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V13, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     8 126
  8P GAIN WILD-TYPE  16 305
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      8  126
  8P GAIN WILD-TYPE   16  305
                        clus
vv                       8P GAIN MUTATED 8P GAIN WILD-TYPE
  HISPANIC OR LATINO                   8                16
  NOT HISPANIC OR LATINO             126               305
[1] 2 2
[1] FALSE

Clustering(16) Variable = 8Q GAIN MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                 0   1
  8Q GAIN MUTATED   178  65
  8Q GAIN WILD-TYPE 123  48
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              243               171 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               65                48 
$`8Q GAIN MUTATED`
TCGA-4P-AA8J TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-5152 TCGA-BA-5555 
         102          283         1983          248         1288          520 
TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6871 
         623         1636         1747          190          451           63 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II 
         384          113          236          855          622          918 
TCGA-BA-A6DA TCGA-BA-A6DG TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 
         351         1976          623          142          187         2878 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7863 
         278          140          133          558          310          423 
TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A47Z 
         687         1153          436         1955          624            5 
TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4731 
           4          799          721         1151          392          993 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4742 
         395          625         1960         1330          811         1988 
TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5370 
        1007         1045         1977         1980         1966         1975 
TCGA-CN-5373 TCGA-CN-6012 TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6988 
         683          629           98          202          224          318 
TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A499 
         394          735          432           46          443          535 
TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W 
         391          904          225          526          484          348 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5334 TCGA-CQ-6218 
        1207          654         1422         1393          129         1253 
TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7065 TCGA-CQ-7067 
         985         1959         1959         1179         1007          509 
TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
        1309         1274         1950         1353         1960          707 
TCGA-CQ-A4CB TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 
         893          785          391          950         2562          358 
TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6473 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6482 
        1777         1521         1125          514         1969          345 
TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6493 TCGA-CR-7365 TCGA-CR-7367 
         354          234          379         1956         1191         1440 
TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7372 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 
        1960          105          759          972         1968         1036 
TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7397 
         796         1954         1430         1951          392          216 
TCGA-CR-7399 TCGA-CR-7401 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5435 
         181         1077         1955          522         1950         1438 
TCGA-CV-5436 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5444 TCGA-CV-5966 
         584         1978         2886         2327         2437          519 
TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 
        1478         1840          215         1665          641         1899 
TCGA-CV-6934 TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 
        1948         1952         1959         3835         1948         1969 
TCGA-CV-6952 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7102 
        1966         3837         1959         1970         1970         1945 
TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7243 TCGA-CV-7245 
        1987         1979         1952         1444          954          797 
TCGA-CV-7248 TCGA-CV-7254 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7434 
        1967         1976         1947         1937         1973         1958 
TCGA-CV-A45R TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A468 
        5480         1960         1940         1954         1722         1977 
TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CX-7082 
        1075          906         1959          714          606          317 
TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6826 
         237          828          773          292          701          154 
TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EO 
         106          128          539          376          483          435 
TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 
         424          368          389         1778         1081          516 
TCGA-DQ-5630 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7592 TCGA-F7-7848 TCGA-F7-8298 
        1030         1965          575          299         1131          490 
TCGA-F7-8489 TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A620 TCGA-H7-8501 
         658           92          585            3           13           58 
TCGA-H7-A6C4 TCGA-H7-A76A TCGA-HD-7917 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 
         414          206           37           44           24           25 
TCGA-HD-A634 TCGA-HL-7533 TCGA-IQ-A61E TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S 
          10         1057          588          351          360          224 
TCGA-KU-A66T TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67D TCGA-MT-A67G TCGA-MZ-A7D7 
         552           14           34           56          112          240 
TCGA-P3-A5QA TCGA-P3-A5QE TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IG TCGA-QK-A6IH 
        1726         1559          553          357          218          228 
TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A8ZB TCGA-QK-AA3K TCGA-UF-A718 TCGA-UF-A719 
         225          387          135          168         1326         1663 
TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF 
        1278         1043         1894          484          735         1497 
TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JS 
         665          214          413 

$`8Q GAIN WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5151 TCGA-BA-5153 TCGA-BA-5556 
         462          415          276          722         1762          725 
TCGA-BA-6869 TCGA-BA-A4IF TCGA-BA-A6D8 TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DJ 
         644          895          850          216          182          314 
TCGA-BB-7862 TCGA-BB-7866 TCGA-BB-7871 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 
         536          638          428         1157          142         1230 
TCGA-CN-4730 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4741 TCGA-CN-5358 TCGA-CN-5359 
         817          642         1250         1268          173         1980 
TCGA-CN-5360 TCGA-CN-5367 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6013 
        1081         1966          290          630          933          628 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6021 TCGA-CN-6023 
         594          629           45          432         1970         1110 
TCGA-CN-6989 TCGA-CN-6997 TCGA-CN-A49C TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A6V1 
         611          429          645          175          367          223 
TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-5327 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 
         298         1466         1660         1399          317          341 
TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7071 TCGA-CQ-A4CA 
        1000         1057         1750         1560          877         1963 
TCGA-CQ-A4CD TCGA-CQ-A4CH TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6471 
         998          303         1663         1152          799         1966 
TCGA-CR-6472 TCGA-CR-6474 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6491 TCGA-CR-6492 
        1050         1971          362          311          350          479 
TCGA-CR-7364 TCGA-CR-7368 TCGA-CR-7371 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7385 
        1435         1245         1979          889           30          997 
TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 
         907          913          946          908          898          930 
TCGA-CR-7398 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5434 TCGA-CV-5439 TCGA-CV-5443 
         156          911         1472         3295          546         1958 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5979 TCGA-CV-6441 TCGA-CV-6935 
         406          701         2641         1315         1970         1969 
TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 
        1957         1969         1959         1936         1959         1939 
TCGA-CV-7242 TCGA-CV-7250 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 
        1095         1960         1099         1974         1948         1955 
TCGA-CV-7422 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7435 TCGA-CV-7440 
        1957         1972         1937         1984         1959         1981 
TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A460 TCGA-CV-A6JD TCGA-CV-A6JT TCGA-CV-A6JU 
         851         1945         1946         1970          670          110 
TCGA-CV-A6JY TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-D6-6824 TCGA-D6-6825 
         646          685         1950          321           77          491 
TCGA-D6-6827 TCGA-D6-A6EM TCGA-D6-A74Q TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 
         568          232          338          548          775          622 
TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-A50G TCGA-F7-A61V 
         369          368          324          340           15          384 
TCGA-F7-A61W TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8502 TCGA-H7-A6C5 TCGA-HD-7229 
          14            6          407          133          403            2 
TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-8224 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A6HZ 
           5           25           55           11           49          111 
TCGA-HD-A6I0 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61G TCGA-IQ-A61H 
          33          485          122          441          360          412 
TCGA-IQ-A61J TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A67A TCGA-MT-A67F TCGA-MZ-A6I9 
         440          378          168          392          111          254 
TCGA-P3-A5Q5 TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T4 
         910         1120         1954          578         1917         1968 
TCGA-P3-A6T8 TCGA-QK-A6IF TCGA-QK-A6V9 TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-QK-A8ZA 
         400          245          567          198          149          135 
TCGA-QK-AA3J TCGA-UF-A71B TCGA-UF-A71D 
         157         1319         1252 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                3                 2 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             5480              3295 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              721               646 
[1] "3.0 - 5480.0 (721.0)" "2.0 - 3295.0 (646.0)"
[1] "hr=" "1.3"
D16V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  8Q GAIN MUTATED        16       42        50       138        10         0
  8Q GAIN WILD-TYPE      10       33        24        97         2         1
D16V3, multiclass
           clus
vv          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  STAGE I                16                10
  STAGE II               42                33
  STAGE III              50                24
  STAGE IVA             138                97
  STAGE IVB              10                 2
  STAGE IVC               0                 1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1 T2 T3 T4
  8Q GAIN MUTATED      31 73 60 95
  8Q GAIN WILD-TYPE    16 54 34 67
D16V4, multiclass
       clus
vv      8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T0+T1              31                16
  T2                 73                54
  T3                 60                34
  T4                 95                67
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  8Q GAIN MUTATED   96 39 95  7
  8Q GAIN WILD-TYPE 74 24 57  1
D16V5, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  N0              96                74
  N1              39                24
  N2              95                57
  N3               7                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1  MX
  8Q GAIN MUTATED   102   0  33
  8Q GAIN WILD-TYPE  65   1  25
D16V6, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  M0             102                65
  M1               0                 1
  MX              33                25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V7, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED    79 212
  8Q GAIN WILD-TYPE  53 144
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     79  212
  8Q GAIN WILD-TYPE   53  144
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE              79                53
  MALE               212               144
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  8Q GAIN MUTATED                                     284
  8Q GAIN WILD-TYPE                                   193
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  8Q GAIN MUTATED                                                             1
  8Q GAIN WILD-TYPE                                                           0
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  8Q GAIN MUTATED                                                     6
  8Q GAIN WILD-TYPE                                                   4
D16V8, multiclass
                                                             clus
vv                                                            8Q GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                   284
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       6
                                                             clus
vv                                                            8Q GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     193
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                 0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         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"
D16V9, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED    45 246
  8Q GAIN WILD-TYPE  34 163
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     45  246
  8Q GAIN WILD-TYPE   34  163
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NO               45                34
  YES             246               163
[1] 2 2
[1] FALSE
D16V10, continuous
D16V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8Q GAIN MUTATED                                  2     7
  8Q GAIN WILD-TYPE                                0     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8Q GAIN MUTATED                          28   240
  8Q GAIN WILD-TYPE                        16   175
D16V12, multiclass
                                  clus
vv                                 8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               2                 0
  ASIAN                                          7                 4
  BLACK OR AFRICAN AMERICAN                     28                16
  WHITE                                        240               175
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V13, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED    17 252
  8Q GAIN WILD-TYPE   7 179
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     17  252
  8Q GAIN WILD-TYPE    7  179
                        clus
vv                       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  HISPANIC OR LATINO                  17                 7
  NOT HISPANIC OR LATINO             252               179
[1] 2 2
[1] FALSE

Clustering(17) Variable = 9P GAIN MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                 0   1
  9P GAIN MUTATED    57  18
  9P GAIN WILD-TYPE 244  95
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               75               339 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               18                95 
$`9P GAIN MUTATED`
TCGA-BA-5149 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6873 TCGA-BA-A6DA 
         248          725          623         1747          113          351 
TCGA-BA-A6DJ TCGA-BB-7870 TCGA-CN-5355 TCGA-CN-5359 TCGA-CN-5363 TCGA-CN-5370 
         314         1153         1007         1980         1977         1975 
TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6023 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-A499 
         630          933         1110          735          432          535 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-6223 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7068 
        1422         1393         1057         1179         1750         1309 
TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CD TCGA-CR-6467 TCGA-CR-6487 TCGA-CR-7370 
        1353         1960          998         1777          234          105 
TCGA-CR-7371 TCGA-CR-7373 TCGA-CR-7395 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 
        1979          889          930         1978         2886         2327 
TCGA-CV-5966 TCGA-CV-5977 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6941 TCGA-CV-6952 
         519         1840          641         1899         1959         1966 
TCGA-CV-7099 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7427 
        1936         1952         1444         1976         1099         1937 
TCGA-CV-A45Q TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JO TCGA-CV-A6JZ TCGA-CX-7219 
        1945         1977         1970         1959          714          828 
TCGA-D6-6516 TCGA-D6-A6EM TCGA-D6-A6EQ TCGA-DQ-5625 TCGA-F7-A61S TCGA-H7-7774 
         773          232          368         1081            3          407 
TCGA-H7-8502 TCGA-HD-7917 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-A61L 
         133           37           10           33         1057          351 
TCGA-MT-A51W TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G TCGA-P3-A6SW TCGA-P3-A6T2 
          14          392          111          112         1120         1917 
TCGA-QK-A6IG TCGA-QK-A8Z9 TCGA-UF-A7J9 
         218          149         1043 

$`9P GAIN WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 
         102          462          283          415         1983          276 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5558 TCGA-BA-6868 
         722         1288         1762          520         1636          190 
TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A4IF 
         644          451           63          384          236          895 
TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DB TCGA-BA-A6DE 
         855          622          918          850          216          182 
TCGA-BA-A6DG TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 
        1976          623          142          187         2878          278 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 
         140          133          558          310          536          423 
TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 
         687          638          428          436         1955          624 
TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 
           5            4          799          721         1157          142 
TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
        1230         1151          392          817          993          642 
TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 
        1250          395          625         1960         1330          811 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5365 
        1268         1988         1045          173         1081         1980 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6012 TCGA-CN-6013 
        1966         1966          683          290          629          628 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 
         594          629           45          432           98         1970 
TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6997 
         202          224          318          611          394          429 
TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T 
          46          443          391          904          645          225 
TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A6V1 
         526          484          348          175          367          223 
TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5331 
         298         1466         1207          654         1660         1399 
TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6224 
         317          341          129         1253         1000          985 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7069 
        1959         1959         1560         1007          509         1274 
TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CE 
         877         1950          707         1963          893          785 
TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 
         391          303          950         2562          358         1663 
TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 
        1152          799         1521         1966         1050         1125 
TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 
        1971          514         1969          362          311          345 
TCGA-CR-6484 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 
         354          379          350          479         1956         1435 
TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7372 TCGA-CR-7374 
        1191         1440         1245         1960          759           30 
TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 
         972         1968         1036          796         1954          997 
TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 
        1430         1951          392          907          913          946 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 
         908          898          216          156          181         1077 
TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 
         911         1472         1955          522         1950         3295 
TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5970 
        1438          584          546         1958         2437          406 
TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 
         701         2641         1478          215         1315         1665 
TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6942 TCGA-CV-6943 
        1970         1948         1969         1952         3835         1948 
TCGA-CV-6945 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 
        1969         1957         1969         1959         3837         1959 
TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7180 
        1970         1970         1959         1939         1945         1987 
TCGA-CV-7183 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 
        1979         1095          954          797         1967         1960 
TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7428 
        1974         1948         1955         1957         1947         1973 
TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7440 
        1972         1937         1984         1958         1959         1981 
TCGA-CV-A45O TCGA-CV-A45R TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 
         851         5480         1960         1940         1946         1954 
TCGA-CV-A464 TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY 
        1722         1075          906          670          110          646 
TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 
         606          685         1950          317          321          237 
TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 
         292          701           77          491          154          568 
TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EO 
         106          128          539          376          483          435 
TCGA-D6-A6EP TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5629 TCGA-DQ-5630 
         424          389          338         1778          516         1030 
TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 
         548         1965          575          775          622          299 
TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 
         369          368          324          340         1131          490 
TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61V TCGA-F7-A61W 
         658           15           92          585          384           14 
TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-8501 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A 
          13            6           58          414          403          206 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 
           2            5           25           55           44           24 
TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A6HZ TCGA-IQ-7630 TCGA-IQ-7631 
          25           11           49          111          485          122 
TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61O 
         441          588          360          412          440          360 
TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51X TCGA-MT-A67D 
         224          552          378          168           34           56 
TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SX 
         254          240          910         1726         1559         1954 
TCGA-P3-A6T0 TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF 
         578         1968          400          553          357          245 
TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A8Z7 TCGA-QK-A8ZA 
         228          225          387          567          198          135 
TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71B 
         135          157          168         1326         1663         1319 
TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF 
        1252         1278         1894          484          735         1497 
TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JS 
         665          214          413 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                3                 2 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
             2886              5480 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
             1043               644 
[1] "3.0 - 2886.0 (1043.0)" "2.0 - 5480.0 (644.0)" 
[1] "hr=" "1.5"
D17V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  9P GAIN MUTATED         5       20        12        46         4         0
  9P GAIN WILD-TYPE      21       55        62       189         8         1
D17V3, multiclass
           clus
vv          9P GAIN MUTATED 9P GAIN WILD-TYPE
  STAGE I                 5                21
  STAGE II               20                55
  STAGE III              12                62
  STAGE IVA              46               189
  STAGE IVB               4                 8
  STAGE IVC               0                 1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  9P GAIN MUTATED       7  23  21  36
  9P GAIN WILD-TYPE    40 104  73 126
D17V4, multiclass
       clus
vv      9P GAIN MUTATED 9P GAIN WILD-TYPE
  T0+T1               7                40
  T2                 23               104
  T3                 21                73
  T4                 36               126
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  9P GAIN MUTATED    35  11  28   4
  9P GAIN WILD-TYPE 135  52 124   4
D17V5, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  N0              35               135
  N1              11                52
  N2              28               124
  N3               4                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1  MX
  9P GAIN MUTATED    31   0  12
  9P GAIN WILD-TYPE 136   1  46
D17V6, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  M0              31               136
  M1               0                 1
  MX              12                46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V7, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    34  59
  9P GAIN WILD-TYPE  98 297
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     34   59
  9P GAIN WILD-TYPE   98  297
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE              34                98
  MALE                59               297
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  9P GAIN MUTATED                                      92
  9P GAIN WILD-TYPE                                   385
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  9P GAIN MUTATED                                                             0
  9P GAIN WILD-TYPE                                                           1
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  9P GAIN MUTATED                                                     1
  9P GAIN WILD-TYPE                                                   9
D17V8, multiclass
                                                             clus
vv                                                            9P GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    92
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       1
                                                             clus
vv                                                            9P GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     385
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                 1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V9, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    11  82
  9P GAIN WILD-TYPE  68 327
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     11   82
  9P GAIN WILD-TYPE   68  327
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  NO               11                68
  YES              82               327
[1] 2 2
[1] FALSE
D17V10, continuous
D17V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9P GAIN MUTATED                                  0     2
  9P GAIN WILD-TYPE                                2     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9P GAIN MUTATED                           5    83
  9P GAIN WILD-TYPE                        39   332
D17V12, multiclass
                                  clus
vv                                 9P GAIN MUTATED 9P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          2                 9
  BLACK OR AFRICAN AMERICAN                      5                39
  WHITE                                         83               332
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V13, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     7  83
  9P GAIN WILD-TYPE  17 348
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      7   83
  9P GAIN WILD-TYPE   17  348
                        clus
vv                       9P GAIN MUTATED 9P GAIN WILD-TYPE
  HISPANIC OR LATINO                   7                17
  NOT HISPANIC OR LATINO              83               348
[1] 2 2
[1] FALSE

Clustering(18) Variable = 9Q GAIN MUTATION ANALYSIS
D18V1, survival
                   sevent
clus2                 0   1
  9Q GAIN MUTATED    76  28
  9Q GAIN WILD-TYPE 225  85
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
              104               310 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               28                85 
$`9Q GAIN MUTATED`
TCGA-BA-5149 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6873 
         248          520          725          623         1747          113 
TCGA-BA-A6DA TCGA-BA-A6DJ TCGA-BB-4224 TCGA-BB-7864 TCGA-BB-7870 TCGA-CN-4723 
         351          314          278          687         1153          721 
TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4741 TCGA-CN-5355 TCGA-CN-5359 TCGA-CN-5363 
        1230         1151         1268         1007         1980         1977 
TCGA-CN-5367 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6021 TCGA-CN-6023 TCGA-CN-6994 
        1966          630          933         1970         1110          735 
TCGA-CN-6996 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A63T TCGA-CN-A6V3 TCGA-CQ-5323 
         432          535          391          225          298         1466 
TCGA-CQ-5325 TCGA-CQ-5330 TCGA-CQ-6223 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7068 
         654         1393         1057         1179         1750         1309 
TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CA TCGA-CQ-A4CD TCGA-CQ-A4CG TCGA-CR-6467 
        1353         1960         1963          998          391         1777 
TCGA-CR-6477 TCGA-CR-7368 TCGA-CR-7373 TCGA-CR-7379 TCGA-CR-7389 TCGA-CV-5432 
         514         1245          889         1036          392         1950 
TCGA-CV-5434 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5444 TCGA-CV-5966 
        3295          546         1978         2327         2437          519 
TCGA-CV-5970 TCGA-CV-5977 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6941 TCGA-CV-6952 
         406         1840          641         1899         1959         1966 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7245 TCGA-CV-7261 
        1936         1959         1952         1444          797         1099 
TCGA-CV-7422 TCGA-CV-7427 TCGA-CV-7432 TCGA-CV-7434 TCGA-CV-A45Q TCGA-CV-A45Z 
        1957         1937         1937         1958         1945         1940 
TCGA-CV-A461 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JZ TCGA-CX-7219 TCGA-D6-6516 
        1954         1977         1970          714          828          773 
TCGA-D6-8569 TCGA-D6-A6EM TCGA-D6-A6EQ TCGA-D6-A74Q TCGA-DQ-5625 TCGA-F7-A61S 
         128          232          368          338         1081            3 
TCGA-H7-7774 TCGA-H7-8502 TCGA-HD-7917 TCGA-HD-8314 TCGA-HD-A634 TCGA-HD-A6I0 
         407          133           37           44           10           33 
TCGA-IQ-7630 TCGA-IQ-A61L TCGA-MT-A51W TCGA-MT-A67A TCGA-MT-A67G TCGA-P3-A6SW 
         485          351           14          392          112         1120 
TCGA-P3-A6T2 TCGA-QK-A64Z TCGA-QK-A6IG TCGA-QK-A8Z9 TCGA-UF-A71E TCGA-UF-A7J9 
        1917          553          218          149         1278         1043 
TCGA-UF-A7JA TCGA-UF-A7JS 
        1894          413 

$`9Q GAIN WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 
         102          462          283          415         1983          276 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 
         722         1288         1762         1636          190          644 
TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG 
         451           63          384          236          895          855 
TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DG 
         622          918          850          216          182         1976 
TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-4227 
         623          142          187         2878          140          133 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7866 TCGA-BB-7871 
         558          310          536          423          638          428 
TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 
         436         1955          624            5            4          799 
TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
        1157          142          392          817          993          642 
TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 
        1250          395          625         1960         1330          811 
TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5365 TCGA-CN-5366 
        1988         1045          173         1081         1980         1966 
TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 
        1975          683          290          629          628          594 
TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-6024 
         629           45          432           98          202          224 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 
         318          611          394          429           46          443 
TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y 
         904          645          526          484          348          175 
TCGA-CN-A641 TCGA-CN-A6V1 TCGA-CQ-5324 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5331 
         367          223         1207         1660         1422         1399 
TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6224 
         317          341          129         1253         1000          985 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7069 
        1959         1959         1560         1007          509         1274 
TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CE TCGA-CQ-A4CH 
         877         1950          707          893          785          303 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 
         950         2562          358         1663         1152          799 
TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6478 
        1521         1966         1050         1125         1971         1969 
TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 
         362          311          345          354          234          379 
TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 
         350          479         1956         1435         1191         1440 
TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7374 TCGA-CR-7376 
        1960          105         1979          759           30          972 
TCGA-CR-7377 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 
        1968          796         1954          997         1430         1951 
TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 
         907          913          946          908          898          930 
TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 
         216          156          181         1077          911         1472 
TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5441 TCGA-CV-5443 
        1955          522         1438          584         2886         1958 
TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 
         701         2641         1478          215         1315         1665 
TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6942 TCGA-CV-6943 
        1970         1948         1969         1952         3835         1948 
TCGA-CV-6945 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 
        1969         1957         1969         1959         3837         1959 
TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7183 
        1970         1970         1939         1945         1987         1979 
TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7406 
        1095          954         1967         1960         1976         1974 
TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7424 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7433 
        1948         1955         1947         1973         1972         1984 
TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45R TCGA-CV-A45Y TCGA-CV-A460 
        1959         1981          851         5480         1960         1946 
TCGA-CV-A464 TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU 
        1722         1075          906         1959          670          110 
TCGA-CV-A6JY TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 
         646          606          685         1950          317          321 
TCGA-CX-7086 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 
         237          292          701           77          491          154 
TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EO 
         568          106          539          376          483          435 
TCGA-D6-A6EP TCGA-D6-A6ES TCGA-DQ-5624 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 
         424          389         1778          516         1030          548 
TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 
        1965          575          775          622          299          369 
TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 
         368          324          340         1131          490          658 
TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 
          15           92          585          384           14           13 
TCGA-F7-A623 TCGA-H7-8501 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 
           6           58          414          403          206            2 
TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-8224 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 
           5           25           55           24           25           11 
TCGA-HD-A633 TCGA-HD-A6HZ TCGA-HL-7533 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E 
          49          111         1057          122          441          588 
TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T 
         360          412          440          360          224          552 
TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51X TCGA-MT-A67D TCGA-MT-A67F TCGA-MZ-A6I9 
         378          168           34           56          111          254 
TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SX TCGA-P3-A6T0 
         240          910         1726         1559         1954          578 
TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IH TCGA-QK-A6II 
        1968          400          357          245          228          225 
TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A8Z7 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J 
         387          567          198          135          135          157 
TCGA-QK-AA3K TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A7JC 
         168         1326         1663         1319         1252          484 
TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ 
         735         1497          665          214 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                3                 2 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             3295              5480 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           1002.5             640.0 
[1] "3.0 - 3295.0 (1002.5)" "2.0 - 5480.0 (640.0)" 
[1] "hr=" "1.1"
D18V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  9Q GAIN MUTATED         6       24        15        70         6         0
  9Q GAIN WILD-TYPE      20       51        59       165         6         1
D18V3, multiclass
           clus
vv          9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  STAGE I                 6                20
  STAGE II               24                51
  STAGE III              15                59
  STAGE IVA              70               165
  STAGE IVB               6                 6
  STAGE IVC               0                 1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  9Q GAIN MUTATED      10  29  26  56
  9Q GAIN WILD-TYPE    37  98  68 106
D18V4, multiclass
       clus
vv      9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  T0+T1              10                37
  T2                 29                98
  T3                 26                68
  T4                 56               106
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  9Q GAIN MUTATED    50  16  40   4
  9Q GAIN WILD-TYPE 120  47 112   4
D18V5, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  N0              50               120
  N1              16                47
  N2              40               112
  N3               4                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1  MX
  9Q GAIN MUTATED    40   0  14
  9Q GAIN WILD-TYPE 127   1  44
D18V6, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  M0              40               127
  M1               0                 1
  MX              14                44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V7, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    38  91
  9Q GAIN WILD-TYPE  94 265
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     38   91
  9Q GAIN WILD-TYPE   94  265
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE              38                94
  MALE                91               265
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  9Q GAIN MUTATED                                     126
  9Q GAIN WILD-TYPE                                   351
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  9Q GAIN MUTATED                                                             0
  9Q GAIN WILD-TYPE                                                           1
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  9Q GAIN MUTATED                                                     3
  9Q GAIN WILD-TYPE                                                   7
D18V8, multiclass
                                                             clus
vv                                                            9Q GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                   126
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       3
                                                             clus
vv                                                            9Q GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     351
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                 1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V9, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    19 110
  9Q GAIN WILD-TYPE  60 299
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     19  110
  9Q GAIN WILD-TYPE   60  299
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  NO               19                60
  YES             110               299
[1] 2 2
[1] FALSE
D18V10, continuous
D18V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9Q GAIN MUTATED                                  0     2
  9Q GAIN WILD-TYPE                                2     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9Q GAIN MUTATED                          11   112
  9Q GAIN WILD-TYPE                        33   303
D18V12, multiclass
                                  clus
vv                                 9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          2                 9
  BLACK OR AFRICAN AMERICAN                     11                33
  WHITE                                        112               303
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V13, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    10 110
  9Q GAIN WILD-TYPE  14 321
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     10  110
  9Q GAIN WILD-TYPE   14  321
                        clus
vv                       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  HISPANIC OR LATINO                  10                14
  NOT HISPANIC OR LATINO             110               321
[1] 2 2
[1] FALSE

Clustering(19) Variable = 10P GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                  0   1
  10P GAIN MUTATED    25   6
  10P GAIN WILD-TYPE 276 107
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                31                383 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 6                107 
$`10P GAIN MUTATED`
TCGA-BA-5151 TCGA-BA-5555 TCGA-BA-6869 TCGA-BA-6872 TCGA-BA-A6DL TCGA-BB-7861 
         722          520          644          384          623          310 
TCGA-CN-4727 TCGA-CN-5356 TCGA-CN-6013 TCGA-CN-6994 TCGA-CN-A63T TCGA-CQ-7067 
        1230         1045          628          735          225          509 
TCGA-CR-5247 TCGA-CR-6488 TCGA-CR-7399 TCGA-CV-5441 TCGA-CV-6003 TCGA-CV-6934 
         358          379          181         2886         1665         1948 
TCGA-CV-7091 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7435 TCGA-CV-A45Z TCGA-CV-A6JY 
        1959         1960         1976         1959         1940          646 
TCGA-DQ-7589 TCGA-F7-7848 TCGA-HD-7917 TCGA-HD-A6HZ TCGA-P3-A5QE TCGA-QK-A6IG 
         575         1131           37          111         1559          218 
TCGA-UF-A71D 
        1252 

$`10P GAIN WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 
         102          462          283          415         1983          276 
TCGA-BA-5149 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 
         248         1288         1762          725          623         1636 
TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6873 TCGA-BA-7269 
        1747          190          451           63          113          236 
TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA 
         895          855          622          918          850          351 
TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A8YP TCGA-BB-4217 
         216          182         1976          314          142          187 
TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7862 
        2878          278          140          133          558          536 
TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 
         423          687          638         1153          428          436 
TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 
        1955          624            5            4          799          721 
TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 
        1157          142         1151          392          817          993 
TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 
         642         1250          395          625         1960         1330 
TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5359 
         811         1268         1988         1007          173         1980 
TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 
        1081         1977         1980         1966         1966         1975 
TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6016 
         683          290          630          933          629          594 
TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 
         629           45          432           98         1970          202 
TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6996 
        1110          224          318          611          394          432 
TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B 
         429           46          443          535          391          904 
TCGA-CN-A49C TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 
         645          526          484          348          175          367 
TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 
         223          298         1466         1207          654         1660 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 
        1422         1393         1399          317          341          129 
TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 
        1253         1000         1057          985         1959         1959 
TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7069 
        1179         1750         1560         1007         1309         1274 
TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CA 
         877         1950         1353         1960          707         1963 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI 
         893          998          785          391          303          950 
TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 
        2562         1663         1152          799         1777         1521 
TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 
        1966         1050         1125         1971          514         1969 
TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6491 
         362          311          345          354          234          350 
TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 
         479         1956         1435         1191         1440         1245 
TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 
        1960          105         1979          759          889           30 
TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 
         972         1968         1036          796         1954          997 
TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 
        1430         1951          392          907          913          946 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7401 
         908          898          930          216          156         1077 
TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 
         911         1472         1955          522         1950         3295 
TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5443 
        1438          584          546         1978         2327         1958 
TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 
        2437          519          406          701         2641         1478 
TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 
        1840          215         1315          641         1899         1970 
TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 
        1969         1952         1959         3835         1948         1969 
TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7095 
        1966         1957         1969         1959         3837         1970 
TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7180 
        1970         1936         1959         1939         1945         1987 
TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 
        1979         1952         1444         1095          954          797 
TCGA-CV-7248 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7422 
        1967         1099         1974         1948         1955         1957 
TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 
        1947         1937         1973         1972         1937         1984 
TCGA-CV-7434 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45Y 
        1958         1981          851         1945         5480         1960 
TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE 
        1946         1954         1722         1977         1970         1075 
TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JZ TCGA-CV-A6K0 
         906         1959          670          110          714          606 
TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 
         685         1950          317          321          237          828 
TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 
         773          292          701           77          491          154 
TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK 
         568          106          128          539          376          483 
TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q 
         232          435          424          368          389          338 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 
        1778         1081          516         1030          548         1965 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 
         775          622          299          369          368          324 
TCGA-DQ-7596 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J 
         340          490          658           15           92          585 
TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-7774 
           3          384           14           13            6          407 
TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 
          58          133          414          403          206            2 
TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 
           5           25           55           44           24           25 
TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 
          11           49           10           33         1057          485 
TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J 
         122          441          588          360          412          440 
TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 
         351          360          224          552          378          168 
TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G 
          14           34          392           56          111          112 
TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A6SW TCGA-P3-A6SX 
         254          240          910         1726         1120         1954 
TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 
         578         1917         1968          400          553          357 
TCGA-QK-A6IF TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A8Z7 
         245          228          225          387          567          198 
TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-UF-A718 
         149          135          135          157          168         1326 
TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC 
        1663         1319         1278         1043         1894          484 
TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JS 
         735         1497          665          214          413 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                37                  2 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              2886               5480 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
               646                701 
[1] "37.0 - 2886.0 (646.0)" "2.0 - 5480.0 (701.0)" 
[1] "hr=" "1.4"
D19V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  10P GAIN MUTATED         2        5         7        15         0         0
  10P GAIN WILD-TYPE      24       70        67       220        12         1
D19V3, multiclass
           clus
vv          10P GAIN MUTATED 10P GAIN WILD-TYPE
  STAGE I                  2                 24
  STAGE II                 5                 70
  STAGE III                7                 67
  STAGE IVA               15                220
  STAGE IVB                0                 12
  STAGE IVC                0                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  10P GAIN MUTATED       5   8   7  10
  10P GAIN WILD-TYPE    42 119  87 152
D19V4, multiclass
       clus
vv      10P GAIN MUTATED 10P GAIN WILD-TYPE
  T0+T1                5                 42
  T2                   8                119
  T3                   7                 87
  T4                  10                152
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  10P GAIN MUTATED    16   6   7   0
  10P GAIN WILD-TYPE 154  57 145   8
D19V5, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  N0               16                154
  N1                6                 57
  N2                7                145
  N3                0                  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"
                    vv
clus                  M0  M1  MX
  10P GAIN MUTATED     7   0   3
  10P GAIN WILD-TYPE 160   1  55
D19V6, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  M0                7                160
  M1                0                  1
  MX                3                 55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V7, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     8  26
  10P GAIN WILD-TYPE 124 330
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      8   26
  10P GAIN WILD-TYPE  124  330
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE                8                124
  MALE                 26                330
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  10P GAIN MUTATED                                      33
  10P GAIN WILD-TYPE                                   444
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  10P GAIN MUTATED                                                             0
  10P GAIN WILD-TYPE                                                           1
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  10P GAIN MUTATED                                                     1
  10P GAIN WILD-TYPE                                                   9
D19V8, multiclass
                                                             clus
vv                                                            10P GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     33
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        1
                                                             clus
vv                                                            10P GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      444
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                  1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                          9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V9, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     6  28
  10P GAIN WILD-TYPE  73 381
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      6   28
  10P GAIN WILD-TYPE   73  381
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  NO                 6                 73
  YES               28                381
[1] 2 2
[1] FALSE
D19V10, continuous
D19V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10P GAIN MUTATED                                  0     0
  10P GAIN WILD-TYPE                                2    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10P GAIN MUTATED                           2    32
  10P GAIN WILD-TYPE                        42   383
D19V12, multiclass
                                  clus
vv                                 10P GAIN MUTATED 10P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                 11
  BLACK OR AFRICAN AMERICAN                       2                 42
  WHITE                                          32                383
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V13, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     0  33
  10P GAIN WILD-TYPE  24 398
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      0   33
  10P GAIN WILD-TYPE   24  398
                        clus
vv                       10P GAIN MUTATED 10P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 24
  NOT HISPANIC OR LATINO               33                398
[1] 2 2
[1] FALSE

Clustering(20) Variable = 10Q GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                  0   1
  10Q GAIN MUTATED    22   6
  10Q GAIN WILD-TYPE 279 107
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                28                386 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 6                107 
$`10Q GAIN MUTATED`
TCGA-BA-5151 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-A6DL TCGA-CN-4727 TCGA-CN-6013 
         722          384          113          623         1230          628 
TCGA-CN-6023 TCGA-CN-6994 TCGA-CN-A63T TCGA-CQ-5329 TCGA-CQ-7067 TCGA-CQ-A4C7 
        1110          735          225         1422          509         1960 
TCGA-CR-7390 TCGA-CR-7399 TCGA-CV-5441 TCGA-CV-5966 TCGA-CV-6003 TCGA-CV-6441 
         907          181         2886          519         1665         1970 
TCGA-CV-7091 TCGA-CV-7435 TCGA-CV-A6JY TCGA-D6-6825 TCGA-DQ-5629 TCGA-F7-A620 
        1959         1959          646          491          516           13 
TCGA-HD-7917 TCGA-HD-A6HZ TCGA-QK-A6IG TCGA-UF-A71D 
          37          111          218         1252 

$`10Q GAIN WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 
         102          462          283          415         1983          276 
TCGA-BA-5149 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 
         248         1288         1762          520          725          623 
TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 
        1636         1747          190          644          451           63 
TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 
         236          895          855          622          918          850 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A8YP 
         351          216          182         1976          314          142 
TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 
         187         2878          278          140          133          558 
TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 
         310          536          423          687          638         1153 
TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A47Z TCGA-C9-A480 
         428          436         1955          624            5            4 
TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 
         799          721         1157          142         1151          392 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 
         817          993          642         1250          395          625 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 
        1960         1330          811         1268         1988         1007 
TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 
        1045          173         1980         1081         1977         1980 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 
        1966         1966         1975          683          290          630 
TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 
         933          629          594          629           45          432 
TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 
          98         1970          202          224          318          611 
TCGA-CN-6992 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A499 
         394          432          429           46          443          535 
TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W 
         391          904          645          526          484          348 
TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-5324 
         175          367          223          298         1466         1207 
TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 
         654         1660         1393         1399          317          341 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 
         129         1253         1000         1057          985         1959 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7068 
        1959         1179         1750         1560         1007         1309 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CA 
        1274          877         1950         1353          707         1963 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI 
         893          998          785          391          303          950 
TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 
        2562          358         1663         1152          799         1777 
TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 
        1521         1966         1050         1125         1971          514 
TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 
        1969          362          311          345          354          234 
TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 
         379          350          479         1956         1435         1191 
TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 
        1440         1245         1960          105         1979          759 
TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 
         889           30          972         1968         1036          796 
TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7391 
        1954          997         1430         1951          392          913 
TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 
         946          908          898          930          216          156 
TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 
        1077          911         1472         1955          522         1950 
TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5442 
        3295         1438          584          546         1978         2327 
TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 
        1958         2437          406          701         2641         1478 
TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6934 
        1840          215         1315          641         1899         1948 
TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 
        1969         1952         1959         3835         1948         1969 
TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7095 
        1966         1957         1969         1959         3837         1970 
TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7180 
        1970         1936         1959         1939         1945         1987 
TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 
        1979         1952         1444         1095          954          797 
TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 
        1967         1960         1976         1099         1974         1948 
TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 
        1955         1957         1947         1937         1973         1972 
TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q 
        1937         1984         1958         1981          851         1945 
TCGA-CV-A45R TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A464 
        5480         1960         1940         1946         1954         1722 
TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT 
        1977         1970         1075          906         1959          670 
TCGA-CV-A6JU TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 
         110          714          606          685         1950          317 
TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 
         321          237          828          773          292          701 
TCGA-D6-6824 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 
          77          154          568          106          128          539 
TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ 
         376          483          232          435          424          368 
TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 
         389          338         1778         1081         1030          548 
TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 
        1965          575          775          622          299          369 
TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 
         368          324          340         1131          490          658 
TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W 
          15           92          585            3          384           14 
TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 
           6          407           58          133          414          403 
TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-8224 TCGA-HD-8314 
         206            2            5           25           55           44 
TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6I0 
          24           25           11           49           10           33 
TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G 
        1057          485          122          441          588          360 
TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T 
         412          440          351          360          224          552 
TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D 
         378          168           14           34          392           56 
TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QA 
         111          112          254          240          910         1726 
TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T4 
        1559         1120         1954          578         1917         1968 
TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IH TCGA-QK-A6II 
         400          553          357          245          228          225 
TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB 
         387          567          198          149          135          135 
TCGA-QK-AA3J TCGA-QK-AA3K TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71E 
         157          168         1326         1663         1319         1278 
TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH 
        1043         1894          484          735         1497          665 
TCGA-UF-A7JJ TCGA-UF-A7JS 
         214          413 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                13                  2 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              2886               5480 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
               637                704 
[1] "13.0 - 2886.0 (637.0)" "2.0 - 5480.0 (704.0)" 
[1] "hr=" "1.2"
D20V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  10Q GAIN MUTATED         3        3         6        16         0         0
  10Q GAIN WILD-TYPE      23       72        68       219        12         1
D20V3, multiclass
           clus
vv          10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  STAGE I                  3                 23
  STAGE II                 3                 72
  STAGE III                6                 68
  STAGE IVA               16                219
  STAGE IVB                0                 12
  STAGE IVC                0                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  10Q GAIN MUTATED       4   7   7  11
  10Q GAIN WILD-TYPE    43 120  87 151
D20V4, multiclass
       clus
vv      10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  T0+T1                4                 43
  T2                   7                120
  T3                   7                 87
  T4                  11                151
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  10Q GAIN MUTATED    14   6   9   0
  10Q GAIN WILD-TYPE 156  57 143   8
D20V5, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  N0               14                156
  N1                6                 57
  N2                9                143
  N3                0                  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"
                    vv
clus                  M0  M1  MX
  10Q GAIN MUTATED     9   0   3
  10Q GAIN WILD-TYPE 158   1  55
D20V6, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  M0                9                158
  M1                0                  1
  MX                3                 55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V7, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     8  23
  10Q GAIN WILD-TYPE 124 333
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      8   23
  10Q GAIN WILD-TYPE  124  333
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FEMALE                8                124
  MALE                 23                333
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  10Q GAIN MUTATED                                      31
  10Q GAIN WILD-TYPE                                   446
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  10Q GAIN MUTATED                                                             0
  10Q GAIN WILD-TYPE                                                           1
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  10Q GAIN MUTATED                                                     0
  10Q GAIN WILD-TYPE                                                  10
D20V8, multiclass
                                                             clus
vv                                                            10Q GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     31
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        0
                                                             clus
vv                                                            10Q GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      446
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                  1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V9, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     7  24
  10Q GAIN WILD-TYPE  72 385
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      7   24
  10Q GAIN WILD-TYPE   72  385
     clus
vv    10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  NO                 7                 72
  YES               24                385
[1] 2 2
[1] FALSE
D20V10, continuous
D20V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10Q GAIN MUTATED                                  0     0
  10Q GAIN WILD-TYPE                                2    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10Q GAIN MUTATED                           0    30
  10Q GAIN WILD-TYPE                        44   385
D20V12, multiclass
                                  clus
vv                                 10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                 11
  BLACK OR AFRICAN AMERICAN                       0                 44
  WHITE                                          30                385
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V13, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     2  28
  10Q GAIN WILD-TYPE  22 403
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      2   28
  10Q GAIN WILD-TYPE   22  403
                        clus
vv                       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                 22
  NOT HISPANIC OR LATINO               28                403
[1] 2 2
[1] FALSE

Clustering(21) Variable = 11P GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                  0   1
  11P GAIN MUTATED    37  12
  11P GAIN WILD-TYPE 264 101
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                49                365 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                12                101 
$`11P GAIN MUTATED`
TCGA-BA-4075 TCGA-BA-5556 TCGA-BA-6868 TCGA-BA-A8YP TCGA-BB-4225 TCGA-BB-7861 
         283          725          190          142          140          310 
TCGA-C9-A47Z TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5367 
           5          625         1960         1988         1007         1966 
TCGA-CN-6997 TCGA-CQ-5323 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-7063 TCGA-CQ-7065 
         429         1466          341          129         1750         1007 
TCGA-CQ-7069 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CR-6484 
        1274         1353         1960          785          391          354 
TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7382 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-7254 
        1191         1440          796         1665          641         1976 
TCGA-CV-7261 TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 
        1099          646          714          237          828          773 
TCGA-D6-6827 TCGA-D6-8569 TCGA-D6-A6EP TCGA-DQ-7588 TCGA-F7-A50J TCGA-HD-7229 
         568          128          424         1965          585            2 
TCGA-IQ-7630 TCGA-IQ-A61L TCGA-P3-A5QA TCGA-P3-A6T2 TCGA-QK-A6IG TCGA-QK-A6IJ 
         485          351         1726         1917          218          387 
TCGA-UF-A7JC 
         484 

$`11P GAIN WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
         102          462          415         1983          276          248 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5557 TCGA-BA-5558 
         722         1288         1762          520          623         1636 
TCGA-BA-5559 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 
        1747          644          451           63          384          113 
TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 
         236          895          855          622          918          850 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A6DL 
         351          216          182         1976          314          623 
TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7862 
         187         2878          278          133          558          536 
TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 
         423          687          638         1153          428          436 
TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 
        1955          624            4          799          721         1157 
TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 
         142         1230         1151          392          817          993 
TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 
         642         1250          395         1330          811         1268 
TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 
        1045          173         1980         1081         1977         1980 
TCGA-CN-5366 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 
        1966         1975          683          290          630          933 
TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 
         629          628          594          629           45          432 
TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 
          98         1970          202         1110          224          318 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A498 
         611          394          735          432           46          443 
TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U 
         535          391          904          645          225          526 
TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A6V1 TCGA-CN-A6V3 
         484          348          175          367          223          298 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 
        1207          654         1660         1422         1393         1399 
TCGA-CQ-5332 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 
         317         1253         1000         1057          985         1959 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7071 
        1959         1179         1560          509         1309          877 
TCGA-CQ-7072 TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CH 
        1950          707         1963          893          998          303 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 
         950         2562          358         1663         1152          799 
TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 
        1777         1521         1966         1050         1125         1971 
TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 
         514         1969          362          311          345          234 
TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7368 
         379          350          479         1956         1435         1245 
TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 
        1960          105         1979          759          889           30 
TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 
         972         1968         1036         1954          997         1430 
TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
        1951          392          907          913          946          908 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 
         898          930          216          156          181         1077 
TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 
         911         1472         1955          522         1950         3295 
TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 
        1438          584          546         1978         2886         2327 
TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 
        1958         2437          519          406          701         2641 
TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6436 TCGA-CV-6441 
        1478         1840          215         1315         1899         1970 
TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 
        1948         1969         1952         1959         3835         1948 
TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 
        1969         1966         1957         1969         1959         3837 
TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 
        1959         1970         1970         1936         1959         1939 
TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7242 
        1945         1987         1979         1952         1444         1095 
TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7406 TCGA-CV-7410 
         954          797         1967         1960         1974         1948 
TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 
        1955         1957         1947         1937         1973         1972 
TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45O 
        1937         1984         1958         1959         1981          851 
TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 
        1945         5480         1960         1940         1946         1954 
TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO 
        1722         1977         1970         1075          906         1959 
TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 
         670          110          606          685         1950          317 
TCGA-CX-7085 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 
         321          292          701           77          491          154 
TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO 
         106          539          376          483          232          435 
TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 
         368          389          338         1778         1081          516 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 
        1030          548          575          775          622          299 
TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 
         369          368          324          340         1131          490 
TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W 
         658           15           92            3          384           14 
TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 
          13            6          407           58          133          414 
TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 
         403          206            5           25           37           55 
TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 
          44           24           25           11           49           10 
TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E 
         111           33         1057          122          441          588 
TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T 
         360          412          440          360          224          552 
TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D 
         378          168           14           34          392           56 
TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QE 
         111          112          254          240          910         1559 
TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A64Z 
        1120         1954          578         1968          400          553 
TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6V9 TCGA-QK-A8Z7 
         357          245          228          225          567          198 
TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-UF-A718 
         149          135          135          157          168         1326 
TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA 
        1663         1319         1252         1278         1043         1894 
TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JS 
         735         1497          665          214          413 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 2                  3 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              1988               5480 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
               646                701 
[1] "2.0 - 1988.0 (646.0)" "3.0 - 5480.0 (701.0)"
[1] "hr=" "1.2"
D21V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  11P GAIN MUTATED         5       13        14        23         2         0
  11P GAIN WILD-TYPE      21       62        60       212        10         1
D21V3, multiclass
           clus
vv          11P GAIN MUTATED 11P GAIN WILD-TYPE
  STAGE I                  5                 21
  STAGE II                13                 62
  STAGE III               14                 60
  STAGE IVA               23                212
  STAGE IVB                2                 10
  STAGE IVC                0                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  11P GAIN MUTATED       6  19  16  16
  11P GAIN WILD-TYPE    41 108  78 146
D21V4, multiclass
       clus
vv      11P GAIN MUTATED 11P GAIN WILD-TYPE
  T0+T1                6                 41
  T2                  19                108
  T3                  16                 78
  T4                  16                146
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  11P GAIN MUTATED    29   8  13   2
  11P GAIN WILD-TYPE 141  55 139   6
D21V5, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  N0               29                141
  N1                8                 55
  N2               13                139
  N3                2                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  11P GAIN MUTATED    28   0   4
  11P GAIN WILD-TYPE 139   1  54
D21V6, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  M0               28                139
  M1                0                  1
  MX                4                 54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V7, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    17  43
  11P GAIN WILD-TYPE 115 313
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     17   43
  11P GAIN WILD-TYPE  115  313
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE               17                115
  MALE                 43                313
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  11P GAIN MUTATED                                      60
  11P GAIN WILD-TYPE                                   417
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  11P GAIN MUTATED                                                             0
  11P GAIN WILD-TYPE                                                           1
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  11P GAIN MUTATED                                                     0
  11P GAIN WILD-TYPE                                                  10
D21V8, multiclass
                                                             clus
vv                                                            11P GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     60
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        0
                                                             clus
vv                                                            11P GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      417
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                  1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V9, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    11  49
  11P GAIN WILD-TYPE  68 360
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     11   49
  11P GAIN WILD-TYPE   68  360
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  NO                11                 68
  YES               49                360
[1] 2 2
[1] FALSE
D21V10, continuous
D21V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11P GAIN MUTATED                                  0     4
  11P GAIN WILD-TYPE                                2     7
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11P GAIN MUTATED                           7    47
  11P GAIN WILD-TYPE                        37   368
D21V12, multiclass
                                  clus
vv                                 11P GAIN MUTATED 11P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           4                  7
  BLACK OR AFRICAN AMERICAN                       7                 37
  WHITE                                          47                368
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V13, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     2  55
  11P GAIN WILD-TYPE  22 376
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      2   55
  11P GAIN WILD-TYPE   22  376
                        clus
vv                       11P GAIN MUTATED 11P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                 22
  NOT HISPANIC OR LATINO               55                376
[1] 2 2
[1] FALSE

Clustering(22) Variable = 11Q GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                  0   1
  11Q GAIN MUTATED    41  15
  11Q GAIN WILD-TYPE 260  98
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                56                358 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                15                 98 
$`11Q GAIN MUTATED`
TCGA-BA-4075 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4225 
         283          725         1636          623          142          140 
TCGA-BB-7861 TCGA-CN-4731 TCGA-CN-4737 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5367 
         310          993          625         1988         1007         1966 
TCGA-CN-6018 TCGA-CN-6997 TCGA-CN-A63U TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-7063 
          45          429          526          341          129         1750 
TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4C7 TCGA-CQ-A4CE TCGA-CQ-A4CG 
        1007         1274         1950         1960          785          391 
TCGA-CR-6484 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7372 TCGA-CR-7383 TCGA-CV-6003 
         354         1191         1440          759         1954         1665 
TCGA-CV-6960 TCGA-CV-7235 TCGA-CV-7248 TCGA-CV-7261 TCGA-CV-7440 TCGA-CV-A6JY 
        1969         1952         1967         1099         1981          646 
TCGA-CV-A6JZ TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6826 TCGA-D6-6827 
         714          237          828          773          154          568 
TCGA-D6-A4ZB TCGA-D6-A6EP TCGA-DQ-5631 TCGA-F7-A50J TCGA-HD-7229 TCGA-IQ-7630 
         376          424          548          585            2          485 
TCGA-IQ-A61L TCGA-P3-A5QA TCGA-QK-A6IJ TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71D 
         351         1726          387         1326         1663         1252 
TCGA-UF-A7JC TCGA-UF-A7JJ 
         484          214 

$`11Q GAIN WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
         102          462          415         1983          276          248 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5557 TCGA-BA-5559 
         722         1288         1762          520          623         1747 
TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 
         190          644          451           63          384          113 
TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 
         236          895          855          622          918          850 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BB-4217 
         351          216          182         1976          314          187 
TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7862 TCGA-BB-7863 
        2878          278          133          558          536          423 
TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 
         687          638         1153          428          436         1955 
TCGA-BB-8601 TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 
         624            5            4          799          721         1157 
TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4733 
         142         1230         1151          392          817          642 
TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 
        1250          395         1960         1330          811         1268 
TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 
        1045          173         1980         1081         1977         1980 
TCGA-CN-5366 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 
        1966         1975          683          290          630          933 
TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6020 
         629          628          594          629          432           98 
TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 
        1970          202         1110          224          318          611 
TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A499 
         394          735          432           46          443          535 
TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63W 
         391          904          645          225          484          348 
TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-5324 
         175          367          223          298         1466         1207 
TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 
         654         1660         1422         1393         1399          317 
TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 
        1253         1000         1057          985         1959         1959 
TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-A4C6 
        1179         1560          509         1309          877         1353 
TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CH TCGA-CQ-A4CI 
         707         1963          893          998          303          950 
TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 
        2562          358         1663         1152          799         1777 
TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 
        1521         1966         1050         1125         1971          514 
TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6488 
        1969          362          311          345          234          379 
TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7368 TCGA-CR-7369 
         350          479         1956         1435         1245         1960 
TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 
         105         1979          889           30          972         1968 
TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 
        1036          796          997         1430         1951          392 
TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 
         907          913          946          908          898          930 
TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 
         216          156          181         1077          911         1472 
TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 
        1955          522         1950         3295         1438          584 
TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 
         546         1978         2886         2327         1958         2437 
TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 
         519          406          701         2641         1478         1840 
TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 
         215         1315          641         1899         1970         1948 
TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 
        1969         1952         1959         3835         1948         1969 
TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 
        1966         1957         1959         3837         1959         1970 
TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7180 
        1970         1936         1959         1939         1945         1987 
TCGA-CV-7183 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7250 
        1979         1444         1095          954          797         1960 
TCGA-CV-7254 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 
        1976         1974         1948         1955         1957         1947 
TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 
        1937         1973         1972         1937         1984         1958 
TCGA-CV-7435 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45Y TCGA-CV-A45Z 
        1959          851         1945         5480         1960         1940 
TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE 
        1946         1954         1722         1977         1970         1075 
TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6K0 TCGA-CV-A6K1 
         906         1959          670          110          606          685 
TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 
        1950          317          321          292          701           77 
TCGA-D6-6825 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A6EK TCGA-D6-A6EM 
         491          106          128          539          483          232 
TCGA-D6-A6EO TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 
         435          368          389          338         1778         1081 
TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 
         516         1030         1965          575          775          622 
TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 
         299          369          368          324          340         1131 
TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A61S TCGA-F7-A61V 
         490          658           15           92            3          384 
TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 
          14           13            6          407           58          133 
TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 
         414          403          206            5           25           37 
TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 
          55           44           24           25           11           49 
TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7631 TCGA-IQ-7632 
          10          111           33         1057          122          441 
TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61O TCGA-KU-A66S 
         588          360          412          440          360          224 
TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A 
         552          378          168           14           34          392 
TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 
          56          111          112          254          240          910 
TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T4 
        1559         1120         1954          578         1917         1968 
TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH 
         400          553          357          245          218          228 
TCGA-QK-A6II TCGA-QK-A6V9 TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB 
         225          567          198          149          135          135 
TCGA-QK-AA3J TCGA-QK-AA3K TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA 
         157          168         1319         1278         1043         1894 
TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JS 
         735         1497          665          413 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 2                  3 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              1988               5480 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             719.5              694.0 
[1] "2.0 - 1988.0 (719.5)" "3.0 - 5480.0 (694.0)"
[1] "hr=" "1.2"
D22V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  11Q GAIN MUTATED         6       14        14        30         1         0
  11Q GAIN WILD-TYPE      20       61        60       205        11         1
D22V3, multiclass
           clus
vv          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  STAGE I                  6                 20
  STAGE II                14                 61
  STAGE III               14                 60
  STAGE IVA               30                205
  STAGE IVB                1                 11
  STAGE IVC                0                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  11Q GAIN MUTATED       8  18  18  22
  11Q GAIN WILD-TYPE    39 109  76 140
D22V4, multiclass
       clus
vv      11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T0+T1                8                 39
  T2                  18                109
  T3                  18                 76
  T4                  22                140
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  11Q GAIN MUTATED    35   6  18   1
  11Q GAIN WILD-TYPE 135  57 134   7
D22V5, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  N0               35                135
  N1                6                 57
  N2               18                134
  N3                1                  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"
                    vv
clus                  M0  M1  MX
  11Q GAIN MUTATED    31   0   5
  11Q GAIN WILD-TYPE 136   1  53
D22V6, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  M0               31                136
  M1                0                  1
  MX                5                 53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V7, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    22  47
  11Q GAIN WILD-TYPE 110 309
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     22   47
  11Q GAIN WILD-TYPE  110  309
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE               22                110
  MALE                 47                309
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  11Q GAIN MUTATED                                      69
  11Q GAIN WILD-TYPE                                   408
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  11Q GAIN MUTATED                                                             0
  11Q GAIN WILD-TYPE                                                           1
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  11Q GAIN MUTATED                                                     0
  11Q GAIN WILD-TYPE                                                  10
D22V8, multiclass
                                                             clus
vv                                                            11Q GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     69
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        0
                                                             clus
vv                                                            11Q GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      408
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                  1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V9, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     8  61
  11Q GAIN WILD-TYPE  71 348
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      8   61
  11Q GAIN WILD-TYPE   71  348
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  NO                 8                 71
  YES               61                348
[1] 2 2
[1] FALSE
D22V10, continuous
D22V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11Q GAIN MUTATED                                  0     2
  11Q GAIN WILD-TYPE                                2     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11Q GAIN MUTATED                           7    56
  11Q GAIN WILD-TYPE                        37   359
D22V12, multiclass
                                  clus
vv                                 11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           2                  9
  BLACK OR AFRICAN AMERICAN                       7                 37
  WHITE                                          56                359
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V13, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     2  59
  11Q GAIN WILD-TYPE  22 372
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      2   59
  11Q GAIN WILD-TYPE   22  372
                        clus
vv                       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                 22
  NOT HISPANIC OR LATINO               59                372
[1] 2 2
[1] FALSE

Clustering(23) Variable = 12P GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                  0   1
  12P GAIN MUTATED    88  26
  12P GAIN WILD-TYPE 213  87
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               114                300 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                26                 87 
$`12P GAIN MUTATED`
TCGA-4P-AA8J TCGA-BA-5555 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IF TCGA-BA-A4IH 
         102          520         1747           63          895          622 
TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-7862 
         623          142         2878          278          140          536 
TCGA-BB-7870 TCGA-C9-A47Z TCGA-CN-4725 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4737 
        1153            5         1157         1151          392          625 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-5356 TCGA-CN-5359 TCGA-CN-5366 TCGA-CN-6012 
        1960         1330         1045         1980         1966          629 
TCGA-CN-6018 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6994 TCGA-CN-A499 
          45         1110          224          318          735          535 
TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A63T TCGA-CQ-5329 TCGA-CQ-5332 TCGA-CQ-6224 
         391          904          225         1422          317          985 
TCGA-CQ-7067 TCGA-CQ-A4CE TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-6467 TCGA-CR-6487 
         509          785         2562          358         1777          234 
TCGA-CR-6488 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7372 TCGA-CR-7379 TCGA-CR-7383 
         379         1435         1191          759         1036         1954 
TCGA-CR-7390 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CV-5430 TCGA-CV-5431 
         907          216          156          181         1955          522 
TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5440 TCGA-CV-5978 TCGA-CV-6003 TCGA-CV-6941 
        1950         3295         1978          215         1665         1959 
TCGA-CV-6945 TCGA-CV-7091 TCGA-CV-7102 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 
        1969         1959         1945         1095          954          797 
TCGA-CV-7248 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7435 
        1967         1976         1099         1955         1957         1959 
TCGA-CV-7440 TCGA-CV-A45R TCGA-CV-A45Z TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 
        1981         5480         1940          237          828          773 
TCGA-D6-6823 TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7589 
         701          338         1778          516         1965          575 
TCGA-DQ-7591 TCGA-DQ-7592 TCGA-F7-7848 TCGA-F7-A50J TCGA-F7-A61S TCGA-H7-7774 
         622          299         1131          585            3          407 
TCGA-H7-8501 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-A6HZ TCGA-KU-A66T 
          58            5           25           37          111          552 
TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67G TCGA-MZ-A7D7 
          14           34          392           56          112          240 
TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-QK-A64Z TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A8Z9 
        1917         1968          553          245          218          149 
TCGA-QK-A8ZA TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JC TCGA-UF-A7JH 
         135         1319         1278         1043          484          665 

$`12P GAIN WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
         462          283          415         1983          276          248 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 
         722         1288         1762          725          623         1636 
TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 
         190          644          451          384          113          236 
TCGA-BA-A4IG TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE 
         855          918          850          351          216          182 
TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BB-4217 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 
        1976          314          187          133          558          310 
TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 
         423          687          638          428          436         1955 
TCGA-BB-8601 TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4727 
         624            4          799          721          142         1230 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4740 
         817          993          642         1250          395          811 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5363 
        1268         1988         1007          173         1081         1977 
TCGA-CN-5365 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 
        1980         1966         1975          683          290          630 
TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6020 
         933          628          594          629          432           98 
TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6996 TCGA-CN-6997 
        1970          202          611          394          432          429 
TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49C TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W 
          46          443          645          526          484          348 
TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-5324 
         175          367          223          298         1466         1207 
TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 
         654         1660         1393         1399          341          129 
TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 
        1253         1000         1057         1959         1959         1179 
TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 
        1750         1560         1007         1309         1274          877 
TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB 
        1950         1353         1960          707         1963          893 
TCGA-CQ-A4CD TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5248 TCGA-CR-5249 
         998          391          303          950         1663         1152 
TCGA-CR-5250 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 
         799         1521         1966         1050         1125         1971 
TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 
         514         1969          362          311          345          354 
TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 
         350          479         1956         1440         1245         1960 
TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 
         105         1979          889           30          972         1968 
TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7391 
         796          997         1430         1951          392          913 
TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7401 TCGA-CR-7402 
         946          908          898          930         1077          911 
TCGA-CR-7404 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5441 TCGA-CV-5442 
        1472         1438          584          546         2886         2327 
TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 
        1958         2437          519          406          701         2641 
TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 
        1478         1840         1315          641         1899         1970 
TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6952 
        1948         1969         1952         3835         1948         1966 
TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7095 TCGA-CV-7097 
        1957         1969         1959         3837         1970         1970 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 
        1936         1959         1939         1987         1979         1952 
TCGA-CV-7238 TCGA-CV-7250 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7424 TCGA-CV-7427 
        1444         1960         1974         1948         1947         1937 
TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-A45O 
        1973         1972         1937         1984         1958          851 
TCGA-CV-A45Q TCGA-CV-A45Y TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A468 
        1945         1960         1946         1954         1722         1977 
TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU 
        1970         1075          906         1959          670          110 
TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 
         646          714          606          685         1950          317 
TCGA-CX-7085 TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 
         321          292           77          491          154          568 
TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM 
         106          128          539          376          483          232 
TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-DQ-5625 TCGA-DQ-5630 
         435          424          368          389         1081         1030 
TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
         548          775          369          368          324          340 
TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A61V TCGA-F7-A61W 
         490          658           15           92          384           14 
TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A 
          13            6          133          414          403          206 
TCGA-HD-7229 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 
           2           55           44           24           25           11 
TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 
          49           10           33         1057          485          122 
TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61L 
         441          588          360          412          440          351 
TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A67F TCGA-MZ-A6I9 
         360          224          378          168          111          254 
TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 
         910         1726         1559         1120         1954          578 
TCGA-P3-A6T8 TCGA-QK-A652 TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 
         400          357          228          225          387          567 
TCGA-QK-A8Z7 TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-UF-A718 TCGA-UF-A719 
         198          135          157          168         1326         1663 
TCGA-UF-A71D TCGA-UF-A7JA TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JJ TCGA-UF-A7JS 
        1252         1894          735         1497          214          413 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 3                  2 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              5480               3837 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               683                704 
[1] "3.0 - 5480.0 (683.0)" "2.0 - 3837.0 (704.0)"
[1] "hr=" "1.3"
D23V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  12P GAIN MUTATED         9       20        22        68         4         0
  12P GAIN WILD-TYPE      17       55        52       167         8         1
D23V3, multiclass
           clus
vv          12P GAIN MUTATED 12P GAIN WILD-TYPE
  STAGE I                  9                 17
  STAGE II                20                 55
  STAGE III               22                 52
  STAGE IVA               68                167
  STAGE IVB                4                  8
  STAGE IVC                0                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  12P GAIN MUTATED      13  38  28  45
  12P GAIN WILD-TYPE    34  89  66 117
D23V4, multiclass
       clus
vv      12P GAIN MUTATED 12P GAIN WILD-TYPE
  T0+T1               13                 34
  T2                  38                 89
  T3                  28                 66
  T4                  45                117
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  12P GAIN MUTATED    52  17  43   3
  12P GAIN WILD-TYPE 118  46 109   5
D23V5, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  N0               52                118
  N1               17                 46
  N2               43                109
  N3                3                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  12P GAIN MUTATED    42   0  18
  12P GAIN WILD-TYPE 125   1  40
D23V6, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  M0               42                125
  M1                0                  1
  MX               18                 40
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V7, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    32 107
  12P GAIN WILD-TYPE 100 249
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     32  107
  12P GAIN WILD-TYPE  100  249
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE               32                100
  MALE                107                249
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  12P GAIN MUTATED                                     137
  12P GAIN WILD-TYPE                                   340
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  12P GAIN MUTATED                                                             0
  12P GAIN WILD-TYPE                                                           1
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  12P GAIN MUTATED                                                     2
  12P GAIN WILD-TYPE                                                   8
D23V8, multiclass
                                                             clus
vv                                                            12P GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    137
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        2
                                                             clus
vv                                                            12P GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      340
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                  1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                          8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V9, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    23 116
  12P GAIN WILD-TYPE  56 293
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     23  116
  12P GAIN WILD-TYPE   56  293
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  NO                23                 56
  YES              116                293
[1] 2 2
[1] FALSE
D23V10, continuous
D23V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12P GAIN MUTATED                                  1     1
  12P GAIN WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12P GAIN MUTATED                          16   119
  12P GAIN WILD-TYPE                        28   296
D23V12, multiclass
                                  clus
vv                                 12P GAIN MUTATED 12P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  1
  ASIAN                                           1                 10
  BLACK OR AFRICAN AMERICAN                      16                 28
  WHITE                                         119                296
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V13, binary
                    cls
clus                   0   1
  12P GAIN MUTATED     5 125
  12P GAIN WILD-TYPE  19 306
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      5  125
  12P GAIN WILD-TYPE   19  306
                        clus
vv                       12P GAIN MUTATED 12P GAIN WILD-TYPE
  HISPANIC OR LATINO                    5                 19
  NOT HISPANIC OR LATINO              125                306
[1] 2 2
[1] FALSE

Clustering(24) Variable = 12Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                  0   1
  12Q GAIN MUTATED    54  16
  12Q GAIN WILD-TYPE 247  97
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                70                344 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                16                 97 
$`12Q GAIN MUTATED`
TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IF TCGA-BA-A6DL TCGA-BB-4223 TCGA-BB-4225 
        1747           63          895          623         2878          140 
TCGA-BB-7870 TCGA-C9-A47Z TCGA-CN-4725 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4737 
        1153            5         1157         1230         1151          625 
TCGA-CN-4739 TCGA-CN-5356 TCGA-CN-5359 TCGA-CN-6010 TCGA-CN-6012 TCGA-CN-6023 
        1330         1045         1980          630          629         1110 
TCGA-CN-6988 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A63T TCGA-CQ-5332 
         318          535          391          904          225          317 
TCGA-CQ-6224 TCGA-CQ-7067 TCGA-CQ-A4CE TCGA-CR-5247 TCGA-CR-6467 TCGA-CR-7365 
         985          509          785          358         1777         1191 
TCGA-CR-7379 TCGA-CR-7383 TCGA-CR-7399 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5434 
        1036         1954          181         1955          522         3295 
TCGA-CV-6941 TCGA-CV-7102 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 
        1959         1945         1095          954          797         1967 
TCGA-CV-7422 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45R TCGA-CV-A45Z TCGA-D6-6516 
        1957         1959         1981         5480         1940          773 
TCGA-D6-6823 TCGA-D6-A74Q TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7591 TCGA-F7-A50J 
         701          338         1965          575          622          585 
TCGA-F7-A61S TCGA-H7-7774 TCGA-HD-7753 TCGA-HD-A6HZ TCGA-KU-A66T TCGA-MT-A51W 
           3          407            5          111          552           14 
TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67G TCGA-P3-A6T4 TCGA-QK-A6IF TCGA-QK-A8Z9 
         392           56          112         1968          245          149 
TCGA-QK-A8ZA TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JC 
         135         1278         1043          484 

$`12Q GAIN WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 
         102          462          283          415         1983          276 
TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 
         248          722         1288         1762          520          725 
TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 
         623         1636          190          644          451          384 
TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 
         113          236          855          622          918          850 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A8YP 
         351          216          182         1976          314          142 
TCGA-BB-4217 TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 
         187          278          133          558          310          536 
TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 
         423          687          638          428          436         1955 
TCGA-BB-8601 TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4729 
         624            4          799          721          142          392 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4738 
         817          993          642         1250          395         1960 
TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5360 
         811         1268         1988         1007          173         1081 
TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 
        1977         1980         1966         1966         1975          683 
TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 
         290          933          628          594          629           45 
TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6989 
         432           98         1970          202          224          611 
TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 
         394          735          432          429           46          443 
TCGA-CN-A49C TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 
         645          526          484          348          175          367 
TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 
         223          298         1466         1207          654         1660 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 
        1422         1393         1399          341          129         1253 
TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 
        1000         1057         1959         1959         1179         1750 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 
        1560         1007         1309         1274          877         1950 
TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD 
        1353         1960          707         1963          893          998 
TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 
         391          303          950         2562         1663         1152 
TCGA-CR-5250 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 
         799         1521         1966         1050         1125         1971 
TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 
         514         1969          362          311          345          354 
TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 
         234          379          350          479         1956         1435 
TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 
        1440         1245         1960          105         1979          759 
TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7382 TCGA-CR-7385 
         889           30          972         1968          796          997 
TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 
        1430         1951          392          907          913          946 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7401 
         908          898          930          216          156         1077 
TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5432 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 
         911         1472         1950         1438          584          546 
TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 
        1978         2886         2327         1958         2437          519 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 
         406          701         2641         1478         1840          215 
TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 
        1315         1665          641         1899         1970         1948 
TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6952 
        1969         1952         3835         1948         1969         1966 
TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 
        1957         1969         1959         3837         1959         1970 
TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7180 TCGA-CV-7183 
        1970         1936         1959         1939         1987         1979 
TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7406 
        1952         1444         1960         1976         1099         1974 
TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 
        1948         1955         1947         1937         1973         1972 
TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A45Y 
        1937         1984         1958          851         1945         1960 
TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE 
        1946         1954         1722         1977         1970         1075 
TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ 
         906         1959          670          110          646          714 
TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 
         606          685         1950          317          321          237 
TCGA-CX-7219 TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 
         828          292           77          491          154          568 
TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM 
         106          128          539          376          483          232 
TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-DQ-5624 TCGA-DQ-5625 
         435          424          368          389         1778         1081 
TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7592 TCGA-DQ-7593 
         516         1030          548          775          299          369 
TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 
         368          324          340         1131          490          658 
TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 
          15           92          384           14           13            6 
TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 
          58          133          414          403          206            2 
TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 
          25           37           55           44           24           25 
TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 
          11           49           10           33         1057          485 
TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J 
         122          441          588          360          412          440 
TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51X 
         351          360          224          378          168           34 
TCGA-MT-A67F TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE 
         111          254          240          910         1726         1559 
TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T8 TCGA-QK-A64Z 
        1120         1954          578         1917          400          553 
TCGA-QK-A652 TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 
         357          218          228          225          387          567 
TCGA-QK-A8Z7 TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-UF-A718 TCGA-UF-A719 
         198          135          157          168         1326         1663 
TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A7JA TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH 
        1319         1252         1894          735         1497          665 
TCGA-UF-A7JJ TCGA-UF-A7JS 
         214          413 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 3                  2 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              5480               3837 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               779                686 
[1] "3.0 - 5480.0 (779.0)" "2.0 - 3837.0 (686.0)"
[1] "hr=" "1.3"
D24V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  12Q GAIN MUTATED         6       10        15        39         1         0
  12Q GAIN WILD-TYPE      20       65        59       196        11         1
D24V3, multiclass
           clus
vv          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  STAGE I                  6                 20
  STAGE II                10                 65
  STAGE III               15                 59
  STAGE IVA               39                196
  STAGE IVB                1                 11
  STAGE IVC                0                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  12Q GAIN MUTATED       9  19  18  26
  12Q GAIN WILD-TYPE    38 108  76 136
D24V4, multiclass
       clus
vv      12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T0+T1                9                 38
  T2                  19                108
  T3                  18                 76
  T4                  26                136
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  12Q GAIN MUTATED    36   9  23   0
  12Q GAIN WILD-TYPE 134  54 129   8
D24V5, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  N0               36                134
  N1                9                 54
  N2               23                129
  N3                0                  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"
                    vv
clus                  M0  M1  MX
  12Q GAIN MUTATED    24   0  11
  12Q GAIN WILD-TYPE 143   1  47
D24V6, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  M0               24                143
  M1                0                  1
  MX               11                 47
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V7, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    22  59
  12Q GAIN WILD-TYPE 110 297
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     22   59
  12Q GAIN WILD-TYPE  110  297
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE               22                110
  MALE                 59                297
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  12Q GAIN MUTATED                                      80
  12Q GAIN WILD-TYPE                                   397
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  12Q GAIN MUTATED                                                             0
  12Q GAIN WILD-TYPE                                                           1
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  12Q GAIN MUTATED                                                     1
  12Q GAIN WILD-TYPE                                                   9
D24V8, multiclass
                                                             clus
vv                                                            12Q GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     80
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        1
                                                             clus
vv                                                            12Q GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      397
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                  1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                          9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V9, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    19  62
  12Q GAIN WILD-TYPE  60 347
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     19   62
  12Q GAIN WILD-TYPE   60  347
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  NO                19                 60
  YES               62                347
[1] 2 2
[1] FALSE
D24V10, continuous
D24V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12Q GAIN MUTATED                                  0     1
  12Q GAIN WILD-TYPE                                2    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12Q GAIN MUTATED                           6    73
  12Q GAIN WILD-TYPE                        38   342
D24V12, multiclass
                                  clus
vv                                 12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           1                 10
  BLACK OR AFRICAN AMERICAN                       6                 38
  WHITE                                          73                342
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V13, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED     5  70
  12Q GAIN WILD-TYPE  19 361
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      5   70
  12Q GAIN WILD-TYPE   19  361
                        clus
vv                       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    5                 19
  NOT HISPANIC OR LATINO               70                361
[1] 2 2
[1] FALSE

Clustering(25) Variable = 13Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                  0   1
  13Q GAIN MUTATED    33  10
  13Q GAIN WILD-TYPE 268 103
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                43                371 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                10                103 
$`13Q GAIN MUTATED`
TCGA-BA-4075 TCGA-BA-6870 TCGA-BA-A4IF TCGA-BB-4225 TCGA-CN-4726 TCGA-CN-4728 
         283          451          895          140          142         1151 
TCGA-CN-4729 TCGA-CN-4737 TCGA-CN-4742 TCGA-CN-5370 TCGA-CN-6013 TCGA-CN-6989 
         392          625         1988         1975          628          611 
TCGA-CN-6996 TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CQ-7072 TCGA-CQ-A4CH 
         432          484          348          175         1950          303 
TCGA-CQ-A4CI TCGA-CR-5247 TCGA-CR-6484 TCGA-CR-6488 TCGA-CR-7365 TCGA-CR-7367 
         950          358          354          379         1191         1440 
TCGA-CR-7370 TCGA-CR-7390 TCGA-CV-5440 TCGA-CV-6003 TCGA-CV-7090 TCGA-CV-7095 
         105          907         1978         1665         3837         1970 
TCGA-CV-7097 TCGA-CV-7243 TCGA-D6-6823 TCGA-D6-8569 TCGA-DQ-5629 TCGA-DQ-5631 
        1970          954          701          128          516          548 
TCGA-F7-A50J TCGA-IQ-A61G TCGA-MT-A51W TCGA-MT-A51X TCGA-QK-A6IH TCGA-UF-A719 
         585          360           14           34          228         1663 
TCGA-UF-A7JH 
         665 

$`13Q GAIN WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
         102          462          415         1983          276          248 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 
         722         1288         1762          520          725          623 
TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6871 TCGA-BA-6872 
        1636         1747          190          644           63          384 
TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 
         113          236          855          622          918          850 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A6DL 
         351          216          182         1976          314          623 
TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-4228 
         142          187         2878          278          133          558 
TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 
         310          536          423          687          638         1153 
TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A47Z TCGA-C9-A480 
         428          436         1955          624            5            4 
TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4727 TCGA-CN-4730 TCGA-CN-4731 
         799          721         1157         1230          817          993 
TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 
         642         1250          395         1960         1330          811 
TCGA-CN-4741 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 
        1268         1007         1045          173         1980         1081 
TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5373 TCGA-CN-5374 
        1977         1980         1966         1966          683          290 
TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 
         630          933          629          594          629           45 
TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
         432           98         1970          202         1110          224 
TCGA-CN-6988 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 
         318          394          735          429           46          443 
TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U 
         535          391          904          645          225          526 
TCGA-CN-A641 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
         367          223          298         1466         1207          654 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 
        1660         1422         1393         1399          317          341 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 
         129         1253         1000         1057          985         1959 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 
        1959         1179         1750         1560         1007          509 
TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
        1309         1274          877         1353         1960          707 
TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CR-5243 
        1963          893          998          785          391         2562 
TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 
        1663         1152          799         1777         1521         1966 
TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 
        1050         1125         1971          514         1969          362 
TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 
         311          345          234          350          479         1956 
TCGA-CR-7364 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 
        1435         1245         1960         1979          759          889 
TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 
          30          972         1968         1036          796         1954 
TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7391 TCGA-CR-7392 
         997         1430         1951          392          913          946 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 
         908          898          930          216          156          181 
TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 
        1077          911         1472         1955          522         1950 
TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5441 TCGA-CV-5442 
        3295         1438          584          546         2886         2327 
TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 
        1958         2437          519          406          701         2641 
TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6436 
        1478         1840          215         1315          641         1899 
TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6942 
        1970         1948         1969         1952         1959         3835 
TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 
        1948         1969         1966         1957         1969         1959 
TCGA-CV-7091 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7180 
        1959         1936         1959         1939         1945         1987 
TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7245 TCGA-CV-7248 
        1979         1952         1444         1095          797         1967 
TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 
        1960         1976         1099         1974         1948         1955 
TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 
        1957         1947         1937         1973         1972         1937 
TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q 
        1984         1958         1959         1981          851         1945 
TCGA-CV-A45R TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A464 
        5480         1960         1940         1946         1954         1722 
TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT 
        1977         1970         1075          906         1959          670 
TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 
         110          646          714          606          685         1950 
TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6517 
         317          321          237          828          773          292 
TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-A4Z9 
          77          491          154          568          106          539 
TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ 
         376          483          232          435          424          368 
TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-7588 
         389          338         1778         1081         1030         1965 
TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 
         575          775          622          299          369          368 
TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G 
         324          340         1131          490          658           15 
TCGA-F7-A50I TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 
          92            3          384           14           13            6 
TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A 
         407           58          133          414          403          206 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 
           2            5           25           37           55           44 
TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ 
          24           25           11           49           10          111 
TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E 
          33         1057          485          122          441          588 
TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T 
         412          440          351          360          224          552 
TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G 
         378          168          392           56          111          112 
TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW 
         254          240          910         1726         1559         1120 
TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A64Z 
        1954          578         1917         1968          400          553 
TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 
         357          245          218          225          387          567 
TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K 
         198          149          135          135          157          168 
TCGA-UF-A718 TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA 
        1326         1319         1252         1278         1043         1894 
TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JJ TCGA-UF-A7JS 
         484          735         1497          214          413 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                14                  2 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              3837               5480 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
               585                725 
[1] "14.0 - 3837.0 (585.0)" "2.0 - 5480.0 (725.0)" 
[1] "hr=" "1.3"
D25V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  13Q GAIN MUTATED         1       12        10        23         2         0
  13Q GAIN WILD-TYPE      25       63        64       212        10         1
D25V3, multiclass
           clus
vv          13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  STAGE I                  1                 25
  STAGE II                12                 63
  STAGE III               10                 64
  STAGE IVA               23                212
  STAGE IVB                2                 10
  STAGE IVC                0                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  13Q GAIN MUTATED       2  18  10  18
  13Q GAIN WILD-TYPE    45 109  84 144
D25V4, multiclass
       clus
vv      13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  T0+T1                2                 45
  T2                  18                109
  T3                  10                 84
  T4                  18                144
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  13Q GAIN MUTATED    18   8  16   0
  13Q GAIN WILD-TYPE 152  55 136   8
D25V5, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  N0               18                152
  N1                8                 55
  N2               16                136
  N3                0                  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"
                    vv
clus                  M0  M1  MX
  13Q GAIN MUTATED    19   0   6
  13Q GAIN WILD-TYPE 148   1  52
D25V6, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  M0               19                148
  M1                0                  1
  MX                6                 52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V7, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED    16  39
  13Q GAIN WILD-TYPE 116 317
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     16   39
  13Q GAIN WILD-TYPE  116  317
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE               16                116
  MALE                 39                317
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  13Q GAIN MUTATED                                      54
  13Q GAIN WILD-TYPE                                   423
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  13Q GAIN MUTATED                                                             0
  13Q GAIN WILD-TYPE                                                           1
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  13Q GAIN MUTATED                                                     1
  13Q GAIN WILD-TYPE                                                   9
D25V8, multiclass
                                                             clus
vv                                                            13Q GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     54
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        1
                                                             clus
vv                                                            13Q GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      423
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                  1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                          9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V9, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED    14  41
  13Q GAIN WILD-TYPE  65 368
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     14   41
  13Q GAIN WILD-TYPE   65  368
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  NO                14                 65
  YES               41                368
[1] 2 2
[1] FALSE
D25V10, continuous
D25V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  13Q GAIN MUTATED                                  0     2
  13Q GAIN WILD-TYPE                                2     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  13Q GAIN MUTATED                           4    45
  13Q GAIN WILD-TYPE                        40   370
D25V12, multiclass
                                  clus
vv                                 13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           2                  9
  BLACK OR AFRICAN AMERICAN                       4                 40
  WHITE                                          45                370
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V13, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     4  47
  13Q GAIN WILD-TYPE  20 384
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      4   47
  13Q GAIN WILD-TYPE   20  384
                        clus
vv                       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                 20
  NOT HISPANIC OR LATINO               47                384
[1] 2 2
[1] FALSE

Clustering(26) Variable = 14Q GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                  0   1
  14Q GAIN MUTATED    78  36
  14Q GAIN WILD-TYPE 223  77
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
               114                300 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                36                 77 
$`14Q GAIN MUTATED`
TCGA-BA-4075 TCGA-BA-5555 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF 
         283          520          384          113          236          895 
TCGA-BA-A6DA TCGA-BA-A6DG TCGA-BA-A6DL TCGA-BB-8601 TCGA-C9-A47Z TCGA-C9-A480 
         351         1976          623          624            5            4 
TCGA-CN-4723 TCGA-CN-4730 TCGA-CN-4738 TCGA-CN-4740 TCGA-CN-5356 TCGA-CN-5363 
         721          817         1960          811         1045         1977 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-6021 TCGA-CN-6994 TCGA-CN-A499 TCGA-CN-A49A 
        1966         1966         1970          735          535          391 
TCGA-CN-A63T TCGA-CN-A63W TCGA-CQ-5323 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5334 
         225          348         1466         1422         1393          129 
TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7067 TCGA-CQ-7069 TCGA-CQ-7072 
         985         1959         1179          509         1274         1950 
TCGA-CQ-A4C6 TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6488 
        1353          785          391         1971          514          379 
TCGA-CR-6491 TCGA-CR-7367 TCGA-CR-7370 TCGA-CR-7372 TCGA-CR-7377 TCGA-CR-7379 
         350         1440          105          759         1968         1036 
TCGA-CR-7383 TCGA-CR-7388 TCGA-CR-7390 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5439 
        1954         1951          907         1950         3295          546 
TCGA-CV-5440 TCGA-CV-5444 TCGA-CV-5970 TCGA-CV-5973 TCGA-CV-5977 TCGA-CV-6003 
        1978         2437          406         2641         1840         1665 
TCGA-CV-6934 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6945 TCGA-CV-6954 TCGA-CV-7090 
        1948         1959         3835         1969         1957         3837 
TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7101 TCGA-CV-7180 TCGA-CV-7238 TCGA-CV-7243 
        1959         1970         1939         1987         1444          954 
TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7254 TCGA-CV-7418 TCGA-CV-7434 TCGA-CV-7440 
         797         1967         1976         1955         1958         1981 
TCGA-CV-A45Q TCGA-CV-A6JE TCGA-CV-A6K0 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 
        1945         1075          606          237          828          773 
TCGA-D6-6823 TCGA-D6-6825 TCGA-D6-A4Z9 TCGA-D6-A6EP TCGA-D6-A74Q TCGA-DQ-5625 
         701          491          539          424          338         1081 
TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-F7-A50I 
         516         1965          575          299          369           92 
TCGA-F7-A50J TCGA-HD-7753 TCGA-HD-7917 TCGA-HD-A6HZ TCGA-IQ-A61E TCGA-IQ-A61J 
         585            5           37          111          588          440 
TCGA-IQ-A61L TCGA-KU-A66T TCGA-MT-A51W TCGA-MT-A51X TCGA-P3-A6SX TCGA-P3-A6T4 
         351          552           14           34         1954         1968 
TCGA-QK-A6IG TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-AA3K TCGA-UF-A7JD TCGA-UF-A7JH 
         218          149          135          168          735          665 

$`14Q GAIN WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
         102          462          415         1983          276          248 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 
         722         1288         1762          725          623         1636 
TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-A4IG 
        1747          190          644          451           63          855 
TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DJ 
         622          918          850          216          182          314 
TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 
         142          187         2878          278          140          133 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 
         558          310          536          423          687          638 
TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-CN-4722 TCGA-CN-4725 
        1153          428          436         1955          799         1157 
TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4731 TCGA-CN-4733 
         142         1230         1151          392          993          642 
TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4739 TCGA-CN-4741 TCGA-CN-4742 
        1250          395          625         1330         1268         1988 
TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5365 TCGA-CN-5370 
        1007          173         1980         1081         1980         1975 
TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 
         683          290          630          933          629          628 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6022 
         594          629           45          432           98          202 
TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6996 
        1110          224          318          611          394          432 
TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63U 
         429           46          443          904          645          526 
TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5324 
         484          175          367          223          298         1207 
TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-6218 
         654         1660         1399          317          341         1253 
TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6228 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 
        1000         1057         1959         1750         1560         1007 
TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB 
        1309          877         1960          707         1963          893 
TCGA-CQ-A4CD TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 
         998          303          950         2562          358         1663 
TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 
        1152          799         1777         1521         1966         1050 
TCGA-CR-6473 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 
        1125         1969          362          311          345          354 
TCGA-CR-6487 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7368 
         234          479         1956         1435         1191         1245 
TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7382 
        1960         1979          889           30          972          796 
TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7389 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
         997         1430          392          913          946          908 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 
         898          930          216          156          181         1077 
TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5435 TCGA-CV-5436 
         911         1472         1955          522         1438          584 
TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5966 TCGA-CV-5971 TCGA-CV-5976 
        2886         2327         1958          519          701         1478 
TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6935 
         215         1315          641         1899         1970         1969 
TCGA-CV-6936 TCGA-CV-6943 TCGA-CV-6952 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7097 
        1952         1948         1966         1969         1959         1970 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7242 
        1936         1959         1945         1979         1952         1095 
TCGA-CV-7250 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7422 TCGA-CV-7424 
        1960         1099         1974         1948         1957         1947 
TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7435 
        1937         1973         1972         1937         1984         1959 
TCGA-CV-A45O TCGA-CV-A45R TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 
         851         5480         1960         1940         1946         1954 
TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT 
        1722         1977         1970          906         1959          670 
TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 
         110          646          714          685         1950          317 
TCGA-CX-7085 TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 
         321          292           77          154          568          106 
TCGA-D6-8569 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EQ 
         128          376          483          232          435          368 
TCGA-D6-A6ES TCGA-DQ-5624 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 
         389         1778         1030          548          775          622 
TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 
         368          324          340         1131          490          658 
TCGA-F7-A50G TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 
          15            3          384           14           13            6 
TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A 
         407           58          133          414          403          206 
TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 
           2           25           55           44           24           25 
TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 
          11           49           10           33         1057          485 
TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61O TCGA-KU-A66S 
         122          441          360          412          360          224 
TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G 
         378          168          392           56          111          112 
TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW 
         254          240          910         1726         1559         1120 
TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF 
         578         1917          400          553          357          245 
TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A8Z7 TCGA-QK-A8ZB 
         228          225          387          567          198          135 
TCGA-QK-AA3J TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E 
         157         1326         1663         1319         1252         1278 
TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JF TCGA-UF-A7JJ TCGA-UF-A7JS 
        1043         1894          484         1497          214          413 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 4                  2 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              3837               5480 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             804.0              645.5 
[1] "4.0 - 3837.0 (804.0)" "2.0 - 5480.0 (645.5)"
[1] "hr=" "1.3"
D26V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  14Q GAIN MUTATED        10       22        22        63         4         0
  14Q GAIN WILD-TYPE      16       53        52       172         8         1
D26V3, multiclass
           clus
vv          14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  STAGE I                 10                 16
  STAGE II                22                 53
  STAGE III               22                 52
  STAGE IVA               63                172
  STAGE IVB                4                  8
  STAGE IVC                0                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  14Q GAIN MUTATED      12  37  27  46
  14Q GAIN WILD-TYPE    35  90  67 116
D26V4, multiclass
       clus
vv      14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  T0+T1               12                 35
  T2                  37                 90
  T3                  27                 67
  T4                  46                116
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  14Q GAIN MUTATED    48  16  45   2
  14Q GAIN WILD-TYPE 122  47 107   6
D26V5, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  N0               48                122
  N1               16                 47
  N2               45                107
  N3                2                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  14Q GAIN MUTATED    41   0  18
  14Q GAIN WILD-TYPE 126   1  40
D26V6, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  M0               41                126
  M1                0                  1
  MX               18                 40
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V7, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    42  97
  14Q GAIN WILD-TYPE  90 259
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     42   97
  14Q GAIN WILD-TYPE   90  259
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE               42                 90
  MALE                 97                259
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  14Q GAIN MUTATED                                     139
  14Q GAIN WILD-TYPE                                   338
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  14Q GAIN MUTATED                                                             0
  14Q GAIN WILD-TYPE                                                           1
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  14Q GAIN MUTATED                                                     0
  14Q GAIN WILD-TYPE                                                  10
D26V8, multiclass
                                                             clus
vv                                                            14Q GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    139
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        0
                                                             clus
vv                                                            14Q GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      338
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                  1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V9, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    20 119
  14Q GAIN WILD-TYPE  59 290
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     20  119
  14Q GAIN WILD-TYPE   59  290
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  NO                20                 59
  YES              119                290
[1] 2 2
[1] FALSE
D26V10, continuous
D26V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  14Q GAIN MUTATED                                  1     3
  14Q GAIN WILD-TYPE                                1     8
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  14Q GAIN MUTATED                          19   110
  14Q GAIN WILD-TYPE                        25   305
D26V12, multiclass
                                  clus
vv                                 14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  1
  ASIAN                                           3                  8
  BLACK OR AFRICAN AMERICAN                      19                 25
  WHITE                                         110                305
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V13, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     6 124
  14Q GAIN WILD-TYPE  18 307
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      6  124
  14Q GAIN WILD-TYPE   18  307
                        clus
vv                       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    6                 18
  NOT HISPANIC OR LATINO              124                307
[1] 2 2
[1] FALSE

Clustering(27) Variable = 15Q GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                  0   1
  15Q GAIN MUTATED    42  16
  15Q GAIN WILD-TYPE 259  97
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                58                356 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                16                 97 
$`15Q GAIN MUTATED`
TCGA-BA-6871 TCGA-BA-6873 TCGA-BB-7861 TCGA-BB-8596 TCGA-C9-A47Z TCGA-CN-4729 
          63          113          310         1955            5          392 
TCGA-CN-4737 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-5356 TCGA-CN-5365 TCGA-CN-5366 
         625         1330          811         1045         1980         1966 
TCGA-CN-6010 TCGA-CN-A63U TCGA-CQ-6228 TCGA-CQ-7069 TCGA-CQ-A4C9 TCGA-CR-6474 
         630          526         1959         1274          707         1971 
TCGA-CR-6477 TCGA-CR-6484 TCGA-CR-6491 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7379 
         514          354          350         1435         1191         1036 
TCGA-CR-7390 TCGA-CV-6003 TCGA-CV-6934 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7101 
         907         1665         1948         3837         1959         1939 
TCGA-CV-7235 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7418 TCGA-CV-7427 TCGA-CV-7433 
        1952         1976         1099         1955         1937         1984 
TCGA-CV-A6JD TCGA-CV-A6K2 TCGA-D6-6516 TCGA-D6-8569 TCGA-D6-A6EM TCGA-DQ-5629 
        1970         1950          773          128          232          516 
TCGA-DQ-7588 TCGA-DQ-7589 TCGA-F7-7848 TCGA-H7-8501 TCGA-HD-7753 TCGA-HD-7917 
        1965          575         1131           58            5           37 
TCGA-HD-A633 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-IQ-7632 TCGA-MT-A67A TCGA-MT-A67G 
          49          111           33          441          392          112 
TCGA-QK-A6IH TCGA-QK-A8Z7 TCGA-UF-A71E TCGA-UF-A7JH 
         228          198         1278          665 

$`15Q GAIN WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 
         102          462          283          415         1983          276 
TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 
         248          722         1288         1762          520          725 
TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 
         623         1636         1747          190          644          451 
TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II 
         384          236          895          855          622          918 
TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DJ 
         850          351          216          182         1976          314 
TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 
         623          142          187         2878          278          140 
TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 
         133          558          536          423          687          638 
TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8601 TCGA-C9-A480 TCGA-CN-4722 
        1153          428          436          624            4          799 
TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4730 
         721         1157          142         1230         1151          817 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4741 
         993          642         1250          395         1960         1268 
TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 
        1988         1007          173         1980         1081         1977 
TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6012 
        1966         1975          683          290          933          629 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 
         628          594          629           45          432           98 
TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 
        1970          202         1110          224          318          611 
TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 
         394          735          432          429           46          443 
TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63V 
         535          391          904          645          225          484 
TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 
         348          175          367          223          298         1466 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 
        1207          654         1660         1422         1393         1399 
TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 
         317          341          129         1253         1000         1057 
TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 
         985         1959         1179         1750         1560         1007 
TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 
         509         1309          877         1950         1353         1960 
TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH 
        1963          893          998          785          391          303 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 
         950         2562          358         1663         1152          799 
TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6478 
        1777         1521         1966         1050         1125         1969 
TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6492 
         362          311          345          234          379          479 
TCGA-CR-6493 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 
        1956         1440         1245         1960          105         1979 
TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7382 
         759          889           30          972         1968          796 
TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7391 
        1954          997         1430         1951          392          913 
TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 
         946          908          898          930          216          156 
TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 
         181         1077          911         1472         1955          522 
TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 
        1950         3295         1438          584          546         1978 
TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 
        2886         2327         1958         2437          519          406 
TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 
         701         2641         1478         1840          215         1315 
TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6941 
         641         1899         1970         1969         1952         1959 
TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6960 
        3835         1948         1969         1966         1957         1969 
TCGA-CV-6961 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 
        1959         1970         1970         1936         1959         1945 
TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 
        1987         1979         1444         1095          954          797 
TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7422 TCGA-CV-7424 
        1967         1960         1974         1948         1957         1947 
TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7440 
        1973         1972         1937         1958         1959         1981 
TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 
         851         1945         5480         1960         1940         1946 
TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO 
        1954         1722         1977         1075          906         1959 
TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 
         670          110          646          714          606          685 
TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6517 TCGA-D6-6823 
         317          321          237          828          292          701 
TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-A4Z9 
          77          491          154          568          106          539 
TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES 
         376          483          435          424          368          389 
TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7590 
         338         1778         1081         1030          548          775 
TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
         622          299          369          368          324          340 
TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S 
         490          658           15           92          585            3 
TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8502 
         384           14           13            6          407          133 
TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-8224 
         414          403          206            2           25           55 
TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A634 TCGA-HL-7533 
          44           24           25           11           10         1057 
TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J 
         485          122          588          360          412          440 
TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 
         351          360          224          552          378          168 
TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67D TCGA-MT-A67F TCGA-MZ-A6I9 TCGA-MZ-A7D7 
          14           34           56          111          254          240 
TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 
         910         1726         1559         1120         1954          578 
TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF 
        1917         1968          400          553          357          245 
TCGA-QK-A6IG TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A8Z9 TCGA-QK-A8ZA 
         218          225          387          567          149          135 
TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71B 
         135          157          168         1326         1663         1319 
TCGA-UF-A71D TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF 
        1252         1043         1894          484          735         1497 
TCGA-UF-A7JJ TCGA-UF-A7JS 
         214          413 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 5                  2 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              3837               5480 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
               792                686 
[1] "5.0 - 3837.0 (792.0)" "2.0 - 5480.0 (686.0)"
[1] "hr=" "1.1"
D27V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  15Q GAIN MUTATED         4       11        10        35         3         0
  15Q GAIN WILD-TYPE      22       64        64       200         9         1
D27V3, multiclass
           clus
vv          15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  STAGE I                  4                 22
  STAGE II                11                 64
  STAGE III               10                 64
  STAGE IVA               35                200
  STAGE IVB                3                  9
  STAGE IVC                0                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  15Q GAIN MUTATED       7  19   6  31
  15Q GAIN WILD-TYPE    40 108  88 131
D27V4, multiclass
       clus
vv      15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  T0+T1                7                 40
  T2                  19                108
  T3                   6                 88
  T4                  31                131
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  15Q GAIN MUTATED    27  10  18   1
  15Q GAIN WILD-TYPE 143  53 134   7
D27V5, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  N0               27                143
  N1               10                 53
  N2               18                134
  N3                1                  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"
                    vv
clus                  M0  M1  MX
  15Q GAIN MUTATED    21   0   8
  15Q GAIN WILD-TYPE 146   1  50
D27V6, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  M0               21                146
  M1                0                  1
  MX                8                 50
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V7, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    22  47
  15Q GAIN WILD-TYPE 110 309
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     22   47
  15Q GAIN WILD-TYPE  110  309
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE               22                110
  MALE                 47                309
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  15Q GAIN MUTATED                                      67
  15Q GAIN WILD-TYPE                                   410
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  15Q GAIN MUTATED                                                             0
  15Q GAIN WILD-TYPE                                                           1
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  15Q GAIN MUTATED                                                     2
  15Q GAIN WILD-TYPE                                                   8
D27V8, multiclass
                                                             clus
vv                                                            15Q GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     67
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        2
                                                             clus
vv                                                            15Q GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      410
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                  1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                          8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V9, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    11  58
  15Q GAIN WILD-TYPE  68 351
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     11   58
  15Q GAIN WILD-TYPE   68  351
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  NO                11                 68
  YES               58                351
[1] 2 2
[1] FALSE
D27V10, continuous
D27V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  15Q GAIN MUTATED                                  0     2
  15Q GAIN WILD-TYPE                                2     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  15Q GAIN MUTATED                           5    59
  15Q GAIN WILD-TYPE                        39   356
D27V12, multiclass
                                  clus
vv                                 15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           2                  9
  BLACK OR AFRICAN AMERICAN                       5                 39
  WHITE                                          59                356
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V13, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     1  62
  15Q GAIN WILD-TYPE  23 369
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      1   62
  15Q GAIN WILD-TYPE   23  369
                        clus
vv                       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 23
  NOT HISPANIC OR LATINO               62                369
[1] 2 2
[1] FALSE

Clustering(28) Variable = 16P GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                  0   1
  16P GAIN MUTATED    60  24
  16P GAIN WILD-TYPE 241  89
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                84                330 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                24                 89 
$`16P GAIN MUTATED`
TCGA-BA-4075 TCGA-BA-5555 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 
         283          520         1747          190          644          451 
TCGA-BA-6871 TCGA-BA-6873 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A6DL TCGA-C9-A47Z 
          63          113          895          855          623            5 
TCGA-CN-4728 TCGA-CN-4730 TCGA-CN-4737 TCGA-CN-4739 TCGA-CN-5356 TCGA-CN-6013 
        1151          817          625         1330         1045          628 
TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-A49A TCGA-CN-A63U 
          98          202          735          432          391          526 
TCGA-CQ-5329 TCGA-CQ-6223 TCGA-CQ-7067 TCGA-CQ-7072 TCGA-CQ-A4CA TCGA-CR-5247 
        1422         1057          509         1950         1963          358 
TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6481 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7370 
         514         1969          311         1191         1440          105 
TCGA-CR-7372 TCGA-CR-7379 TCGA-CR-7388 TCGA-CR-7390 TCGA-CV-5431 TCGA-CV-5439 
         759         1036         1951          907          522          546 
TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-6003 TCGA-CV-6941 TCGA-CV-6945 TCGA-CV-6954 
        1840          215         1665         1959         1969         1957 
TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7180 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 
        1959         1970         1987         1095          954          797 
TCGA-CV-7248 TCGA-CV-7433 TCGA-CV-7435 TCGA-CV-A45R TCGA-CV-A461 TCGA-CV-A6JY 
        1967         1984         1959         5480         1954          646 
TCGA-CX-7086 TCGA-D6-6516 TCGA-D6-6823 TCGA-D6-8569 TCGA-D6-A6EP TCGA-DQ-5625 
         237          773          701          128          424         1081 
TCGA-DQ-5631 TCGA-DQ-7588 TCGA-F7-A50J TCGA-F7-A623 TCGA-HD-8634 TCGA-IQ-7631 
         548         1965          585            6           24          122 
TCGA-IQ-A61L TCGA-MT-A51W TCGA-P3-A6T4 TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A8Z7 
         351           14         1968          225          387          198 
TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH 
        1278         1043         1894          735         1497          665 

$`16P GAIN WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
         102          462          415         1983          276          248 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 
         722         1288         1762          725          623         1636 
TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA 
         384          236          622          918          850          351 
TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A8YP TCGA-BB-4217 
         216          182         1976          314          142          187 
TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 
        2878          278          140          133          558          310 
TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 
         536          423          687          638         1153          428 
TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 
         436         1955          624            4          799          721 
TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4729 TCGA-CN-4731 TCGA-CN-4733 
        1157          142         1230          392          993          642 
TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 
        1250          395         1960          811         1268         1988 
TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 
        1007          173         1980         1081         1977         1980 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 
        1966         1966         1975          683          290          630 
TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 
         933          629          594          629           45          432 
TCGA-CN-6021 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 
        1970         1110          224          318          611          394 
TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A49C 
         429           46          443          535          904          645 
TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A6V1 
         225          484          348          175          367          223 
TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5330 
         298         1466         1207          654         1660         1393 
TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 
        1399          317          341          129         1253         1000 
TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 
         985         1959         1959         1179         1750         1560 
TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 
        1007         1309         1274          877         1353         1960 
TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH 
         707          893          998          785          391          303 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 
         950         2562         1663         1152          799         1777 
TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6480 
        1521         1966         1050         1125         1971          362 
TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 
         345          354          234          379          350          479 
TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7373 
        1956         1435         1245         1960         1979          889 
TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 
          30          972         1968          796         1954          997 
TCGA-CR-7386 TCGA-CR-7389 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 
        1430          392          913          946          908          898 
TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 
         930          216          156          181         1077          911 
TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 
        1472         1955         1950         3295         1438          584 
TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 
        1978         2886         2327         1958         2437          519 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5979 TCGA-CV-6433 
         406          701         2641         1478         1315          641 
TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6942 
        1899         1970         1948         1969         1952         3835 
TCGA-CV-6943 TCGA-CV-6952 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7097 
        1948         1966         1969         1959         3837         1970 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7183 TCGA-CV-7235 
        1936         1959         1939         1945         1979         1952 
TCGA-CV-7238 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 
        1444         1960         1976         1099         1974         1948 
TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 
        1955         1957         1947         1937         1973         1972 
TCGA-CV-7432 TCGA-CV-7434 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A45Y 
        1937         1958         1981          851         1945         1960 
TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE 
        1940         1946         1722         1977         1970         1075 
TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JZ TCGA-CV-A6K0 
         906         1959          670          110          714          606 
TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7219 TCGA-D6-6517 
         685         1950          317          321          828          292 
TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-A4Z9 
          77          491          154          568          106          539 
TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EQ TCGA-D6-A6ES 
         376          483          232          435          368          389 
TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-7589 TCGA-DQ-7590 
         338         1778          516         1030          575          775 
TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
         622          299          369          368          324          340 
TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A61S 
        1131          490          658           15           92            3 
TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 
         384           14           13          407           58          133 
TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 
         414          403          206            2            5           25 
TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 
          37           55           44           25           11           49 
TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7632 
          10          111           33         1057          485          441 
TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61O TCGA-KU-A66S 
         588          360          412          440          360          224 
TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D 
         552          378          168           34          392           56 
TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QA 
         111          112          254          240          910         1726 
TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T8 
        1559         1120         1954          578         1917          400 
TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6V9 
         553          357          245          218          228          567 
TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-UF-A718 
         149          135          135          157          168         1326 
TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A7JC TCGA-UF-A7JJ TCGA-UF-A7JS 
        1663         1319         1252          484          214          413 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 5                  2 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              5480               3837 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
               747                684 
[1] "5.0 - 5480.0 (747.0)" "2.0 - 3837.0 (684.0)"
[1] "hr=" "1.1"
D28V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  16P GAIN MUTATED         6       15        16        43         4         0
  16P GAIN WILD-TYPE      20       60        58       192         8         1
D28V3, multiclass
           clus
vv          16P GAIN MUTATED 16P GAIN WILD-TYPE
  STAGE I                  6                 20
  STAGE II                15                 60
  STAGE III               16                 58
  STAGE IVA               43                192
  STAGE IVB                4                  8
  STAGE IVC                0                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  16P GAIN MUTATED       9  23  19  35
  16P GAIN WILD-TYPE    38 104  75 127
D28V4, multiclass
       clus
vv      16P GAIN MUTATED 16P GAIN WILD-TYPE
  T0+T1                9                 38
  T2                  23                104
  T3                  19                 75
  T4                  35                127
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  16P GAIN MUTATED    39  13  26   2
  16P GAIN WILD-TYPE 131  50 126   6
D28V5, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  N0               39                131
  N1               13                 50
  N2               26                126
  N3                2                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  16P GAIN MUTATED    33   0   8
  16P GAIN WILD-TYPE 134   1  50
D28V6, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  M0               33                134
  M1                0                  1
  MX                8                 50
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V7, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    25  78
  16P GAIN WILD-TYPE 107 278
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     25   78
  16P GAIN WILD-TYPE  107  278
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE               25                107
  MALE                 78                278
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  16P GAIN MUTATED                                     101
  16P GAIN WILD-TYPE                                   376
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  16P GAIN MUTATED                                                             0
  16P GAIN WILD-TYPE                                                           1
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  16P GAIN MUTATED                                                     2
  16P GAIN WILD-TYPE                                                   8
D28V8, multiclass
                                                             clus
vv                                                            16P GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    101
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        2
                                                             clus
vv                                                            16P GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      376
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                  1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                          8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V9, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    18  85
  16P GAIN WILD-TYPE  61 324
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     18   85
  16P GAIN WILD-TYPE   61  324
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  NO                18                 61
  YES               85                324
[1] 2 2
[1] FALSE
D28V10, continuous
D28V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16P GAIN MUTATED                                  0     1
  16P GAIN WILD-TYPE                                2    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16P GAIN MUTATED                          15    83
  16P GAIN WILD-TYPE                        29   332
D28V12, multiclass
                                  clus
vv                                 16P GAIN MUTATED 16P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           1                 10
  BLACK OR AFRICAN AMERICAN                      15                 29
  WHITE                                          83                332
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V13, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     7  85
  16P GAIN WILD-TYPE  17 346
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      7   85
  16P GAIN WILD-TYPE   17  346
                        clus
vv                       16P GAIN MUTATED 16P GAIN WILD-TYPE
  HISPANIC OR LATINO                    7                 17
  NOT HISPANIC OR LATINO               85                346
[1] 2 2
[1] FALSE

Clustering(29) Variable = 16Q GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                  0   1
  16Q GAIN MUTATED    56  26
  16Q GAIN WILD-TYPE 245  87
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                82                332 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                26                 87 
$`16Q GAIN MUTATED`
TCGA-BA-4075 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6873 TCGA-BA-A4IF 
         283          190          451           63          113          895 
TCGA-BA-A4IG TCGA-BA-A6DA TCGA-BA-A6DL TCGA-C9-A47Z TCGA-CN-4728 TCGA-CN-4730 
         855          351          623            5         1151          817 
TCGA-CN-4737 TCGA-CN-4739 TCGA-CN-6013 TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-6989 
         625         1330          628           98          202          611 
TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-A49A TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-6223 
         735          432          391         1422         1393         1057 
TCGA-CQ-7067 TCGA-CQ-7072 TCGA-CQ-A4CA TCGA-CR-5247 TCGA-CR-6477 TCGA-CR-6478 
         509         1950         1963          358          514         1969 
TCGA-CR-7365 TCGA-CR-7372 TCGA-CR-7374 TCGA-CR-7379 TCGA-CR-7388 TCGA-CR-7390 
        1191          759           30         1036         1951          907 
TCGA-CV-5431 TCGA-CV-5439 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 
         522          546         1840          215         1315         1665 
TCGA-CV-6941 TCGA-CV-6945 TCGA-CV-6954 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7099 
        1959         1969         1957         1959         1970         1936 
TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 
        1945         1987         1095          954          797         1967 
TCGA-CV-7406 TCGA-CV-7433 TCGA-CV-7435 TCGA-CV-A45R TCGA-CV-A6JY TCGA-D6-6516 
        1974         1984         1959         5480          646          773 
TCGA-D6-6823 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A6EP TCGA-DQ-5631 TCGA-DQ-7588 
         701          106          128          424          548         1965 
TCGA-F7-A50J TCGA-F7-A623 TCGA-HD-7753 TCGA-HD-8314 TCGA-HD-8634 TCGA-IQ-7631 
         585            6            5           44           24          122 
TCGA-IQ-A61L TCGA-MT-A51W TCGA-MT-A51X TCGA-P3-A6T4 TCGA-QK-A6IJ TCGA-QK-A8Z7 
         351           14           34         1968          387          198 
TCGA-UF-A7JA TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH 
        1894          735         1497          665 

$`16Q GAIN WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
         102          462          415         1983          276          248 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 
         722         1288         1762          520          725          623 
TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6869 TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A4IH 
        1636         1747          644          384          236          622 
TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DJ 
         918          850          216          182         1976          314 
TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 
         142          187         2878          278          140          133 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 
         558          310          536          423          687          638 
TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A480 
        1153          428          436         1955          624            4 
TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4729 
         799          721         1157          142         1230          392 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4740 
         993          642         1250          395         1960          811 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 
        1268         1988         1007         1045          173         1980 
TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 
        1081         1977         1980         1966         1966         1975 
TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6016 
         683          290          630          933          629          594 
TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6021 TCGA-CN-6023 TCGA-CN-6024 
         629           45          432         1970         1110          224 
TCGA-CN-6988 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A499 
         318          394          429           46          443          535 
TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W 
         904          645          225          526          484          348 
TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-5324 
         175          367          223          298         1466         1207 
TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 
         654         1660         1399          317          341          129 
TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 
        1253         1000          985         1959         1959         1179 
TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 
        1750         1560         1007         1309         1274          877 
TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE 
        1353         1960          707          893          998          785 
TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 
         391          303          950         2562         1663         1152 
TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 
         799         1777         1521         1966         1050         1125 
TCGA-CR-6474 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 
        1971          362          311          345          354          234 
TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7367 
         379          350          479         1956         1435         1440 
TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7373 TCGA-CR-7376 
        1245         1960          105         1979          889          972 
TCGA-CR-7377 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7389 
        1968          796         1954          997         1430          392 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 
         913          946          908          898          930          216 
TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 
         156          181         1077          911         1472         1955 
TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5440 TCGA-CV-5441 
        1950         3295         1438          584         1978         2886 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 
        2327         1958         2437          519          406          701 
TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 
        2641         1478          641         1899         1970         1948 
TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6952 TCGA-CV-6960 
        1969         1952         3835         1948         1966         1969 
TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7097 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7183 
        1959         3837         1970         1959         1939         1979 
TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7410 
        1952         1444         1960         1976         1099         1948 
TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 
        1955         1957         1947         1937         1973         1972 
TCGA-CV-7432 TCGA-CV-7434 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A45Y 
        1937         1958         1981          851         1945         1960 
TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD 
        1940         1946         1954         1722         1977         1970 
TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JZ 
        1075          906         1959          670          110          714 
TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 
         606          685         1950          317          321          237 
TCGA-CX-7219 TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 
         828          292           77          491          154          568 
TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EQ 
         539          376          483          232          435          368 
TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 
         389          338         1778         1081          516         1030 
TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 
         575          775          622          299          369          368 
TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G 
         324          340         1131          490          658           15 
TCGA-F7-A50I TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-H7-7774 
          92            3          384           14           13          407 
TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 
          58          133          414          403          206            2 
TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 
          25           37           55           25           11           49 
TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7632 
          10          111           33         1057          485          441 
TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61O TCGA-KU-A66S 
         588          360          412          440          360          224 
TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F 
         552          378          168          392           56          111 
TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE 
         112          254          240          910         1726         1559 
TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T8 TCGA-QK-A64Z 
        1120         1954          578         1917          400          553 
TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6V9 
         357          245          218          228          225          567 
TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-UF-A718 
         149          135          135          157          168         1326 
TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JC 
        1663         1319         1252         1278         1043          484 
TCGA-UF-A7JJ TCGA-UF-A7JS 
         214          413 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 5                  2 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              5480               3837 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
               735                686 
[1] "5.0 - 5480.0 (735.0)" "2.0 - 3837.0 (686.0)"
[1] "hr=" "1.2"
D29V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  16Q GAIN MUTATED         7       18        15        45         4         0
  16Q GAIN WILD-TYPE      19       57        59       190         8         1
D29V3, multiclass
           clus
vv          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  STAGE I                  7                 19
  STAGE II                18                 57
  STAGE III               15                 59
  STAGE IVA               45                190
  STAGE IVB                4                  8
  STAGE IVC                0                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  16Q GAIN MUTATED      12  27  19  33
  16Q GAIN WILD-TYPE    35 100  75 129
D29V4, multiclass
       clus
vv      16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T0+T1               12                 35
  T2                  27                100
  T3                  19                 75
  T4                  33                129
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  16Q GAIN MUTATED    37  12  31   2
  16Q GAIN WILD-TYPE 133  51 121   6
D29V5, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  N0               37                133
  N1               12                 51
  N2               31                121
  N3                2                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  16Q GAIN MUTATED    32   0   8
  16Q GAIN WILD-TYPE 135   1  50
D29V6, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  M0               32                135
  M1                0                  1
  MX                8                 50
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V7, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    31  73
  16Q GAIN WILD-TYPE 101 283
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     31   73
  16Q GAIN WILD-TYPE  101  283
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE               31                101
  MALE                 73                283
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  16Q GAIN MUTATED                                     102
  16Q GAIN WILD-TYPE                                   375
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  16Q GAIN MUTATED                                                             0
  16Q GAIN WILD-TYPE                                                           1
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  16Q GAIN MUTATED                                                     2
  16Q GAIN WILD-TYPE                                                   8
D29V8, multiclass
                                                             clus
vv                                                            16Q GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    102
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        2
                                                             clus
vv                                                            16Q GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      375
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                  1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                          8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V9, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    18  86
  16Q GAIN WILD-TYPE  61 323
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     18   86
  16Q GAIN WILD-TYPE   61  323
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  NO                18                 61
  YES               86                323
[1] 2 2
[1] FALSE
D29V10, continuous
D29V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16Q GAIN MUTATED                                  0     1
  16Q GAIN WILD-TYPE                                2    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16Q GAIN MUTATED                          14    85
  16Q GAIN WILD-TYPE                        30   330
D29V12, multiclass
                                  clus
vv                                 16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           1                 10
  BLACK OR AFRICAN AMERICAN                      14                 30
  WHITE                                          85                330
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V13, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     7  87
  16Q GAIN WILD-TYPE  17 344
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      7   87
  16Q GAIN WILD-TYPE   17  344
                        clus
vv                       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    7                 17
  NOT HISPANIC OR LATINO               87                344
[1] 2 2
[1] FALSE

Clustering(30) Variable = 17P GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                  0   1
  17P GAIN MUTATED    42  13
  17P GAIN WILD-TYPE 259 100
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                55                359 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                13                100 
$`17P GAIN MUTATED`
TCGA-BA-4075 TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BB-4225 TCGA-BB-8601 
         283          384          236          895          140          624 
TCGA-C9-A47Z TCGA-CN-4728 TCGA-CN-5356 TCGA-CN-5366 TCGA-CN-5370 TCGA-CN-6023 
           5         1151         1045         1966         1975         1110 
TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-A63U TCGA-CQ-5329 TCGA-CQ-6229 TCGA-CQ-7072 
         611          735          526         1422         1179         1950 
TCGA-CQ-A4CE TCGA-CR-5247 TCGA-CR-6467 TCGA-CR-6478 TCGA-CR-6488 TCGA-CR-7365 
         785          358         1777         1969          379         1191 
TCGA-CR-7370 TCGA-CR-7383 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5434 
         105         1954         1472         1955         1950         3295 
TCGA-CV-5440 TCGA-CV-5977 TCGA-CV-6003 TCGA-CV-6941 TCGA-CV-6945 TCGA-CV-7095 
        1978         1840         1665         1959         1969         1970 
TCGA-CV-7101 TCGA-CV-7248 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-A45R TCGA-CV-A6JZ 
        1939         1967         1976         1099         5480          714 
TCGA-D6-A6EP TCGA-F7-8298 TCGA-F7-A50I TCGA-HD-7917 TCGA-HD-A6HZ TCGA-IQ-A61L 
         424          490           92           37          111          351 
TCGA-IQ-A61O TCGA-MZ-A7D7 TCGA-QK-A6IG TCGA-QK-A8Z7 TCGA-UF-A719 TCGA-UF-A71E 
         360          240          218          198         1663         1278 
TCGA-UF-A7JH 
         665 

$`17P GAIN WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
         102          462          415         1983          276          248 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 
         722         1288         1762          520          725          623 
TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 
        1636         1747          190          644          451           63 
TCGA-BA-6873 TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA 
         113          855          622          918          850          351 
TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP 
         216          182         1976          314          623          142 
TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 
         187         2878          278          133          558          310 
TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 
         536          423          687          638         1153          428 
TCGA-BB-7872 TCGA-BB-8596 TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 
         436         1955            4          799          721         1157 
TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
         142         1230          392          817          993          642 
TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 
        1250          395          625         1960         1330          811 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 
        1268         1988         1007          173         1980         1081 
TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5367 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 
        1977         1980         1966          683          290          630 
TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 
         933          629          628          594          629           45 
TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6988 
         432           98         1970          202          224          318 
TCGA-CN-6992 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A499 
         394          432          429           46          443          535 
TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63W 
         391          904          645          225          484          348 
TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-5324 
         175          367          223          298         1466         1207 
TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 
         654         1660         1393         1399          317          341 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 
         129         1253         1000         1057          985         1959 
TCGA-CQ-6228 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 
        1959         1750         1560         1007          509         1309 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CA 
        1274          877         1353         1960          707         1963 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 
         893          998          391          303          950         2562 
TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 
        1663         1152          799         1521         1966         1050 
TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 
        1125         1971          514          362          311          345 
TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 
         354          234          350          479         1956         1435 
TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 
        1440         1245         1960         1979          759          889 
TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7385 
          30          972         1968         1036          796          997 
TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 
        1430         1951          392          907          913          946 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 
         908          898          930          216          156          181 
TCGA-CR-7401 TCGA-CR-7402 TCGA-CV-5431 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 
        1077          911          522         1438          584          546 
TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 
        2886         2327         1958         2437          519          406 
TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6433 
         701         2641         1478          215         1315          641 
TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6942 
        1899         1970         1948         1969         1952         3835 
TCGA-CV-6943 TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 
        1948         1966         1957         1969         1959         3837 
TCGA-CV-7091 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7180 
        1959         1970         1936         1959         1945         1987 
TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 
        1979         1952         1444         1095          954          797 
TCGA-CV-7250 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 
        1960         1974         1948         1955         1957         1947 
TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 
        1937         1973         1972         1937         1984         1958 
TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A45Y TCGA-CV-A45Z 
        1959         1981          851         1945         1960         1940 
TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE 
        1946         1954         1722         1977         1970         1075 
TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6K0 
         906         1959          670          110          646          606 
TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 
         685         1950          317          321          237          828 
TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 
         773          292          701           77          491          154 
TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK 
         568          106          128          539          376          483 
TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 
         232          435          368          389          338         1778 
TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 
        1081          516         1030          548         1965          575 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 
         775          622          299          369          368          324 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50J TCGA-F7-A61S 
         340         1131          658           15          585            3 
TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8501 
         384           14           13            6          407           58 
TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 
         133          414          403          206            2            5 
TCGA-HD-7754 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 
          25           55           44           24           25           11 
TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 
          49           10           33         1057          485          122 
TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J TCGA-KU-A66S 
         441          588          360          412          440          224 
TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A 
         552          378          168           14           34          392 
TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QA 
          56          111          112          254          910         1726 
TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T4 
        1559         1120         1954          578         1917         1968 
TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IH TCGA-QK-A6II 
         400          553          357          245          228          225 
TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J 
         387          567          149          135          135          157 
TCGA-QK-AA3K TCGA-UF-A718 TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A7J9 TCGA-UF-A7JA 
         168         1326         1319         1252         1043         1894 
TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JJ TCGA-UF-A7JS 
         484          735         1497          214          413 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 5                  2 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              5480               3837 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              1099                658 
[1] "5.0 - 5480.0 (1099.0)" "2.0 - 3837.0 (658.0)" 
[1] "hr=" "1.6"
D30V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  17P GAIN MUTATED         2       13        16        25         0         0
  17P GAIN WILD-TYPE      24       62        58       210        12         1
D30V3, multiclass
           clus
vv          17P GAIN MUTATED 17P GAIN WILD-TYPE
  STAGE I                  2                 24
  STAGE II                13                 62
  STAGE III               16                 58
  STAGE IVA               25                210
  STAGE IVB                0                 12
  STAGE IVC                0                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  17P GAIN MUTATED       2  22  16  16
  17P GAIN WILD-TYPE    45 105  78 146
D30V4, multiclass
       clus
vv      17P GAIN MUTATED 17P GAIN WILD-TYPE
  T0+T1                2                 45
  T2                  22                105
  T3                  16                 78
  T4                  16                146
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  17P GAIN MUTATED    23  11  18   0
  17P GAIN WILD-TYPE 147  52 134   8
D30V5, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  N0               23                147
  N1               11                 52
  N2               18                134
  N3                0                  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"
                    vv
clus                  M0  M1  MX
  17P GAIN MUTATED    23   0   7
  17P GAIN WILD-TYPE 144   1  51
D30V6, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  M0               23                144
  M1                0                  1
  MX                7                 51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V7, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    13  51
  17P GAIN WILD-TYPE 119 305
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     13   51
  17P GAIN WILD-TYPE  119  305
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE               13                119
  MALE                 51                305
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  17P GAIN MUTATED                                      61
  17P GAIN WILD-TYPE                                   416
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  17P GAIN MUTATED                                                             1
  17P GAIN WILD-TYPE                                                           0
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  17P GAIN MUTATED                                                     2
  17P GAIN WILD-TYPE                                                   8
D30V8, multiclass
                                                             clus
vv                                                            17P GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     61
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        2
                                                             clus
vv                                                            17P GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      416
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                  0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                          8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V9, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    11  53
  17P GAIN WILD-TYPE  68 356
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     11   53
  17P GAIN WILD-TYPE   68  356
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  NO                11                 68
  YES               53                356
[1] 2 2
[1] FALSE
D30V10, continuous
D30V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17P GAIN MUTATED                                  0     1
  17P GAIN WILD-TYPE                                2    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17P GAIN MUTATED                           8    52
  17P GAIN WILD-TYPE                        36   363
D30V12, multiclass
                                  clus
vv                                 17P GAIN MUTATED 17P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           1                 10
  BLACK OR AFRICAN AMERICAN                       8                 36
  WHITE                                          52                363
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V13, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     6  53
  17P GAIN WILD-TYPE  18 378
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      6   53
  17P GAIN WILD-TYPE   18  378
                        clus
vv                       17P GAIN MUTATED 17P GAIN WILD-TYPE
  HISPANIC OR LATINO                    6                 18
  NOT HISPANIC OR LATINO               53                378
[1] 2 2
[1] FALSE

Clustering(31) Variable = 17Q GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                  0   1
  17Q GAIN MUTATED    49  19
  17Q GAIN WILD-TYPE 252  94
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                68                346 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                19                 94 
$`17Q GAIN MUTATED`
TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BB-4225 TCGA-BB-8601 TCGA-C9-A47Z 
         384          236          895          140          624            5 
TCGA-CN-4728 TCGA-CN-4737 TCGA-CN-5356 TCGA-CN-5359 TCGA-CN-5366 TCGA-CN-5370 
        1151          625         1045         1980         1966         1975 
TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-A63U 
         202         1110          318          611          735          526 
TCGA-CN-A63W TCGA-CN-A641 TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4C9 TCGA-CQ-A4CE 
         348          367         1274         1950          707          785 
TCGA-CR-5247 TCGA-CR-6467 TCGA-CR-6473 TCGA-CR-6478 TCGA-CR-7365 TCGA-CR-7370 
         358         1777         1125         1969         1191          105 
TCGA-CR-7383 TCGA-CR-7390 TCGA-CR-7399 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5432 
        1954          907          181         1472         1955         1950 
TCGA-CV-5440 TCGA-CV-5970 TCGA-CV-5977 TCGA-CV-6003 TCGA-CV-6941 TCGA-CV-6945 
        1978          406         1840         1665         1959         1969 
TCGA-CV-6952 TCGA-CV-7095 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7248 TCGA-CV-7250 
        1966         1970         1939         1945         1967         1960 
TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7424 TCGA-CV-A45R TCGA-CV-A6JZ TCGA-D6-8569 
        1976         1099         1947         5480          714          128 
TCGA-D6-A6EP TCGA-DQ-7588 TCGA-H7-8502 TCGA-HD-7753 TCGA-HD-7917 TCGA-HD-A6HZ 
         424         1965          133            5           37          111 
TCGA-IQ-A61L TCGA-IQ-A61O TCGA-MT-A67D TCGA-QK-A6IG TCGA-QK-A8Z7 TCGA-QK-AA3K 
         351          360           56          218          198          168 
TCGA-UF-A71E TCGA-UF-A7JH 
        1278          665 

$`17Q GAIN WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 
         102          462          283          415         1983          276 
TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 
         248          722         1288         1762          520          725 
TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 
         623         1636         1747          190          644          451 
TCGA-BA-6871 TCGA-BA-6873 TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 
          63          113          855          622          918          850 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A6DL 
         351          216          182         1976          314          623 
TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-4228 
         142          187         2878          278          133          558 
TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 
         310          536          423          687          638         1153 
TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 
         428          436         1955            4          799          721 
TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 
        1157          142         1230          392          817          993 
TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 
         642         1250          395         1960         1330          811 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5363 
        1268         1988         1007          173         1081         1977 
TCGA-CN-5365 TCGA-CN-5367 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 
        1980         1966          683          290          630          933 
TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 
         629          628          594          629           45          432 
TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6996 TCGA-CN-6997 
          98         1970          224          394          432          429 
TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C 
          46          443          535          391          904          645 
TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 
         225          484          175          223          298         1466 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 
        1207          654         1660         1422         1393         1399 
TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 
         317          341          129         1253         1000         1057 
TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 
         985         1959         1959         1179         1750         1560 
TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 
        1007          509         1309          877         1353         1960 
TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI 
        1963          893          998          391          303          950 
TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6470 TCGA-CR-6471 
        2562         1663         1152          799         1521         1966 
TCGA-CR-6472 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 
        1050         1971          514          362          311          345 
TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 
         354          234          379          350          479         1956 
TCGA-CR-7364 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7372 
        1435         1440         1245         1960         1979          759 
TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 
         889           30          972         1968         1036          796 
TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7391 TCGA-CR-7392 
         997         1430         1951          392          913          946 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7401 
         908          898          930          216          156         1077 
TCGA-CR-7402 TCGA-CV-5431 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 
         911          522         3295         1438          584          546 
TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5971 
        2886         2327         1958         2437          519          701 
TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6436 
        2641         1478          215         1315          641         1899 
TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6942 TCGA-CV-6943 
        1970         1948         1969         1952         3835         1948 
TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7097 
        1957         1969         1959         3837         1959         1970 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 
        1936         1959         1987         1979         1952         1444 
TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 
        1095          954          797         1974         1948         1955 
TCGA-CV-7422 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 
        1957         1937         1973         1972         1937         1984 
TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A45Y 
        1958         1959         1981          851         1945         1960 
TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD 
        1940         1946         1954         1722         1977         1970 
TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY 
        1075          906         1959          670          110          646 
TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 
         606          685         1950          317          321          237 
TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 
         828          773          292          701           77          491 
TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK 
         154          568          106          539          376          483 
TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 
         232          435          368          389          338         1778 
TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7589 TCGA-DQ-7590 
        1081          516         1030          548          575          775 
TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
         622          299          369          368          324          340 
TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J 
        1131          490          658           15           92          585 
TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-7774 
           3          384           14           13            6          407 
TCGA-H7-8501 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7754 
          58          414          403          206            2           25 
TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 
          55           44           24           25           11           49 
TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 
          10           33         1057          485          122          441 
TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J TCGA-KU-A66S TCGA-KU-A66T 
         588          360          412          440          224          552 
TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67F 
         378          168           14           34          392          111 
TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE 
         112          254          240          910         1726         1559 
TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-P3-A6T8 
        1120         1954          578         1917         1968          400 
TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ 
         553          357          245          228          225          387 
TCGA-QK-A6V9 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-UF-A718 
         567          149          135          135          157         1326 
TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC 
        1663         1319         1252         1043         1894          484 
TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JJ TCGA-UF-A7JS 
         735         1497          214          413 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 5                  2 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              5480               3837 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               901                664 
[1] "5.0 - 5480.0 (901.0)" "2.0 - 3837.0 (664.0)"
[1] "hr=" "1.2"
D31V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  17Q GAIN MUTATED         2       12        18        38         0         1
  17Q GAIN WILD-TYPE      24       63        56       197        12         0
D31V3, multiclass
           clus
vv          17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  STAGE I                  2                 24
  STAGE II                12                 63
  STAGE III               18                 56
  STAGE IVA               38                197
  STAGE IVB                0                 12
  STAGE IVC                1                  0
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  17Q GAIN MUTATED       2  23  22  24
  17Q GAIN WILD-TYPE    45 104  72 138
D31V4, multiclass
       clus
vv      17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T0+T1                2                 45
  T2                  23                104
  T3                  22                 72
  T4                  24                138
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  17Q GAIN MUTATED    25  14  28   0
  17Q GAIN WILD-TYPE 145  49 124   8
D31V5, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  N0               25                145
  N1               14                 49
  N2               28                124
  N3                0                  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"
                    vv
clus                  M0  M1  MX
  17Q GAIN MUTATED    28   1  10
  17Q GAIN WILD-TYPE 139   0  48
D31V6, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  M0               28                139
  M1                1                  0
  MX               10                 48
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V7, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    17  64
  17Q GAIN WILD-TYPE 115 292
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     17   64
  17Q GAIN WILD-TYPE  115  292
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE               17                115
  MALE                 64                292
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  17Q GAIN MUTATED                                      78
  17Q GAIN WILD-TYPE                                   399
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  17Q GAIN MUTATED                                                             1
  17Q GAIN WILD-TYPE                                                           0
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  17Q GAIN MUTATED                                                     2
  17Q GAIN WILD-TYPE                                                   8
D31V8, multiclass
                                                             clus
vv                                                            17Q GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     78
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        2
                                                             clus
vv                                                            17Q GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      399
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                  0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                          8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V9, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    12  69
  17Q GAIN WILD-TYPE  67 340
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     12   69
  17Q GAIN WILD-TYPE   67  340
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  NO                12                 67
  YES               69                340
[1] 2 2
[1] FALSE
D31V10, continuous
D31V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17Q GAIN MUTATED                                  0     2
  17Q GAIN WILD-TYPE                                2     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17Q GAIN MUTATED                           9    67
  17Q GAIN WILD-TYPE                        35   348
D31V12, multiclass
                                  clus
vv                                 17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           2                  9
  BLACK OR AFRICAN AMERICAN                       9                 35
  WHITE                                          67                348
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V13, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     8  69
  17Q GAIN WILD-TYPE  16 362
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      8   69
  17Q GAIN WILD-TYPE   16  362
                        clus
vv                       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    8                 16
  NOT HISPANIC OR LATINO               69                362
[1] 2 2
[1] FALSE

Clustering(32) Variable = 18P GAIN MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                  0   1
  18P GAIN MUTATED    67  27
  18P GAIN WILD-TYPE 234  86
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                94                320 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                27                 86 
$`18P GAIN MUTATED`
TCGA-BA-4076 TCGA-BA-5151 TCGA-BA-5555 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6869 
         415          722          520         1636         1747          644 
TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-A4IG TCGA-BA-A6DL TCGA-BB-4223 
          63          384          113          855          623         2878 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7870 TCGA-C9-A47Z 
         278          140          310          536         1153            5 
TCGA-CN-4728 TCGA-CN-4730 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-5363 TCGA-CN-5366 
        1151          817          395          625         1977         1966 
TCGA-CN-6012 TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-A63T 
         629           98          202          224          318          225 
TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A641 TCGA-CQ-5332 TCGA-CQ-6227 TCGA-CQ-7067 
         526          348          367          317         1959          509 
TCGA-CQ-A4C9 TCGA-CR-5247 TCGA-CR-6467 TCGA-CR-6482 TCGA-CR-6493 TCGA-CR-7364 
         707          358         1777          345         1956         1435 
TCGA-CR-7365 TCGA-CR-7370 TCGA-CR-7372 TCGA-CR-7390 TCGA-CR-7399 TCGA-CR-7401 
        1191          105          759          907          181         1077 
TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5440 TCGA-CV-5441 
         911         1472         1950         3295         1978         2886 
TCGA-CV-5973 TCGA-CV-5977 TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6441 TCGA-CV-6935 
        2641         1840         1315          641         1970         1969 
TCGA-CV-6941 TCGA-CV-6945 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7243 
        1959         1969         1939         1945         1987          954 
TCGA-CV-7406 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45Z TCGA-CV-A461 
        1974         1958         1959         1981         1940         1954 
TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A6EO TCGA-D6-A6EP TCGA-DQ-5631 TCGA-DQ-7590 
         106          128          435          424          548          775 
TCGA-DQ-7595 TCGA-H7-8502 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-A634 TCGA-HD-A6HZ 
         324          133          403          206           10          111 
TCGA-IQ-A61G TCGA-KU-A66T TCGA-MZ-A7D7 TCGA-QK-A8Z7 TCGA-QK-A8ZA TCGA-QK-A8ZB 
         360          552          240          198          135          135 
TCGA-UF-A719 TCGA-UF-A71E TCGA-UF-A7JA TCGA-UF-A7JD 
        1663         1278         1894          735 

$`18P GAIN WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
         102          462          283         1983          276          248 
TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-6868 TCGA-BA-6870 
        1288         1762          725          623          190          451 
TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA 
         236          895          622          918          850          351 
TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A8YP TCGA-BB-4217 
         216          182         1976          314          142          187 
TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7871 
         133          558          423          687          638          428 
TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 
         436         1955          624            4          799          721 
TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4729 TCGA-CN-4731 TCGA-CN-4733 
        1157          142         1230          392          993          642 
TCGA-CN-4735 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 
        1250         1960         1330          811         1268         1988 
TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5365 
        1007         1045          173         1980         1081         1980 
TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 
        1966         1975          683          290          630          933 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6021 
         628          594          629           45          432         1970 
TCGA-CN-6023 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 
        1110          611          394          735          432          429 
TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C 
          46          443          535          391          904          645 
TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-5324 
         484          175          223          298         1466         1207 
TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 
         654         1660         1422         1393         1399          341 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6228 
         129         1253         1000         1057          985         1959 
TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7069 
        1179         1750         1560         1007         1309         1274 
TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CA TCGA-CQ-A4CB 
         877         1950         1353         1960         1963          893 
TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 
         998          785          391          303          950         2562 
TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 
        1663         1152          799         1521         1966         1050 
TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 
        1125         1971          514         1969          362          311 
TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-7367 
         354          234          379          350          479         1440 
TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 
        1245         1960         1979          889           30          972 
TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 
        1968         1036          796         1954          997         1430 
TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 
        1951          392          913          946          908          898 
TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5435 
         930          216          156         1955          522         1438 
TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 
         584          546         2327         1958         2437          519 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5976 TCGA-CV-5978 TCGA-CV-6003 TCGA-CV-6436 
         406          701         1478          215         1665         1899 
TCGA-CV-6934 TCGA-CV-6936 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6952 TCGA-CV-6954 
        1948         1952         3835         1948         1966         1957 
TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 
        1969         1959         3837         1959         1970         1970 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7242 
        1936         1959         1979         1952         1444         1095 
TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7410 
         797         1967         1960         1976         1099         1948 
TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 
        1955         1957         1947         1937         1973         1972 
TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45Y 
        1937         1984          851         1945         5480         1960 
TCGA-CV-A460 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN 
        1946         1722         1977         1970         1075          906 
TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 
        1959          670          110          646          714          606 
TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 
         685         1950          317          321          237          828 
TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 
         773          292          701           77          491          154 
TCGA-D6-6827 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EQ 
         568          539          376          483          232          368 
TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 
         389          338         1778         1081          516         1030 
TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 
        1965          575          622          299          369          368 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I 
         340         1131          490          658           15           92 
TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 
         585            3          384           14           13            6 
TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-A6C4 TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 
         407           58          414            2            5           25 
TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 
          37           55           44           24           25           11 
TCGA-HD-A633 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 
          49           33         1057          485          122          441 
TCGA-IQ-A61E TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S 
         588          412          440          351          360          224 
TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D 
         378          168           14           34          392           56 
TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE 
         111          112          254          910         1726         1559 
TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-P3-A6T8 
        1120         1954          578         1917         1968          400 
TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II 
         553          357          245          218          228          225 
TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A8Z9 TCGA-QK-AA3J TCGA-QK-AA3K TCGA-UF-A718 
         387          567          149          157          168         1326 
TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A7J9 TCGA-UF-A7JC TCGA-UF-A7JF TCGA-UF-A7JH 
        1319         1252         1043          484         1497          665 
TCGA-UF-A7JJ TCGA-UF-A7JS 
         214          413 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 5                  2 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              3295               5480 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             675.5              701.0 
[1] "5.0 - 3295.0 (675.5)" "2.0 - 5480.0 (701.0)"
[1] "hr=" "1.2"
D32V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  18P GAIN MUTATED         3       12        16        58         2         1
  18P GAIN WILD-TYPE      23       63        58       177        10         0
D32V3, multiclass
           clus
vv          18P GAIN MUTATED 18P GAIN WILD-TYPE
  STAGE I                  3                 23
  STAGE II                12                 63
  STAGE III               16                 58
  STAGE IVA               58                177
  STAGE IVB                2                 10
  STAGE IVC                1                  0
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  18P GAIN MUTATED       8  23  28  36
  18P GAIN WILD-TYPE    39 104  66 126
D32V4, multiclass
       clus
vv      18P GAIN MUTATED 18P GAIN WILD-TYPE
  T0+T1                8                 39
  T2                  23                104
  T3                  28                 66
  T4                  36                126
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  18P GAIN MUTATED    31  13  43   2
  18P GAIN WILD-TYPE 139  50 109   6
D32V5, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  N0               31                139
  N1               13                 50
  N2               43                109
  N3                2                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  18P GAIN MUTATED    29   1  15
  18P GAIN WILD-TYPE 138   0  43
D32V6, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  M0               29                138
  M1                1                  0
  MX               15                 43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V7, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    15  97
  18P GAIN WILD-TYPE 117 259
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     15   97
  18P GAIN WILD-TYPE  117  259
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE               15                117
  MALE                 97                259
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  18P GAIN MUTATED                                     110
  18P GAIN WILD-TYPE                                   367
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  18P GAIN MUTATED                                                             0
  18P GAIN WILD-TYPE                                                           1
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  18P GAIN MUTATED                                                     2
  18P GAIN WILD-TYPE                                                   8
D32V8, multiclass
                                                             clus
vv                                                            18P GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    110
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        2
                                                             clus
vv                                                            18P GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      367
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                  1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                          8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V9, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    16  96
  18P GAIN WILD-TYPE  63 313
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     16   96
  18P GAIN WILD-TYPE   63  313
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  NO                16                 63
  YES               96                313
[1] 2 2
[1] FALSE
D32V10, continuous
D32V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18P GAIN MUTATED                                  0     1
  18P GAIN WILD-TYPE                                2    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18P GAIN MUTATED                          13    93
  18P GAIN WILD-TYPE                        31   322
D32V12, multiclass
                                  clus
vv                                 18P GAIN MUTATED 18P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           1                 10
  BLACK OR AFRICAN AMERICAN                      13                 31
  WHITE                                          93                322
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V13, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     4 100
  18P GAIN WILD-TYPE  20 331
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      4  100
  18P GAIN WILD-TYPE   20  331
                        clus
vv                       18P GAIN MUTATED 18P GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                 20
  NOT HISPANIC OR LATINO              100                331
[1] 2 2
[1] FALSE

Clustering(33) Variable = 18Q GAIN MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                  0   1
  18Q GAIN MUTATED    29   9
  18Q GAIN WILD-TYPE 272 104
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                38                376 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 9                104 
$`18Q GAIN MUTATED`
TCGA-BA-5151 TCGA-BA-5555 TCGA-BA-5559 TCGA-BA-6871 TCGA-BB-4223 TCGA-BB-4225 
         722          520         1747           63         2878          140 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7870 TCGA-CN-4730 TCGA-CN-4736 TCGA-CN-6012 
         558          310         1153          817          395          629 
TCGA-CN-6020 TCGA-CN-6024 TCGA-CN-6988 TCGA-CR-6467 TCGA-CR-6482 TCGA-CR-7367 
          98          224          318         1777          345         1440 
TCGA-CR-7370 TCGA-CR-7372 TCGA-CR-7401 TCGA-CR-7404 TCGA-CV-5432 TCGA-CV-5434 
         105          759         1077         1472         1950         3295 
TCGA-CV-6433 TCGA-CV-6441 TCGA-CV-7406 TCGA-CV-A45Z TCGA-CV-A461 TCGA-D6-A6EO 
         641         1970         1974         1940         1954          435 
TCGA-DQ-7590 TCGA-H7-A76A TCGA-HD-A634 TCGA-QK-A6IG TCGA-QK-A8Z7 TCGA-UF-A719 
         775          206           10          218          198         1663 
TCGA-UF-A71E TCGA-UF-A7JA 
        1278         1894 

$`18Q GAIN WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 
         102          462          283          415         1983          276 
TCGA-BA-5149 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 
         248         1288         1762          725          623         1636 
TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 
         190          644          451          384          113          236 
TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA 
         895          855          622          918          850          351 
TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP 
         216          182         1976          314          623          142 
TCGA-BB-4217 TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 
         187          278          133          536          423          687 
TCGA-BB-7866 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A47Z 
         638          428          436         1955          624            5 
TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 
           4          799          721         1157          142         1230 
TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4737 
        1151          392          993          642         1250          625 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 
        1960         1330          811         1268         1988         1007 
TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 
        1045          173         1980         1081         1977         1980 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 
        1966         1966         1975          683          290          630 
TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 
         933          628          594          629           45          432 
TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 
        1970          202         1110          611          394          735 
TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A 
         432          429           46          443          535          391 
TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W 
         904          645          225          526          484          348 
TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-5324 
         175          367          223          298         1466         1207 
TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 
         654         1660         1422         1393         1399          317 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 
         341          129         1253         1000         1057          985 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 
        1959         1959         1179         1750         1560         1007 
TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 
         509         1309         1274          877         1950         1353 
TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE 
        1960          707         1963          893          998          785 
TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 
         391          303          950         2562          358         1663 
TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 
        1152          799         1521         1966         1050         1125 
TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6484 
        1971          514         1969          362          311          354 
TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 
         234          379          350          479         1956         1435 
TCGA-CR-7365 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7373 TCGA-CR-7374 
        1191         1245         1960         1979          889           30 
TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 
         972         1968         1036          796         1954          997 
TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 
        1430         1951          392          907          913          946 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 
         908          898          930          216          156          181 
TCGA-CR-7402 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 
         911         1955          522         1438          584          546 
TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 
        1978         2886         2327         1958         2437          519 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 
         406          701         2641         1478         1840          215 
TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6436 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 
        1315         1665         1899         1948         1969         1952 
TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-6954 
        1959         3835         1948         1969         1966         1957 
TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 
        1969         1959         3837         1959         1970         1970 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7183 
        1936         1959         1939         1945         1987         1979 
TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 
        1952         1444         1095          954          797         1967 
TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7422 
        1960         1976         1099         1948         1955         1957 
TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 
        1947         1937         1973         1972         1937         1984 
TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A45R 
        1958         1959         1981          851         1945         5480 
TCGA-CV-A45Y TCGA-CV-A460 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE 
        1960         1946         1722         1977         1970         1075 
TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ 
         906         1959          670          110          646          714 
TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 
         606          685         1950          317          321          237 
TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 
         828          773          292          701           77          491 
TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB 
         154          568          106          128          539          376 
TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q 
         483          232          424          368          389          338 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 
        1778         1081          516         1030          548         1965 
TCGA-DQ-7589 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 
         575          622          299          369          368          324 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I 
         340         1131          490          658           15           92 
TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 
         585            3          384           14           13            6 
TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-HD-7229 
         407           58          133          414          403            2 
TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 
           5           25           37           55           44           24 
TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 
          25           11           49          111           33         1057 
TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H 
         485          122          441          588          360          412 
TCGA-IQ-A61J TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 
         440          351          360          224          552          378 
TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F 
         168           14           34          392           56          111 
TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE 
         112          254          240          910         1726         1559 
TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-P3-A6T8 
        1120         1954          578         1917         1968          400 
TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ 
         553          357          245          228          225          387 
TCGA-QK-A6V9 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K 
         567          149          135          135          157          168 
TCGA-UF-A718 TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A7J9 TCGA-UF-A7JC TCGA-UF-A7JD 
        1326         1319         1252         1043          484          735 
TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JS 
        1497          665          214          413 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                10                  2 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              3295               5480 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             740.5              694.0 
[1] "10.0 - 3295.0 (740.5)" "2.0 - 5480.0 (694.0)" 
[1] "hr=" "1.2"
D33V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  18Q GAIN MUTATED         2        5         7        22         0         1
  18Q GAIN WILD-TYPE      24       70        67       213        12         0
D33V3, multiclass
           clus
vv          18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  STAGE I                  2                 24
  STAGE II                 5                 70
  STAGE III                7                 67
  STAGE IVA               22                213
  STAGE IVB                0                 12
  STAGE IVC                1                  0
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  18Q GAIN MUTATED       5   9   8  16
  18Q GAIN WILD-TYPE    42 118  86 146
D33V4, multiclass
       clus
vv      18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  T0+T1                5                 42
  T2                   9                118
  T3                   8                 86
  T4                  16                146
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  18Q GAIN MUTATED    14   8  14   0
  18Q GAIN WILD-TYPE 156  55 138   8
D33V5, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  N0               14                156
  N1                8                 55
  N2               14                138
  N3                0                  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"
                    vv
clus                  M0  M1  MX
  18Q GAIN MUTATED    13   1   3
  18Q GAIN WILD-TYPE 154   0  55
D33V6, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  M0               13                154
  M1                1                  0
  MX                3                 55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V7, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     4  44
  18Q GAIN WILD-TYPE 128 312
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      4   44
  18Q GAIN WILD-TYPE  128  312
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE                4                128
  MALE                 44                312
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  18Q GAIN MUTATED                                      46
  18Q GAIN WILD-TYPE                                   431
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  18Q GAIN MUTATED                                                             0
  18Q GAIN WILD-TYPE                                                           1
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  18Q GAIN MUTATED                                                     2
  18Q GAIN WILD-TYPE                                                   8
D33V8, multiclass
                                                             clus
vv                                                            18Q GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     46
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        2
                                                             clus
vv                                                            18Q GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      431
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                  1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                          8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V9, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     7  41
  18Q GAIN WILD-TYPE  72 368
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      7   41
  18Q GAIN WILD-TYPE   72  368
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  NO                 7                 72
  YES               41                368
[1] 2 2
[1] FALSE
D33V10, continuous
D33V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18Q GAIN MUTATED                                  0     0
  18Q GAIN WILD-TYPE                                2    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18Q GAIN MUTATED                           6    41
  18Q GAIN WILD-TYPE                        38   374
D33V12, multiclass
                                  clus
vv                                 18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                 11
  BLACK OR AFRICAN AMERICAN                       6                 38
  WHITE                                          41                374
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V13, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     2  42
  18Q GAIN WILD-TYPE  22 389
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      2   42
  18Q GAIN WILD-TYPE   22  389
                        clus
vv                       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                 22
  NOT HISPANIC OR LATINO               42                389
[1] 2 2
[1] FALSE

Clustering(34) Variable = 19P GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                  0   1
  19P GAIN MUTATED    36   7
  19P GAIN WILD-TYPE 265 106
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                43                371 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 7                106 
$`19P GAIN MUTATED`
TCGA-BA-5559 TCGA-BA-A8YP TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-7861 TCGA-BB-7871 
        1747          142         2878          140          310          428 
TCGA-BB-8601 TCGA-CN-6021 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6989 TCGA-CN-A63T 
         624         1970         1110          224          611          225 
TCGA-CN-A63V TCGA-CN-A641 TCGA-CQ-5323 TCGA-CR-6467 TCGA-CR-6487 TCGA-CR-6488 
         484          367         1466         1777          234          379 
TCGA-CR-7370 TCGA-CR-7389 TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5440 TCGA-CV-5442 
         105          392         1472          522         1978         2327 
TCGA-CV-5977 TCGA-CV-7101 TCGA-CV-7235 TCGA-CV-7245 TCGA-CV-7261 TCGA-CV-A45Z 
        1840         1939         1952          797         1099         1940 
TCGA-CV-A6K2 TCGA-CX-7219 TCGA-F7-8298 TCGA-F7-A50J TCGA-F7-A623 TCGA-H7-A76A 
        1950          828          490          585            6          206 
TCGA-HD-A6HZ TCGA-MT-A67G TCGA-P3-A6T4 TCGA-QK-A6V9 TCGA-QK-A8Z7 TCGA-QK-AA3K 
         111          112         1968          567          198          168 
TCGA-UF-A71E 
        1278 

$`19P GAIN WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 
         102          462          283          415         1983          276 
TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 
         248          722         1288         1762          520          725 
TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 
         623         1636          190          644          451           63 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH 
         384          113          236          895          855          622 
TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DG 
         918          850          351          216          182         1976 
TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BB-4217 TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-4228 
         314          623          187          278          133          558 
TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7872 
         536          423          687          638         1153          436 
TCGA-BB-8596 TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 
        1955            5            4          799          721         1157 
TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 
         142         1230         1151          392          817          993 
TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 
         642         1250          395          625         1960         1330 
TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 
         811         1268         1988         1007         1045          173 
TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 
        1980         1081         1977         1980         1966         1966 
TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 
        1975          683          290          630          933          629 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 
         628          594          629           45          432           98 
TCGA-CN-6022 TCGA-CN-6988 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 
         202          318          394          735          432          429 
TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C 
          46          443          535          391          904          645 
TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5324 
         526          348          175          223          298         1207 
TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 
         654         1660         1422         1393         1399          317 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 
         341          129         1253         1000         1057          985 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 
        1959         1959         1179         1750         1560         1007 
TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 
         509         1309         1274          877         1950         1353 
TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE 
        1960          707         1963          893          998          785 
TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 
         391          303          950         2562          358         1663 
TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 
        1152          799         1521         1966         1050         1125 
TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 
        1971          514         1969          362          311          345 
TCGA-CR-6484 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 
         354          350          479         1956         1435         1191 
TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 
        1440         1245         1960         1979          759          889 
TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 
          30          972         1968         1036          796         1954 
TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 
         997         1430         1951          907          913          946 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 
         908          898          930          216          156          181 
TCGA-CR-7401 TCGA-CR-7402 TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 
        1077          911         1955         1950         3295         1438 
TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5441 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 
         584          546         2886         1958         2437          519 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5978 TCGA-CV-5979 
         406          701         2641         1478          215         1315 
TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 
        1665          641         1899         1970         1948         1969 
TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6952 
        1952         1959         3835         1948         1969         1966 
TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 
        1957         1969         1959         3837         1959         1970 
TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7183 
        1970         1936         1959         1945         1987         1979 
TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7254 
        1444         1095          954         1967         1960         1976 
TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7427 
        1974         1948         1955         1957         1947         1937 
TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 
        1973         1972         1937         1984         1958         1959 
TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45Y TCGA-CV-A460 
        1981          851         1945         5480         1960         1946 
TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN 
        1954         1722         1977         1970         1075          906 
TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 
        1959          670          110          646          714          606 
TCGA-CV-A6K1 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-D6-6516 TCGA-D6-6517 
         685          317          321          237          773          292 
TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 
         701           77          491          154          568          106 
TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO 
         128          539          376          483          232          435 
TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 
         424          368          389          338         1778         1081 
TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 
         516         1030          548         1965          575          775 
TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
         622          299          369          368          324          340 
TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A61S TCGA-F7-A61V 
        1131          658           15           92            3          384 
TCGA-F7-A61W TCGA-F7-A620 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 
          14           13          407           58          133          414 
TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 
         403            2            5           25           37           55 
TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 
          44           24           25           11           49           10 
TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E 
          33         1057          485          122          441          588 
TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S 
         360          412          440          351          360          224 
TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A 
         552          378          168           14           34          392 
TCGA-MT-A67D TCGA-MT-A67F TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QA 
          56          111          254          240          910         1726 
TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T8 
        1559         1120         1954          578         1917          400 
TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II 
         553          357          245          218          228          225 
TCGA-QK-A6IJ TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-UF-A718 
         387          149          135          135          157         1326 
TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC 
        1663         1319         1252         1043         1894          484 
TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JS 
         735         1497          665          214          413 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 6                  2 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              2878               5480 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
               585                714 
[1] "6.0 - 2878.0 (585.0)" "2.0 - 5480.0 (714.0)"
[1] "hr=" "1.7"
D34V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  19P GAIN MUTATED         3        5         6        26         1         0
  19P GAIN WILD-TYPE      23       70        68       209        11         1
D34V3, multiclass
           clus
vv          19P GAIN MUTATED 19P GAIN WILD-TYPE
  STAGE I                  3                 23
  STAGE II                 5                 70
  STAGE III                6                 68
  STAGE IVA               26                209
  STAGE IVB                1                 11
  STAGE IVC                0                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  19P GAIN MUTATED       7   7  10  17
  19P GAIN WILD-TYPE    40 120  84 145
D34V4, multiclass
       clus
vv      19P GAIN MUTATED 19P GAIN WILD-TYPE
  T0+T1                7                 40
  T2                   7                120
  T3                  10                 84
  T4                  17                145
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  19P GAIN MUTATED    13   5  21   1
  19P GAIN WILD-TYPE 157  58 131   7
D34V5, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  N0               13                157
  N1                5                 58
  N2               21                131
  N3                1                  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"
                    vv
clus                  M0  M1  MX
  19P GAIN MUTATED    15   0  10
  19P GAIN WILD-TYPE 152   1  48
D34V6, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  M0               15                152
  M1                0                  1
  MX               10                 48
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V7, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     9  41
  19P GAIN WILD-TYPE 123 315
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      9   41
  19P GAIN WILD-TYPE  123  315
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE                9                123
  MALE                 41                315
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  19P GAIN MUTATED                                      48
  19P GAIN WILD-TYPE                                   429
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  19P GAIN MUTATED                                                             0
  19P GAIN WILD-TYPE                                                           1
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  19P GAIN MUTATED                                                     2
  19P GAIN WILD-TYPE                                                   8
D34V8, multiclass
                                                             clus
vv                                                            19P GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     48
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        2
                                                             clus
vv                                                            19P GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      429
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                  1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                          8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V9, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     7  43
  19P GAIN WILD-TYPE  72 366
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      7   43
  19P GAIN WILD-TYPE   72  366
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  NO                 7                 72
  YES               43                366
[1] 2 2
[1] FALSE
D34V10, continuous
D34V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19P GAIN MUTATED                                  0     0
  19P GAIN WILD-TYPE                                2    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19P GAIN MUTATED                           6    44
  19P GAIN WILD-TYPE                        38   371
D34V12, multiclass
                                  clus
vv                                 19P GAIN MUTATED 19P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                 11
  BLACK OR AFRICAN AMERICAN                       6                 38
  WHITE                                          44                371
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V13, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     3  45
  19P GAIN WILD-TYPE  21 386
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      3   45
  19P GAIN WILD-TYPE   21  386
                        clus
vv                       19P GAIN MUTATED 19P GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                 21
  NOT HISPANIC OR LATINO               45                386
[1] 2 2
[1] FALSE

Clustering(35) Variable = 19Q GAIN MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                  0   1
  19Q GAIN MUTATED    48  11
  19Q GAIN WILD-TYPE 253 102
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                59                355 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                11                102 
$`19Q GAIN MUTATED`
TCGA-4P-AA8J TCGA-BA-5153 TCGA-BA-5559 TCGA-BA-7269 TCGA-BA-A6DL TCGA-BA-A8YP 
         102         1762         1747          236          623          142 
TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-7861 TCGA-CN-6012 TCGA-CN-6020 TCGA-CN-6021 
        2878          140          310          629           98         1970 
TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A641 TCGA-CQ-5324 
        1110          224          225          484          367         1207 
TCGA-CQ-5330 TCGA-CQ-6223 TCGA-CR-6467 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-7367 
        1393         1057         1777          234          379         1440 
TCGA-CR-7370 TCGA-CR-7389 TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5440 TCGA-CV-5442 
         105          392         1472          522         1978         2327 
TCGA-CV-5977 TCGA-CV-7101 TCGA-CV-7235 TCGA-CV-7243 TCGA-CV-7406 TCGA-CV-7435 
        1840         1939         1952          954         1974         1959 
TCGA-CV-A45Z TCGA-CV-A6K2 TCGA-CX-7219 TCGA-D6-6825 TCGA-DQ-7592 TCGA-F7-8298 
        1940         1950          828          491          299          490 
TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A623 TCGA-H7-A76A TCGA-HD-A6HZ TCGA-HL-7533 
          92          585            6          206          111         1057 
TCGA-IQ-7631 TCGA-IQ-A61G TCGA-KU-A66T TCGA-MT-A67G TCGA-P3-A5Q5 TCGA-P3-A6T4 
         122          360          552          112          910         1968 
TCGA-QK-A6V9 TCGA-QK-A8Z7 TCGA-QK-AA3K TCGA-UF-A71E TCGA-UF-A7JJ 
         567          198          168         1278          214 

$`19Q GAIN WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
         462          283          415         1983          276          248 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 
         722         1288          520          725          623         1636 
TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 
         190          644          451           63          384          113 
TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA 
         895          855          622          918          850          351 
TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BB-4217 TCGA-BB-4224 
         216          182         1976          314          187          278 
TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 
         133          558          536          423          687          638 
TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A47Z 
        1153          428          436         1955          624            5 
TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 
           4          799          721         1157          142         1230 
TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 
        1151          392          817          993          642         1250 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 
         395          625         1960         1330          811         1268 
TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 
        1988         1007         1045          173         1980         1081 
TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 
        1977         1980         1966         1966         1975          683 
TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 
         290          630          933          628          594          629 
TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6022 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 
          45          432          202          318          611          394 
TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A499 
         735          432          429           46          443          535 
TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A63Y 
         391          904          645          526          348          175 
TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 
         223          298         1466          654         1660         1422 
TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 
        1399          317          341          129         1253         1000 
TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 
         985         1959         1959         1179         1750         1560 
TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 
        1007          509         1309         1274          877         1950 
TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD 
        1353         1960          707         1963          893          998 
TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 
         785          391          303          950         2562          358 
TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 
        1663         1152          799         1521         1966         1050 
TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 
        1125         1971          514         1969          362          311 
TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 
         345          354          350          479         1956         1435 
TCGA-CR-7365 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 
        1191         1245         1960         1979          759          889 
TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 
          30          972         1968         1036          796         1954 
TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 
         997         1430         1951          907          913          946 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 
         908          898          930          216          156          181 
TCGA-CR-7401 TCGA-CR-7402 TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 
        1077          911         1955         1950         3295         1438 
TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5441 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 
         584          546         2886         1958         2437          519 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5978 TCGA-CV-5979 
         406          701         2641         1478          215         1315 
TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 
        1665          641         1899         1970         1948         1969 
TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6952 
        1952         1959         3835         1948         1969         1966 
TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 
        1957         1969         1959         3837         1959         1970 
TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7183 
        1970         1936         1959         1945         1987         1979 
TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7254 
        1444         1095          797         1967         1960         1976 
TCGA-CV-7261 TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7427 
        1099         1948         1955         1957         1947         1937 
TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7440 
        1973         1972         1937         1984         1958         1981 
TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45Y TCGA-CV-A460 TCGA-CV-A461 
         851         1945         5480         1960         1946         1954 
TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO 
        1722         1977         1970         1075          906         1959 
TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 
         670          110          646          714          606          685 
TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 
         317          321          237          773          292          701 
TCGA-D6-6824 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 
          77          154          568          106          128          539 
TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ 
         376          483          232          435          424          368 
TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 
         389          338         1778         1081          516         1030 
TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7593 
         548         1965          575          775          622          369 
TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G 
         368          324          340         1131          658           15 
TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-H7-7774 TCGA-H7-8501 
           3          384           14           13          407           58 
TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 
         133          414          403            2            5           25 
TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 
          37           55           44           24           25           11 
TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-IQ-7630 TCGA-IQ-7632 TCGA-IQ-A61E 
          49           10           33          485          441          588 
TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A6H7 
         412          440          351          360          224          378 
TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F 
         168           14           34          392           56          111 
TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX 
         254          240         1726         1559         1120         1954 
TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF 
         578         1917          400          553          357          245 
TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A8Z9 TCGA-QK-A8ZA 
         218          228          225          387          149          135 
TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71D 
         135          157         1326         1663         1319         1252 
TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH 
        1043         1894          484          735         1497          665 
TCGA-UF-A7JS 
         413 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 6                  2 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              2878               5480 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
               567                721 
[1] "6.0 - 2878.0 (567.0)" "2.0 - 5480.0 (721.0)"
[1] "hr=" "1.4"
D35V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  19Q GAIN MUTATED         3       11        10        32         2         0
  19Q GAIN WILD-TYPE      23       64        64       203        10         1
D35V3, multiclass
           clus
vv          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  STAGE I                  3                 23
  STAGE II                11                 64
  STAGE III               10                 64
  STAGE IVA               32                203
  STAGE IVB                2                 10
  STAGE IVC                0                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  19Q GAIN MUTATED       8  19  13  20
  19Q GAIN WILD-TYPE    39 108  81 142
D35V4, multiclass
       clus
vv      19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  T0+T1                8                 39
  T2                  19                108
  T3                  13                 81
  T4                  20                142
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  19Q GAIN MUTATED    22   8  24   2
  19Q GAIN WILD-TYPE 148  55 128   6
D35V5, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  N0               22                148
  N1                8                 55
  N2               24                128
  N3                2                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  19Q GAIN MUTATED    19   0  12
  19Q GAIN WILD-TYPE 148   1  46
D35V6, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  M0               19                148
  M1                0                  1
  MX               12                 46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V7, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    13  58
  19Q GAIN WILD-TYPE 119 298
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     13   58
  19Q GAIN WILD-TYPE  119  298
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE               13                119
  MALE                 58                298
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  19Q GAIN MUTATED                                      68
  19Q GAIN WILD-TYPE                                   409
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  19Q GAIN MUTATED                                                             0
  19Q GAIN WILD-TYPE                                                           1
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  19Q GAIN MUTATED                                                     3
  19Q GAIN WILD-TYPE                                                   7
D35V8, multiclass
                                                             clus
vv                                                            19Q GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     68
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        3
                                                             clus
vv                                                            19Q GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      409
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                  1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                          7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V9, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    12  59
  19Q GAIN WILD-TYPE  67 350
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     12   59
  19Q GAIN WILD-TYPE   67  350
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  NO                12                 67
  YES               59                350
[1] 2 2
[1] FALSE
D35V10, continuous
D35V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19Q GAIN MUTATED                                  1     0
  19Q GAIN WILD-TYPE                                1    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19Q GAIN MUTATED                           9    59
  19Q GAIN WILD-TYPE                        35   356
D35V12, multiclass
                                  clus
vv                                 19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  1
  ASIAN                                           0                 11
  BLACK OR AFRICAN AMERICAN                       9                 35
  WHITE                                          59                356
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V13, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     3  63
  19Q GAIN WILD-TYPE  21 368
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      3   63
  19Q GAIN WILD-TYPE   21  368
                        clus
vv                       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                 21
  NOT HISPANIC OR LATINO               63                368
[1] 2 2
[1] FALSE

Clustering(36) Variable = 20P GAIN MUTATION ANALYSIS
D36V1, survival
                    sevent
clus2                  0   1
  20P GAIN MUTATED   112  31
  20P GAIN WILD-TYPE 189  82
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               143                271 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                31                 82 
$`20P GAIN MUTATED`
TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5556 TCGA-BA-5559 TCGA-BA-6868 
         276          248          722          725         1747          190 
TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A6DB TCGA-BA-A6DG TCGA-BB-4224 TCGA-BB-4225 
         384          236          216         1976          278          140 
TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7872 TCGA-C9-A47Z TCGA-CN-4728 TCGA-CN-4730 
         310          536          436            5         1151          817 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 
         993          642          395          625         1960         1330 
TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5359 TCGA-CN-5360 
         811         1268         1988         1045         1980         1081 
TCGA-CN-5363 TCGA-CN-5366 TCGA-CN-5374 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6020 
        1977         1966          290          629          628           98 
TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-A63T 
         202         1110          224          318          611          225 
TCGA-CN-A63U TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6229 
         526         1422         1393         1057          985         1179 
TCGA-CQ-7064 TCGA-CQ-7067 TCGA-CQ-7069 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
        1560          509         1274         1353         1960          707 
TCGA-CQ-A4CE TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-6467 TCGA-CR-6484 
         785          950         2562          358         1777          354 
TCGA-CR-6488 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7370 TCGA-CR-7372 TCGA-CR-7373 
         379         1191         1440          105          759          889 
TCGA-CR-7377 TCGA-CR-7389 TCGA-CR-7392 TCGA-CR-7399 TCGA-CR-7401 TCGA-CV-5430 
        1968          392          946          181         1077         1955 
TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5442 TCGA-CV-5444 TCGA-CV-5970 
        3295         1438          584         2327         2437          406 
TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-6003 TCGA-CV-6945 
         701         2641         1840          215         1665         1969 
TCGA-CV-6954 TCGA-CV-7090 TCGA-CV-7095 TCGA-CV-7180 TCGA-CV-7242 TCGA-CV-7243 
        1957         3837         1970         1987         1095          954 
TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-A45R TCGA-CV-A45Z TCGA-CV-A464 TCGA-CV-A6JE 
         797         1967         5480         1940         1722         1075 
TCGA-CV-A6JN TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CX-7082 
         906          110          646          714          606          317 
TCGA-CX-7086 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6825 TCGA-D6-8569 TCGA-D6-A4ZB 
         237          773          292          491          128          376 
TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-DQ-5624 TCGA-DQ-7588 TCGA-DQ-7591 TCGA-DQ-7592 
         424          368         1778         1965          622          299 
TCGA-F7-A50J TCGA-F7-A61S TCGA-H7-8501 TCGA-HD-7753 TCGA-HD-8314 TCGA-HD-A634 
         585            3           58            5           44           10 
TCGA-HD-A6HZ TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61L TCGA-KU-A66T 
         111          441          588          360          351          552 
TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67G TCGA-MZ-A7D7 TCGA-P3-A5QA TCGA-P3-A6T0 
         392           56          112          240         1726          578 
TCGA-P3-A6T4 TCGA-QK-A652 TCGA-QK-A6IG TCGA-QK-A6IJ TCGA-QK-A8Z7 TCGA-QK-A8Z9 
        1968          357          218          387          198          149 
TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JF TCGA-UF-A7JJ 
        1278         1043         1894         1497          214 

$`20P GAIN WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-5152 
         102          462          283          415         1983         1288 
TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6869 TCGA-BA-6870 
        1762          520          623         1636          644          451 
TCGA-BA-6871 TCGA-BA-6873 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II 
          63          113          895          855          622          918 
TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DE TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP 
         850          351          182          314          623          142 
TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7863 TCGA-BB-7864 
         187         2878          133          558          423          687 
TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A480 
         638         1153          428         1955          624            4 
TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4729 
         799          721         1157          142         1230          392 
TCGA-CN-4735 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5365 TCGA-CN-5367 TCGA-CN-5370 
        1250         1007          173         1980         1966         1975 
TCGA-CN-5373 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 
         683          630          933          594          629           45 
TCGA-CN-6019 TCGA-CN-6021 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 
         432         1970          394          735          432          429 
TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C 
          46          443          535          391          904          645 
TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A6V1 TCGA-CN-A6V3 
         484          348          175          367          223          298 
TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5331 TCGA-CQ-5332 
        1466         1207          654         1660         1399          317 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6227 TCGA-CQ-6228 
         341          129         1253         1000         1959         1959 
TCGA-CQ-7063 TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4CA 
        1750         1007         1309          877         1950         1963 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5248 TCGA-CR-5249 
         893          998          391          303         1663         1152 
TCGA-CR-5250 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 
         799         1521         1966         1050         1125         1971 
TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 
         514         1969          362          311          345          234 
TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7368 TCGA-CR-7369 
         350          479         1956         1435         1245         1960 
TCGA-CR-7371 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 
        1979           30          972         1036          796         1954 
TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7393 
         997         1430         1951          907          913          908 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7402 TCGA-CR-7404 
         898          930          216          156          911         1472 
TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5443 
         522         1950          546         1978         2886         1958 
TCGA-CV-5966 TCGA-CV-5976 TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 
         519         1478         1315          641         1899         1970 
TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 
        1948         1969         1952         1959         3835         1948 
TCGA-CV-6952 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7091 TCGA-CV-7097 TCGA-CV-7099 
        1966         1969         1959         1959         1970         1936 
TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 
        1959         1939         1945         1979         1952         1444 
TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 
        1960         1976         1099         1974         1948         1955 
TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 
        1957         1947         1937         1973         1972         1937 
TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q 
        1984         1958         1959         1981          851         1945 
TCGA-CV-A45Y TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JO 
        1960         1946         1954         1977         1970         1959 
TCGA-CV-A6JT TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7219 TCGA-D6-6823 
         670          685         1950          321          828          701 
TCGA-D6-6824 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-D6-A6EK 
          77          154          568          106          539          483 
TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5625 TCGA-DQ-5629 
         232          435          389          338         1081          516 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7593 TCGA-DQ-7594 
        1030          548          575          775          369          368 
TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G 
         324          340         1131          490          658           15 
TCGA-F7-A50I TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-7774 
          92          384           14           13            6          407 
TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7754 
         133          414          403          206            2           25 
TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 
          37           55           24           25           11           49 
TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-A61H TCGA-IQ-A61J 
          33         1057          485          122          412          440 
TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X 
         360          224          378          168           14           34 
TCGA-MT-A67F TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX 
         111          254          910         1559         1120         1954 
TCGA-P3-A6T2 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A6IF TCGA-QK-A6IH TCGA-QK-A6II 
        1917          400          553          245          228          225 
TCGA-QK-A6V9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-UF-A718 
         567          135          135          157          168         1326 
TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JH 
        1663         1319         1252          484          735          665 
TCGA-UF-A7JS 
         413 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 3                  2 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              5480               3835 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               701                701 
[1] "3.0 - 5480.0 (701.0)" "2.0 - 3835.0 (701.0)"
[1] "hr=" "1.7"
D36V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  20P GAIN MUTATED        12       23        35        84         5         0
  20P GAIN WILD-TYPE      14       52        39       151         7         1
D36V3, multiclass
           clus
vv          20P GAIN MUTATED 20P GAIN WILD-TYPE
  STAGE I                 12                 14
  STAGE II                23                 52
  STAGE III               35                 39
  STAGE IVA               84                151
  STAGE IVB                5                  7
  STAGE IVC                0                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  20P GAIN MUTATED      21 41 35 63
  20P GAIN WILD-TYPE    26 86 59 99
D36V4, multiclass
       clus
vv      20P GAIN MUTATED 20P GAIN WILD-TYPE
  T0+T1               21                 26
  T2                  41                 86
  T3                  35                 59
  T4                  63                 99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  20P GAIN MUTATED    58  32  54   3
  20P GAIN WILD-TYPE 112  31  98   5
D36V5, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  N0               58                112
  N1               32                 31
  N2               54                 98
  N3                3                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  20P GAIN MUTATED    66   0  19
  20P GAIN WILD-TYPE 101   1  39
D36V6, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  M0               66                101
  M1                0                  1
  MX               19                 39
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V7, binary
                    cls
clus                   0   1
  20P GAIN MUTATED    49 129
  20P GAIN WILD-TYPE  83 227
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     49  129
  20P GAIN WILD-TYPE   83  227
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE               49                 83
  MALE                129                227
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  20P GAIN MUTATED                                     174
  20P GAIN WILD-TYPE                                   303
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  20P GAIN MUTATED                                                             0
  20P GAIN WILD-TYPE                                                           1
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  20P GAIN MUTATED                                                     4
  20P GAIN WILD-TYPE                                                   6
D36V8, multiclass
                                                             clus
vv                                                            20P GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    174
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        4
                                                             clus
vv                                                            20P GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      303
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                  1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                          6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V9, binary
                    cls
clus                   0   1
  20P GAIN MUTATED    34 144
  20P GAIN WILD-TYPE  45 265
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     34  144
  20P GAIN WILD-TYPE   45  265
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  NO                34                 45
  YES              144                265
[1] 2 2
[1] FALSE
D36V10, continuous
D36V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20P GAIN MUTATED                                  1     4
  20P GAIN WILD-TYPE                                1     7
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20P GAIN MUTATED                          17   148
  20P GAIN WILD-TYPE                        27   267
D36V12, multiclass
                                  clus
vv                                 20P GAIN MUTATED 20P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  1
  ASIAN                                           4                  7
  BLACK OR AFRICAN AMERICAN                      17                 27
  WHITE                                         148                267
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V13, binary
                    cls
clus                   0   1
  20P GAIN MUTATED    12 151
  20P GAIN WILD-TYPE  12 280
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     12  151
  20P GAIN WILD-TYPE   12  280
                        clus
vv                       20P GAIN MUTATED 20P GAIN WILD-TYPE
  HISPANIC OR LATINO                   12                 12
  NOT HISPANIC OR LATINO              151                280
[1] 2 2
[1] FALSE

Clustering(37) Variable = 20Q GAIN MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                  0   1
  20Q GAIN MUTATED   115  39
  20Q GAIN WILD-TYPE 186  74
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               154                260 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                39                 74 
$`20Q GAIN MUTATED`
TCGA-BA-4075 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5556 TCGA-BA-6868 
         283          276          248          722          725          190 
TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A6DB TCGA-BA-A6DG TCGA-BB-4225 
         384          236          895          216         1976          140 
TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7864 TCGA-BB-7872 TCGA-C9-A47Z TCGA-CN-4725 
         310          536          687          436            5         1157 
TCGA-CN-4728 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4736 TCGA-CN-4737 
        1151          817          993          642          395          625 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5356 
        1960         1330          811         1268         1988         1045 
TCGA-CN-5359 TCGA-CN-5363 TCGA-CN-5366 TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6012 
        1980         1977         1966          290          933          629 
TCGA-CN-6013 TCGA-CN-6018 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 
         628           45          202         1110          224          318 
TCGA-CN-6994 TCGA-CN-A49A TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A6V3 TCGA-CQ-5329 
         735          391          225          526          298         1422 
TCGA-CQ-5330 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7067 
        1393         1057          985         1179         1560          509 
TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CE 
        1274         1950         1353         1960          707          785 
TCGA-CQ-A4CG TCGA-CR-5247 TCGA-CR-6467 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6484 
         391          358         1777         1971          514          354 
TCGA-CR-6488 TCGA-CR-6493 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7372 TCGA-CR-7373 
         379         1956         1191         1440          759          889 
TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7383 TCGA-CR-7389 TCGA-CR-7392 TCGA-CR-7401 
        1968         1036         1954          392          946         1077 
TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5442 
        1955         1950         3295         1438          584         2327 
TCGA-CV-5444 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-6003 TCGA-CV-6936 TCGA-CV-6945 
        2437         1840          215         1665         1952         1969 
TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-7090 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7180 
        1957         1969         3837         1970         1970         1987 
TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-A45R TCGA-CV-A45Z 
        1095          954          797         1967         5480         1940 
TCGA-CV-A464 TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ 
        1722         1075          906          110          646          714 
TCGA-CV-A6K0 TCGA-CX-7086 TCGA-D6-6516 TCGA-D6-6823 TCGA-D6-6825 TCGA-D6-8569 
         606          237          773          701          491          128 
TCGA-D6-A6EP TCGA-DQ-5624 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7592 
         424         1778          548         1965          575          299 
TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A623 TCGA-H7-8501 TCGA-HD-7753 TCGA-HD-8314 
         585            3            6           58            5           44 
TCGA-HD-A634 TCGA-HD-A6HZ TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61L 
          10          111          441          588          360          351 
TCGA-KU-A66T TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67G 
         552           14           34          392           56          112 
TCGA-MZ-A7D7 TCGA-P3-A5QA TCGA-P3-A6T0 TCGA-P3-A6T4 TCGA-QK-A652 TCGA-QK-A6IG 
         240         1726          578         1968          357          218 
TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-UF-A71D TCGA-UF-A71E 
         387          567          198          149         1252         1278 
TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JF TCGA-UF-A7JJ 
        1043         1894         1497          214 

$`20Q GAIN WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-5152 TCGA-BA-5153 
         102          462          415         1983         1288         1762 
TCGA-BA-5555 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6869 TCGA-BA-6870 
         520          623         1636         1747          644          451 
TCGA-BA-6871 TCGA-BA-6873 TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 
          63          113          855          622          918          850 
TCGA-BA-A6DA TCGA-BA-A6DE TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 
         351          182          314          623          142          187 
TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7863 TCGA-BB-7866 
        2878          278          133          558          423          638 
TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A480 TCGA-CN-4722 
        1153          428         1955          624            4          799 
TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4729 TCGA-CN-4735 TCGA-CN-5355 
         721          142         1230          392         1250         1007 
TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5365 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 
         173         1081         1980         1966         1975          683 
TCGA-CN-6010 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 
         630          594          629          432           98         1970 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 
         611          394          432          429           46          443 
TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y 
         535          904          645          484          348          175 
TCGA-CN-A641 TCGA-CN-A6V1 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 
         367          223         1466         1207          654         1660 
TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 
        1399          317          341          129         1253         1000 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-7063 TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7071 
        1959         1959         1750         1007         1309          877 
TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 
        1963          893          998          303          950         2562 
TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 
        1663         1152          799         1521         1966         1050 
TCGA-CR-6473 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 
        1125         1969          362          311          345          234 
TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-7364 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 
         350          479         1435         1245         1960          105 
TCGA-CR-7371 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7386 
        1979           30          972          796          997         1430 
TCGA-CR-7388 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 
        1951          907          913          908          898          930 
TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5431 
         216          156          181          911         1472          522 
TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5443 TCGA-CV-5966 TCGA-CV-5970 
         546         1978         2886         1958          519          406 
TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6436 
         701         2641         1478         1315          641         1899 
TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 
        1970         1948         1969         1959         3835         1948 
TCGA-CV-6952 TCGA-CV-6961 TCGA-CV-7091 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 
        1966         1959         1959         1936         1959         1939 
TCGA-CV-7102 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7250 TCGA-CV-7254 
        1945         1979         1952         1444         1960         1976 
TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 
        1099         1974         1948         1955         1957         1947 
TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 
        1937         1973         1972         1937         1984         1958 
TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A45Y TCGA-CV-A460 
        1959         1981          851         1945         1960         1946 
TCGA-CV-A461 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6K1 
        1954         1977         1970         1959          670          685 
TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7219 TCGA-D6-6517 TCGA-D6-6824 
        1950          317          321          828          292           77 
TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK 
         154          568          106          539          376          483 
TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5625 
         232          435          368          389          338         1081 
TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7593 TCGA-DQ-7594 
         516         1030          775          622          369          368 
TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G 
         324          340         1131          490          658           15 
TCGA-F7-A50I TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-H7-7774 TCGA-H7-8502 
          92          384           14           13          407          133 
TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7917 
         414          403          206            2           25           37 
TCGA-HD-8224 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A6I0 
          55           24           25           11           49           33 
TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61O 
        1057          485          122          412          440          360 
TCGA-KU-A66S TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A67F TCGA-MZ-A6I9 TCGA-P3-A5Q5 
         224          378          168          111          254          910 
TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T2 TCGA-P3-A6T8 TCGA-QK-A64Z 
        1559         1120         1954         1917          400          553 
TCGA-QK-A6IF TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J 
         245          228          225          135          135          157 
TCGA-QK-AA3K TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A7JC TCGA-UF-A7JD 
         168         1326         1663         1319          484          735 
TCGA-UF-A7JH TCGA-UF-A7JS 
         665          413 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 3                  2 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              5480               3835 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             723.5              667.5 
[1] "3.0 - 5480.0 (723.5)" "2.0 - 3835.0 (667.5)"
[1] "hr=" "1.2"
D37V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  20Q GAIN MUTATED        14       27        34        88         7         0
  20Q GAIN WILD-TYPE      12       48        40       147         5         1
D37V3, multiclass
           clus
vv          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  STAGE I                 14                 12
  STAGE II                27                 48
  STAGE III               34                 40
  STAGE IVA               88                147
  STAGE IVB                7                  5
  STAGE IVC                0                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  20Q GAIN MUTATED      24 44 36 67
  20Q GAIN WILD-TYPE    23 83 58 95
D37V4, multiclass
       clus
vv      20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T0+T1               24                 23
  T2                  44                 83
  T3                  36                 58
  T4                  67                 95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  20Q GAIN MUTATED    68  28  56   4
  20Q GAIN WILD-TYPE 102  35  96   4
D37V5, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  N0               68                102
  N1               28                 35
  N2               56                 96
  N3                4                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1 MX
  20Q GAIN MUTATED   71  0 21
  20Q GAIN WILD-TYPE 96  1 37
D37V6, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  M0               71                 96
  M1                0                  1
  MX               21                 37
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V7, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED    52 137
  20Q GAIN WILD-TYPE  80 219
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     52  137
  20Q GAIN WILD-TYPE   80  219
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE               52                 80
  MALE                137                219
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  20Q GAIN MUTATED                                     186
  20Q GAIN WILD-TYPE                                   291
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  20Q GAIN MUTATED                                                             0
  20Q GAIN WILD-TYPE                                                           1
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  20Q GAIN MUTATED                                                     3
  20Q GAIN WILD-TYPE                                                   7
D37V8, multiclass
                                                             clus
vv                                                            20Q GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    186
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        3
                                                             clus
vv                                                            20Q GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      291
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                  1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                          7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V9, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED    35 154
  20Q GAIN WILD-TYPE  44 255
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     35  154
  20Q GAIN WILD-TYPE   44  255
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  NO                35                 44
  YES              154                255
[1] 2 2
[1] FALSE
D37V10, continuous
D37V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20Q GAIN MUTATED                                  1     4
  20Q GAIN WILD-TYPE                                1     7
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20Q GAIN MUTATED                          20   156
  20Q GAIN WILD-TYPE                        24   259
D37V12, multiclass
                                  clus
vv                                 20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  1
  ASIAN                                           4                  7
  BLACK OR AFRICAN AMERICAN                      20                 24
  WHITE                                         156                259
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V13, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED    11 163
  20Q GAIN WILD-TYPE  13 268
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     11  163
  20Q GAIN WILD-TYPE   13  268
                        clus
vv                       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   11                 13
  NOT HISPANIC OR LATINO              163                268
[1] 2 2
[1] FALSE

Clustering(38) Variable = 21Q GAIN MUTATION ANALYSIS
D38V1, survival
                    sevent
clus2                  0   1
  21Q GAIN MUTATED    19   7
  21Q GAIN WILD-TYPE 282 106
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                26                388 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 7                106 
$`21Q GAIN MUTATED`
TCGA-BA-6873 TCGA-BA-A6DL TCGA-BB-4225 TCGA-CN-4727 TCGA-CN-4729 TCGA-CN-4740 
         113          623          140         1230          392          811 
TCGA-CN-5356 TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-A63U TCGA-CR-6467 TCGA-CR-6478 
        1045          224          394          526         1777         1969 
TCGA-CR-7402 TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5441 TCGA-CV-6945 TCGA-CV-7433 
         911         1955         1950         2886         1969         1984 
TCGA-CV-A461 TCGA-D6-A6EP TCGA-DQ-7591 TCGA-HD-8224 TCGA-HD-8314 TCGA-IQ-A61O 
        1954          424          622           55           44          360 
TCGA-P3-A6SW TCGA-UF-A7JA 
        1120         1894 

$`21Q GAIN WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 
         102          462          283          415         1983          276 
TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 
         248          722         1288         1762          520          725 
TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 
         623         1636         1747          190          644          451 
TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH 
          63          384          236          895          855          622 
TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DG 
         918          850          351          216          182         1976 
TCGA-BA-A6DJ TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4227 
         314          142          187         2878          278          133 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 
         558          310          536          423          687          638 
TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A47Z 
        1153          428          436         1955          624            5 
TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 
           4          799          721         1157          142         1151 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 
         817          993          642         1250          395          625 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 
        1960         1330         1268         1988         1007          173 
TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 
        1980         1081         1977         1980         1966         1966 
TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 
        1975          683          290          630          933          629 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 
         628          594          629           45          432           98 
TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 
        1970          202         1110          318          611          735 
TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A 
         432          429           46          443          535          391 
TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y 
         904          645          225          484          348          175 
TCGA-CN-A641 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
         367          223          298         1466         1207          654 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 
        1660         1422         1393         1399          317          341 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 
         129         1253         1000         1057          985         1959 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 
        1959         1179         1750         1560         1007          509 
TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 
        1309         1274          877         1950         1353         1960 
TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG 
         707         1963          893          998          785          391 
TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 
         303          950         2562          358         1663         1152 
TCGA-CR-5250 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 
         799         1521         1966         1050         1125         1971 
TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 
         514          362          311          345          354          234 
TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 
         379          350          479         1956         1435         1191 
TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 
        1440         1245         1960          105         1979          759 
TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 
         889           30          972         1968         1036          796 
TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 
        1954          997         1430         1951          392          907 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 
         913          946          908          898          930          216 
TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5434 
         156          181         1077         1472          522         3295 
TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5443 
        1438          584          546         1978         2327         1958 
TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 
        2437          519          406          701         2641         1478 
TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 
        1840          215         1315         1665          641         1899 
TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6942 
        1970         1948         1969         1952         1959         3835 
TCGA-CV-6943 TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 
        1948         1966         1957         1969         1959         3837 
TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 
        1959         1970         1970         1936         1959         1939 
TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7242 
        1945         1987         1979         1952         1444         1095 
TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 
         954          797         1967         1960         1976         1099 
TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7427 
        1974         1948         1955         1957         1947         1937 
TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7440 
        1973         1972         1937         1958         1959         1981 
TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 
         851         1945         5480         1960         1940         1946 
TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO 
        1722         1977         1970         1075          906         1959 
TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 
         670          110          646          714          606          685 
TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 
        1950          317          321          237          828          773 
TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 
         292          701           77          491          154          568 
TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM 
         106          128          539          376          483          232 
TCGA-D6-A6EO TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 
         435          368          389          338         1778         1081 
TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 
         516         1030          548         1965          575          775 
TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 
         299          369          368          324          340         1131 
TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S 
         490          658           15           92          585            3 
TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8501 
         384           14           13            6          407           58 
TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 
         133          414          403          206            2            5 
TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 
          25           37           24           25           11           49 
TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 
          10          111           33         1057          485          122 
TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61L 
         441          588          360          412          440          351 
TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X 
         224          552          378          168           14           34 
TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-MZ-A7D7 
         392           56          111          112          254          240 
TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 
         910         1726         1559         1954          578         1917 
TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG 
        1968          400          553          357          245          218 
TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A8Z7 TCGA-QK-A8Z9 
         228          225          387          567          198          149 
TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-UF-A718 TCGA-UF-A719 
         135          135          157          168         1326         1663 
TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JC TCGA-UF-A7JD 
        1319         1252         1278         1043          484          735 
TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JS 
        1497          665          214          413 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                44                  2 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              2886               5480 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
               861                694 
[1] "44.0 - 2886.0 (861.0)" "2.0 - 5480.0 (694.0)" 
[1] "hr=" "1.3"
D38V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  21Q GAIN MUTATED         0        0         7        16         1         0
  21Q GAIN WILD-TYPE      26       75        67       219        11         1
D38V3, multiclass
           clus
vv          21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  STAGE I                  0                 26
  STAGE II                 0                 75
  STAGE III                7                 67
  STAGE IVA               16                219
  STAGE IVB                1                 11
  STAGE IVC                0                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  21Q GAIN MUTATED       2   4   7  12
  21Q GAIN WILD-TYPE    45 123  87 150
D38V4, multiclass
       clus
vv      21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  T0+T1                2                 45
  T2                   4                123
  T3                   7                 87
  T4                  12                150
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  21Q GAIN MUTATED     7   5  12   1
  21Q GAIN WILD-TYPE 163  58 140   7
D38V5, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  N0                7                163
  N1                5                 58
  N2               12                140
  N3                1                  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"
                    vv
clus                  M0  M1  MX
  21Q GAIN MUTATED     8   0   3
  21Q GAIN WILD-TYPE 159   1  55
D38V6, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  M0                8                159
  M1                0                  1
  MX                3                 55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V7, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     4  28
  21Q GAIN WILD-TYPE 128 328
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      4   28
  21Q GAIN WILD-TYPE  128  328
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE                4                128
  MALE                 28                328
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  21Q GAIN MUTATED                                      29
  21Q GAIN WILD-TYPE                                   448
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  21Q GAIN MUTATED                                                             1
  21Q GAIN WILD-TYPE                                                           0
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  21Q GAIN MUTATED                                                     2
  21Q GAIN WILD-TYPE                                                   8
D38V8, multiclass
                                                             clus
vv                                                            21Q GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     29
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        2
                                                             clus
vv                                                            21Q GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      448
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                  0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                          8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V9, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     7  25
  21Q GAIN WILD-TYPE  72 384
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      7   25
  21Q GAIN WILD-TYPE   72  384
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  NO                 7                 72
  YES               25                384
[1] 2 2
[1] FALSE
D38V10, continuous
D38V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  21Q GAIN MUTATED                                  0     0
  21Q GAIN WILD-TYPE                                2    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  21Q GAIN MUTATED                           1    30
  21Q GAIN WILD-TYPE                        43   385
D38V12, multiclass
                                  clus
vv                                 21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                 11
  BLACK OR AFRICAN AMERICAN                       1                 43
  WHITE                                          30                385
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V13, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     4  26
  21Q GAIN WILD-TYPE  20 405
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      4   26
  21Q GAIN WILD-TYPE   20  405
                        clus
vv                       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                 20
  NOT HISPANIC OR LATINO               26                405
[1] 2 2
[1] FALSE

Clustering(39) Variable = 22Q GAIN MUTATION ANALYSIS
D39V1, survival
                    sevent
clus2                  0   1
  22Q GAIN MUTATED    59  29
  22Q GAIN WILD-TYPE 242  84
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                88                326 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                29                 84 
$`22Q GAIN MUTATED`
TCGA-BA-4074 TCGA-BA-4078 TCGA-BA-5555 TCGA-BA-5557 TCGA-BA-7269 TCGA-BA-A6DA 
         462          276          520          623          236          351 
TCGA-BA-A6DL TCGA-BB-7870 TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A480 TCGA-CN-4728 
         623         1153         1955          624            4         1151 
TCGA-CN-4737 TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5367 TCGA-CN-6010 TCGA-CN-6012 
         625         1988         1045         1966          630          629 
TCGA-CN-6016 TCGA-CN-6024 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-A498 TCGA-CN-A49A 
         594          224          611          735          443          391 
TCGA-CQ-5332 TCGA-CQ-6221 TCGA-CQ-6224 TCGA-CQ-6229 TCGA-CQ-7067 TCGA-CQ-7069 
         317         1000          985         1179          509         1274 
TCGA-CQ-7072 TCGA-CR-6471 TCGA-CR-6474 TCGA-CR-6482 TCGA-CR-7365 TCGA-CR-7370 
        1950         1966         1971          345         1191          105 
TCGA-CR-7371 TCGA-CR-7383 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7397 TCGA-CR-7401 
        1979         1954          392          907          216         1077 
TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5970 TCGA-CV-5978 TCGA-CV-6941 
        1955         1950         3295          406          215         1959 
TCGA-CV-7090 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 
        3837         1939         1945          797         1967         1960 
TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7433 TCGA-CV-7434 
        1976         1099         1957         1947         1984         1958 
TCGA-CV-7440 TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A6JE TCGA-CX-7219 TCGA-D6-A4ZB 
        1981         1960         1940         1075          828          376 
TCGA-D6-A6EP TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-7589 TCGA-HD-7753 TCGA-HD-7917 
         424         1081          516          575            5           37 
TCGA-HD-8634 TCGA-IQ-A61H TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66T TCGA-MT-A51X 
          24          412          351          360          552           34 
TCGA-MZ-A7D7 TCGA-P3-A6SX TCGA-P3-A6T4 TCGA-QK-A8Z7 TCGA-QK-A8ZA TCGA-UF-A719 
         240         1954         1968          198          135         1663 
TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JD 
        1319         1278         1043          735 

$`22Q GAIN WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-5151 
         102          283          415         1983          248          722 
TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 
        1288         1762          725         1636         1747          190 
TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-A4IF 
         644          451           63          384          113          895 
TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DB TCGA-BA-A6DE 
         855          622          918          850          216          182 
TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 
        1976          314          142          187         2878          278 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 
         140          133          558          310          536          423 
TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7871 TCGA-BB-7872 TCGA-C9-A47Z TCGA-CN-4722 
         687          638          428          436            5          799 
TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4729 TCGA-CN-4730 
         721         1157          142         1230          392          817 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4739 
         993          642         1250          395         1960         1330 
TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 
         811         1268         1007          173         1980         1081 
TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 
        1977         1980         1966         1975          683          290 
TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 
         933          628          629           45          432           98 
TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6988 TCGA-CN-6992 TCGA-CN-6996 
        1970          202         1110          318          394          432 
TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T 
         429           46          535          904          645          225 
TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A6V1 
         526          484          348          175          367          223 
TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 
         298         1466         1207          654         1660         1422 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6223 
        1393         1399          341          129         1253         1057 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7068 
        1959         1959         1750         1560         1007         1309 
TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB 
         877         1353         1960          707         1963          893 
TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 
         998          785          391          303          950         2562 
TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 
         358         1663         1152          799         1777         1521 
TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 
        1050         1125          514         1969          362          311 
TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 
         354          234          379          350          479         1956 
TCGA-CR-7364 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7372 TCGA-CR-7373 
        1435         1440         1245         1960          759          889 
TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7385 
          30          972         1968         1036          796          997 
TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 
        1430         1951          913          946          908          898 
TCGA-CR-7395 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5431 
         930          156          181          911         1472          522 
TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 
        1438          584          546         1978         2886         2327 
TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 
        1958         2437          519          701         2641         1478 
TCGA-CV-5977 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 
        1840         1315         1665          641         1899         1970 
TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 
        1948         1969         1952         3835         1948         1969 
TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7091 TCGA-CV-7095 
        1966         1957         1969         1959         1959         1970 
TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 
        1970         1936         1959         1987         1979         1952 
TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 
        1444         1095          954         1974         1948         1955 
TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7435 TCGA-CV-A45O 
        1937         1973         1972         1937         1959          851 
TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A468 
        1945         5480         1946         1954         1722         1977 
TCGA-CV-A6JD TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY 
        1970          906         1959          670          110          646 
TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 
         714          606          685         1950          317          321 
TCGA-CX-7086 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 
         237          773          292          701           77          491 
TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A6EK 
         154          568          106          128          539          483 
TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 
         232          435          368          389          338         1778 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 
        1030          548         1965          775          622          299 
TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 
         369          368          324          340         1131          490 
TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V 
         658           15           92          585            3          384 
TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 
          14           13            6          407           58          133 
TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-8224 
         414          403          206            2           25           55 
TCGA-HD-8314 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ 
          44           25           11           49           10          111 
TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E 
          33         1057          485          122          441          588 
TCGA-IQ-A61G TCGA-IQ-A61J TCGA-KU-A66S TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W 
         360          440          224          378          168           14 
TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A5Q5 
         392           56          111          112          254          910 
TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T8 
        1726         1559         1120          578         1917          400 
TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II 
         553          357          245          218          228          225 
TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A8Z9 TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K 
         387          567          149          135          157          168 
TCGA-UF-A718 TCGA-UF-A71D TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JF TCGA-UF-A7JH 
        1326         1252         1894          484         1497          665 
TCGA-UF-A7JJ TCGA-UF-A7JS 
         214          413 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 4                  2 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              3837               5480 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             867.5              676.5 
[1] "4.0 - 3837.0 (867.5)" "2.0 - 5480.0 (676.5)"
[1] "hr=" "1"  
D39V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  22Q GAIN MUTATED         5       15        17        56         2         0
  22Q GAIN WILD-TYPE      21       60        57       179        10         1
D39V3, multiclass
           clus
vv          22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  STAGE I                  5                 21
  STAGE II                15                 60
  STAGE III               17                 57
  STAGE IVA               56                179
  STAGE IVB                2                 10
  STAGE IVC                0                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  22Q GAIN MUTATED       9  25  23  40
  22Q GAIN WILD-TYPE    38 102  71 122
D39V4, multiclass
       clus
vv      22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  T0+T1                9                 38
  T2                  25                102
  T3                  23                 71
  T4                  40                122
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  22Q GAIN MUTATED    39  12  37   1
  22Q GAIN WILD-TYPE 131  51 115   7
D39V5, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  N0               39                131
  N1               12                 51
  N2               37                115
  N3                1                  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"
                    vv
clus                  M0  M1  MX
  22Q GAIN MUTATED    32   0  16
  22Q GAIN WILD-TYPE 135   1  42
D39V6, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  M0               32                135
  M1                0                  1
  MX               16                 42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V7, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    24  84
  22Q GAIN WILD-TYPE 108 272
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     24   84
  22Q GAIN WILD-TYPE  108  272
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE               24                108
  MALE                 84                272
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  22Q GAIN MUTATED                                     105
  22Q GAIN WILD-TYPE                                   372
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  22Q GAIN MUTATED                                                             1
  22Q GAIN WILD-TYPE                                                           0
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  22Q GAIN MUTATED                                                     2
  22Q GAIN WILD-TYPE                                                   8
D39V8, multiclass
                                                             clus
vv                                                            22Q GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    105
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        2
                                                             clus
vv                                                            22Q GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      372
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                  0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                          8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V9, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    20  88
  22Q GAIN WILD-TYPE  59 321
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     20   88
  22Q GAIN WILD-TYPE   59  321
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  NO                20                 59
  YES               88                321
[1] 2 2
[1] FALSE
D39V10, continuous
D39V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  22Q GAIN MUTATED                                  1     2
  22Q GAIN WILD-TYPE                                1     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  22Q GAIN MUTATED                          12    89
  22Q GAIN WILD-TYPE                        32   326
D39V12, multiclass
                                  clus
vv                                 22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  1
  ASIAN                                           2                  9
  BLACK OR AFRICAN AMERICAN                      12                 32
  WHITE                                          89                326
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V13, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED     9  92
  22Q GAIN WILD-TYPE  15 339
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      9   92
  22Q GAIN WILD-TYPE   15  339
                        clus
vv                       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    9                 15
  NOT HISPANIC OR LATINO               92                339
[1] 2 2
[1] FALSE

Clustering(40) Variable = XQ GAIN MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                 0   1
  XQ GAIN MUTATED    43  21
  XQ GAIN WILD-TYPE 258  92
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               64               350 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               21                92 
$`XQ GAIN MUTATED`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-6872 TCGA-BA-7269 TCGA-BB-4223 
         283         1983          248          384          236         2878 
TCGA-BB-4225 TCGA-BB-4227 TCGA-CN-4728 TCGA-CN-4737 TCGA-CN-4740 TCGA-CN-4742 
         140          133         1151          625          811         1988 
TCGA-CN-5359 TCGA-CN-5367 TCGA-CN-6012 TCGA-CN-6023 TCGA-CN-6988 TCGA-CN-6989 
        1980         1966          629         1110          318          611 
TCGA-CN-A49B TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-6229 TCGA-CQ-7072 TCGA-CQ-A4C7 
         904         1660         1422         1179         1950         1960 
TCGA-CQ-A4CG TCGA-CR-5247 TCGA-CR-6467 TCGA-CR-6477 TCGA-CR-6493 TCGA-CR-7370 
         391          358         1777          514         1956          105 
TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5442 TCGA-CV-5444 TCGA-CV-5970 TCGA-CV-5977 
        3295         1438         2327         2437          406         1840 
TCGA-CV-6936 TCGA-CV-7102 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7250 TCGA-CV-7254 
        1952         1945          954          797         1960         1976 
TCGA-CV-A45Q TCGA-CV-A6JY TCGA-CX-7086 TCGA-D6-6516 TCGA-D6-6823 TCGA-D6-8568 
        1945          646          237          773          701          106 
TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5631 TCGA-DQ-7592 TCGA-HD-7917 TCGA-HD-A6I0 
        1081          516          548          299           37           33 
TCGA-IQ-A61G TCGA-IQ-A61J TCGA-KU-A66T TCGA-MT-A51X TCGA-QK-A8ZA TCGA-UF-A719 
         360          440          552           34          135         1663 
TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7JA TCGA-UF-A7JH 
        1319         1278         1894          665 

$`XQ GAIN WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5151 TCGA-BA-5152 
         102          462          415          276          722         1288 
TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 
        1762          520          725          623         1636         1747 
TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6873 TCGA-BA-A4IF 
         190          644          451           63          113          895 
TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB 
         855          622          918          850          351          216 
TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 
         182         1976          314          623          142          187 
TCGA-BB-4224 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 
         278          558          310          536          423          687 
TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 
         638         1153          428          436         1955          624 
TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 
           5            4          799          721         1157          142 
TCGA-CN-4727 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 
        1230          392          817          993          642         1250 
TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4741 TCGA-CN-5355 TCGA-CN-5356 
         395         1960         1330         1268         1007         1045 
TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5370 
         173         1081         1977         1980         1966         1975 
TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6016 
         683          290          630          933          628          594 
TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 
         629           45          432           98         1970          202 
TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 
         224          394          735          432          429           46 
TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U 
         443          535          391          645          225          526 
TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A6V1 TCGA-CN-A6V3 
         484          348          175          367          223          298 
TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 
        1466         1207          654         1393         1399          317 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 
         341          129         1253         1000         1057          985 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 
        1959         1959         1750         1560         1007          509 
TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CA 
        1309         1274          877         1353          707         1963 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 
         893          998          785          303          950         2562 
TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 
        1663         1152          799         1521         1966         1050 
TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 
        1125         1971         1969          362          311          345 
TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-7364 
         354          234          379          350          479         1435 
TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7372 
        1191         1440         1245         1960         1979          759 
TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 
         889           30          972         1968         1036          796 
TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 
        1954          997         1430         1951          392          907 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 
         913          946          908          898          930          216 
TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 
         156          181         1077          911         1472         1955 
TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 
         522         1950          584          546         1978         2886 
TCGA-CV-5443 TCGA-CV-5966 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5978 
        1958          519          701         2641         1478          215 
TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 
        1315         1665          641         1899         1970         1948 
TCGA-CV-6935 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6952 
        1969         1959         3835         1948         1969         1966 
TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 
        1957         1969         1959         3837         1959         1970 
TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7180 TCGA-CV-7183 
        1970         1936         1959         1939         1987         1979 
TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7248 TCGA-CV-7261 TCGA-CV-7406 
        1952         1444         1095         1967         1099         1974 
TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7428 
        1948         1955         1957         1947         1937         1973 
TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7440 
        1972         1937         1984         1958         1959         1981 
TCGA-CV-A45O TCGA-CV-A45R TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 
         851         5480         1960         1940         1946         1954 
TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO 
        1722         1977         1970         1075          906         1959 
TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 
         670          110          714          606          685         1950 
TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7219 TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 
         317          321          828          292           77          491 
TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK 
         154          568          128          539          376          483 
TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q 
         232          435          424          368          389          338 
TCGA-DQ-5624 TCGA-DQ-5630 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 
        1778         1030         1965          575          775          622 
TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 
         369          368          324          340         1131          490 
TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V 
         658           15           92          585            3          384 
TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 
          14           13            6          407           58          133 
TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 
         414          403          206            2            5           25 
TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 
          55           44           24           25           11           49 
TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 
          10          111         1057          485          122          441 
TCGA-IQ-A61E TCGA-IQ-A61H TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A6H7 
         588          412          351          360          224          378 
TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G 
         168           14          392           56          111          112 
TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW 
         254          240          910         1726         1559         1120 
TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A64Z 
        1954          578         1917         1968          400          553 
TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ 
         357          245          218          228          225          387 
TCGA-QK-A6V9 TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K 
         567          198          149          135          157          168 
TCGA-UF-A718 TCGA-UF-A71D TCGA-UF-A7J9 TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF 
        1326         1252         1043          484          735         1497 
TCGA-UF-A7JJ TCGA-UF-A7JS 
         214          413 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               33                 2 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             3295              5480 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
              804               684 
[1] "33.0 - 3295.0 (804.0)" "2.0 - 5480.0 (684.0)" 
[1] "hr=" "1.2"
D40V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  XQ GAIN MUTATED         1       10        11        46         2         0
  XQ GAIN WILD-TYPE      25       65        63       189        10         1
D40V3, multiclass
           clus
vv          XQ GAIN MUTATED XQ GAIN WILD-TYPE
  STAGE I                 1                25
  STAGE II               10                65
  STAGE III              11                63
  STAGE IVA              46               189
  STAGE IVB               2                10
  STAGE IVC               0                 1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  XQ GAIN MUTATED       2  18  17  33
  XQ GAIN WILD-TYPE    45 109  77 129
D40V4, multiclass
       clus
vv      XQ GAIN MUTATED XQ GAIN WILD-TYPE
  T0+T1               2                45
  T2                 18               109
  T3                 17                77
  T4                 33               129
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  XQ GAIN MUTATED    25   9  30   1
  XQ GAIN WILD-TYPE 145  54 122   7
D40V5, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  N0              25               145
  N1               9                54
  N2              30               122
  N3               1                 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"
                   vv
clus                 M0  M1  MX
  XQ GAIN MUTATED    22   0   8
  XQ GAIN WILD-TYPE 145   1  50
D40V6, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  M0              22               145
  M1               0                 1
  MX               8                50
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V7, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    19  62
  XQ GAIN WILD-TYPE 113 294
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     19   62
  XQ GAIN WILD-TYPE  113  294
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE              19               113
  MALE                62               294
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  XQ GAIN MUTATED                                      80
  XQ GAIN WILD-TYPE                                   397
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  XQ GAIN MUTATED                                                             0
  XQ GAIN WILD-TYPE                                                           1
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  XQ GAIN MUTATED                                                     1
  XQ GAIN WILD-TYPE                                                   9
D40V8, multiclass
                                                             clus
vv                                                            XQ GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    80
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       1
                                                             clus
vv                                                            XQ GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     397
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                 1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V9, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    22  59
  XQ GAIN WILD-TYPE  57 350
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     22   59
  XQ GAIN WILD-TYPE   57  350
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  NO               22                57
  YES              59               350
[1] 2 2
[1] FALSE
D40V10, continuous
D40V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XQ GAIN MUTATED                                  1     1
  XQ GAIN WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XQ GAIN MUTATED                           9    68
  XQ GAIN WILD-TYPE                        35   347
D40V12, multiclass
                                  clus
vv                                 XQ GAIN MUTATED XQ GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 1
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      9                35
  WHITE                                         68               347
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V13, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     4  70
  XQ GAIN WILD-TYPE  20 361
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      4   70
  XQ GAIN WILD-TYPE   20  361
                        clus
vv                       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                20
  NOT HISPANIC OR LATINO              70               361
[1] 2 2
[1] FALSE

Clustering(41) Variable = 1P LOSS MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                 0   1
  1P LOSS MUTATED    33  15
  1P LOSS WILD-TYPE 268  98
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               48               366 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               15                98 
$`1P LOSS MUTATED`
TCGA-4P-AA8J TCGA-BA-4075 TCGA-BA-5152 TCGA-BA-6871 TCGA-BA-7269 TCGA-BA-A6D8 
         102          283         1288           63          236          850 
TCGA-CN-4736 TCGA-CN-5355 TCGA-CN-5360 TCGA-CN-6012 TCGA-CN-6018 TCGA-CN-6021 
         395         1007         1081          629           45         1970 
TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6997 TCGA-CN-A63T TCGA-CN-A63W 
         224          394          735          429          225          348 
TCGA-CQ-5332 TCGA-CQ-7072 TCGA-CQ-A4CA TCGA-CQ-A4CI TCGA-CR-7365 TCGA-CR-7370 
         317         1950         1963          950         1191          105 
TCGA-CR-7371 TCGA-CR-7372 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5439 TCGA-CV-5440 
        1979          759         1950         3295          546         1978 
TCGA-CV-6003 TCGA-CV-6935 TCGA-CV-7101 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7424 
        1665         1969         1939         1976         1099         1947 
TCGA-D6-6516 TCGA-D6-A6EM TCGA-DQ-7589 TCGA-F7-8489 TCGA-F7-A61W TCGA-HD-8634 
         773          232          575          658           14           24 
TCGA-HD-A6HZ TCGA-IQ-A61L TCGA-MZ-A6I9 TCGA-P3-A6T8 TCGA-UF-A7J9 TCGA-UF-A7JD 
         111          351          254          400         1043          735 

$`1P LOSS WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 
         462          415         1983          276          248          722 
TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 
        1762          520          725          623         1636         1747 
TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-A4IF 
         190          644          451          384          113          895 
TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE 
         855          622          918          351          216          182 
TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 
        1976          314          623          142          187         2878 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 
         278          140          133          558          310          536 
TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 
         423          687          638         1153          428          436 
TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 
        1955          624            5            4          799          721 
TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 
        1157          142         1230         1151          392          817 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 
         993          642         1250          625         1960         1330 
TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 
         811         1268         1988         1045          173         1980 
TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 
        1977         1980         1966         1966         1975          683 
TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 
         290          630          933          628          594          629 
TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6988 TCGA-CN-6989 
         432           98          202         1110          318          611 
TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B 
         432           46          443          535          391          904 
TCGA-CN-A49C TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A6V1 
         645          526          484          175          367          223 
TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 
         298         1466         1207          654         1660         1422 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 
        1393         1399          341          129         1253         1000 
TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 
        1057          985         1959         1959         1179         1750 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 
        1560         1007          509         1309         1274          877 
TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE 
        1353         1960          707          893          998          785 
TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 
         391          303         2562          358         1663         1152 
TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 
         799         1777         1521         1966         1050         1125 
TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 
        1971          514         1969          362          311          345 
TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 
         354          234          379          350          479         1956 
TCGA-CR-7364 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7373 TCGA-CR-7374 
        1435         1440         1245         1960          889           30 
TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 
         972         1968         1036          796         1954          997 
TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 
        1430         1951          392          907          913          946 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 
         908          898          930          216          156          181 
TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5435 
        1077          911         1472         1955          522         1438 
TCGA-CV-5436 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 
         584         2886         2327         1958         2437          519 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 
         406          701         2641         1478         1840          215 
TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6936 
        1315          641         1899         1970         1948         1952 
TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-6954 
        1959         3835         1948         1969         1966         1957 
TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 
        1969         1959         3837         1959         1970         1970 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 
        1936         1959         1945         1987         1979         1952 
TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 
        1444         1095          954          797         1967         1960 
TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7427 TCGA-CV-7428 
        1974         1948         1955         1957         1937         1973 
TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7440 
        1972         1937         1984         1958         1959         1981 
TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 
         851         1945         5480         1960         1940         1946 
TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN 
        1954         1722         1977         1970         1075          906 
TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 
        1959          670          110          646          714          606 
TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 
         685         1950          317          321          237          828 
TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 
         292          701           77          491          154          568 
TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EO 
         106          128          539          376          483          435 
TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 
         424          368          389          338         1778         1081 
TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7590 TCGA-DQ-7591 
         516         1030          548         1965          775          622 
TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 
         299          369          368          324          340         1131 
TCGA-F7-8298 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V 
         490           15           92          585            3          384 
TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 
          13            6          407           58          133          414 
TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 
         403          206            2            5           25           37 
TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 
          55           44           25           11           49           10 
TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E 
          33         1057          485          122          441          588 
TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T 
         360          412          440          360          224          552 
TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D 
         378          168           14           34          392           56 
TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE 
         111          112          240          910         1726         1559 
TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-QK-A64Z 
        1120         1954          578         1917         1968          553 
TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ 
         357          245          218          228          225          387 
TCGA-QK-A6V9 TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J 
         567          198          149          135          135          157 
TCGA-QK-AA3K TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E 
         168         1326         1663         1319         1252         1278 
TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JS 
        1894          484         1497          665          214          413 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               14                 2 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             3295              5480 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            696.5             701.0 
[1] "14.0 - 3295.0 (696.5)" "2.0 - 5480.0 (701.0)" 
[1] "hr=" "1.1"
D41V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  1P LOSS MUTATED         3        7        10        29         0         0
  1P LOSS WILD-TYPE      23       68        64       206        12         1
D41V3, multiclass
           clus
vv          1P LOSS MUTATED 1P LOSS WILD-TYPE
  STAGE I                 3                23
  STAGE II                7                68
  STAGE III              10                64
  STAGE IVA              29               206
  STAGE IVB               0                12
  STAGE IVC               0                 1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  1P LOSS MUTATED       4  14  13  19
  1P LOSS WILD-TYPE    43 113  81 143
D41V4, multiclass
       clus
vv      1P LOSS MUTATED 1P LOSS WILD-TYPE
  T0+T1               4                43
  T2                 14               113
  T3                 13                81
  T4                 19               143
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  1P LOSS MUTATED    20   7  19   0
  1P LOSS WILD-TYPE 150  56 133   8
D41V5, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  N0              20               150
  N1               7                56
  N2              19               133
  N3               0                 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"
                   vv
clus                 M0  M1  MX
  1P LOSS MUTATED    18   0   7
  1P LOSS WILD-TYPE 149   1  51
D41V6, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  M0              18               149
  M1               0                 1
  MX               7                51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V7, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    13  42
  1P LOSS WILD-TYPE 119 314
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     13   42
  1P LOSS WILD-TYPE  119  314
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE              13               119
  MALE                42               314
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  1P LOSS MUTATED                                      54
  1P LOSS WILD-TYPE                                   423
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  1P LOSS MUTATED                                                             0
  1P LOSS WILD-TYPE                                                           1
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  1P LOSS MUTATED                                                     1
  1P LOSS WILD-TYPE                                                   9
D41V8, multiclass
                                                             clus
vv                                                            1P LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    54
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       1
                                                             clus
vv                                                            1P LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     423
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                 1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V9, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    10  45
  1P LOSS WILD-TYPE  69 364
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     10   45
  1P LOSS WILD-TYPE   69  364
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  NO               10                69
  YES              45               364
[1] 2 2
[1] FALSE
D41V10, continuous
D41V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1P LOSS MUTATED                                  0     2
  1P LOSS WILD-TYPE                                2     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1P LOSS MUTATED                           5    46
  1P LOSS WILD-TYPE                        39   369
D41V12, multiclass
                                  clus
vv                                 1P LOSS MUTATED 1P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          2                 9
  BLACK OR AFRICAN AMERICAN                      5                39
  WHITE                                         46               369
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V13, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     2  47
  1P LOSS WILD-TYPE  22 384
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      2   47
  1P LOSS WILD-TYPE   22  384
                        clus
vv                       1P LOSS MUTATED 1P LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                22
  NOT HISPANIC OR LATINO              47               384
[1] 2 2
[1] FALSE

Clustering(42) Variable = 1Q LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                 0   1
  1Q LOSS MUTATED    20  10
  1Q LOSS WILD-TYPE 281 103
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               30               384 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               10               103 
$`1Q LOSS MUTATED`
TCGA-4P-AA8J TCGA-BA-5149 TCGA-BA-5152 TCGA-C9-A47Z TCGA-CN-4736 TCGA-CN-5355 
         102          248         1288            5          395         1007 
TCGA-CN-6012 TCGA-CN-6018 TCGA-CN-6994 TCGA-CN-A63T TCGA-CN-A63W TCGA-CQ-6227 
         629           45          735          225          348         1959 
TCGA-CQ-A4C7 TCGA-CQ-A4CA TCGA-CR-7365 TCGA-CR-7372 TCGA-CV-5432 TCGA-CV-5439 
        1960         1963         1191          759         1950          546 
TCGA-CV-5441 TCGA-CV-6003 TCGA-CV-7424 TCGA-DQ-7588 TCGA-F7-8489 TCGA-F7-A61W 
        2886         1665         1947         1965          658           14 
TCGA-HD-8634 TCGA-HD-A6HZ TCGA-IQ-A61L TCGA-MZ-A6I9 TCGA-P3-A6T8 TCGA-UF-A7JC 
          24          111          351          254          400          484 

$`1Q LOSS WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5151 
         462          283          415         1983          276          722 
TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 
        1762          520          725          623         1636         1747 
TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 
         190          644          451           63          384          113 
TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 
         236          895          855          622          918          850 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A6DL 
         351          216          182         1976          314          623 
TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 
         142          187         2878          278          140          133 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 
         558          310          536          423          687          638 
TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A480 
        1153          428          436         1955          624            4 
TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 
         799          721         1157          142         1230         1151 
TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4737 
         392          817          993          642         1250          625 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5356 
        1960         1330          811         1268         1988         1045 
TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 
         173         1980         1081         1977         1980         1966 
TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 
        1966         1975          683          290          630          933 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 
         628          594          629          432           98         1970 
TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 
         202         1110          224          318          611          394 
TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A 
         432          429           46          443          535          391 
TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A641 
         904          645          526          484          175          367 
TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 
         223          298         1466         1207          654         1660 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 
        1422         1393         1399          317          341          129 
TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6228 TCGA-CQ-6229 
        1253         1000         1057          985         1959         1179 
TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 
        1750         1560         1007          509         1309         1274 
TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD 
         877         1950         1353          707          893          998 
TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 
         785          391          303          950         2562          358 
TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 
        1663         1152          799         1777         1521         1966 
TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 
        1050         1125         1971          514         1969          362 
TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 
         311          345          354          234          379          350 
TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 
         479         1956         1435         1440         1245         1960 
TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 
         105         1979          889           30          972         1968 
TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 
        1036          796         1954          997         1430         1951 
TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 
         392          907          913          946          908          898 
TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 
         930          216          156          181         1077          911 
TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 
        1472         1955          522         3295         1438          584 
TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 
        1978         2327         1958         2437          519          406 
TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 
         701         2641         1478         1840          215         1315 
TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 
         641         1899         1970         1948         1969         1952 
TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-6954 
        1959         3835         1948         1969         1966         1957 
TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 
        1969         1959         3837         1959         1970         1970 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7183 
        1936         1959         1939         1945         1987         1979 
TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 
        1952         1444         1095          954          797         1967 
TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 
        1960         1976         1099         1974         1948         1955 
TCGA-CV-7422 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 
        1957         1937         1973         1972         1937         1984 
TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A45R 
        1958         1959         1981          851         1945         5480 
TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A468 
        1960         1940         1946         1954         1722         1977 
TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU 
        1970         1075          906         1959          670          110 
TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 
         646          714          606          685         1950          317 
TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 
         321          237          828          773          292          701 
TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 
          77          491          154          568          106          128 
TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP 
         539          376          483          232          435          424 
TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 
         368          389          338         1778         1081          516 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 
        1030          548          575          775          622          299 
TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 
         369          368          324          340         1131          490 
TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A620 
          15           92          585            3          384           13 
TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 
           6          407           58          133          414          403 
TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 
         206            2            5           25           37           55 
TCGA-HD-8314 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6I0 
          44           25           11           49           10           33 
TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G 
        1057          485          122          441          588          360 
TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 
         412          440          360          224          552          378 
TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F 
         168           14           34          392           56          111 
TCGA-MT-A67G TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW 
         112          240          910         1726         1559         1120 
TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-QK-A64Z TCGA-QK-A652 
        1954          578         1917         1968          553          357 
TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 
         245          218          228          225          387          567 
TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K 
         198          149          135          135          157          168 
TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 
        1326         1663         1319         1252         1278         1043 
TCGA-UF-A7JA TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JS 
        1894          735         1497          665          214          413 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                5                 2 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             2886              5480 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            587.5             710.5 
[1] "5.0 - 2886.0 (587.5)" "2.0 - 5480.0 (710.5)"
[1] "hr=" "1.5"
D42V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  1Q LOSS MUTATED         2        3         7        21         0         0
  1Q LOSS WILD-TYPE      24       72        67       214        12         1
D42V3, multiclass
           clus
vv          1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  STAGE I                 2                24
  STAGE II                3                72
  STAGE III               7                67
  STAGE IVA              21               214
  STAGE IVB               0                12
  STAGE IVC               0                 1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  1Q LOSS MUTATED       3   8  12  11
  1Q LOSS WILD-TYPE    44 119  82 151
D42V4, multiclass
       clus
vv      1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  T0+T1               3                44
  T2                  8               119
  T3                 12                82
  T4                 11               151
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  1Q LOSS MUTATED    13   4  15   0
  1Q LOSS WILD-TYPE 157  59 137   8
D42V5, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  N0              13               157
  N1               4                59
  N2              15               137
  N3               0                 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"
                   vv
clus                 M0  M1  MX
  1Q LOSS MUTATED    11   0   6
  1Q LOSS WILD-TYPE 156   1  52
D42V6, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  M0              11               156
  M1               0                 1
  MX               6                52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V7, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     9  27
  1Q LOSS WILD-TYPE 123 329
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      9   27
  1Q LOSS WILD-TYPE  123  329
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE               9               123
  MALE                27               329
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  1Q LOSS MUTATED                                      36
  1Q LOSS WILD-TYPE                                   441
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  1Q LOSS MUTATED                                                             0
  1Q LOSS WILD-TYPE                                                           1
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  1Q LOSS MUTATED                                                     0
  1Q LOSS WILD-TYPE                                                  10
D42V8, multiclass
                                                             clus
vv                                                            1Q LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    36
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       0
                                                             clus
vv                                                            1Q LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     441
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                 1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V9, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     6  30
  1Q LOSS WILD-TYPE  73 379
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      6   30
  1Q LOSS WILD-TYPE   73  379
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  NO                6                73
  YES              30               379
[1] 2 2
[1] FALSE
D42V10, continuous
D42V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1Q LOSS MUTATED                                  0     3
  1Q LOSS WILD-TYPE                                2     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1Q LOSS MUTATED                           2    30
  1Q LOSS WILD-TYPE                        42   385
D42V12, multiclass
                                  clus
vv                                 1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          3                 8
  BLACK OR AFRICAN AMERICAN                      2                42
  WHITE                                         30               385
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V13, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     1  32
  1Q LOSS WILD-TYPE  23 399
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      1   32
  1Q LOSS WILD-TYPE   23  399
                        clus
vv                       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                23
  NOT HISPANIC OR LATINO              32               399
[1] 2 2
[1] FALSE

Clustering(43) Variable = 2P LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                 0   1
  2P LOSS MUTATED    20   7
  2P LOSS WILD-TYPE 281 106
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               27               387 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                7               106 
$`2P LOSS MUTATED`
TCGA-BA-4076 TCGA-BA-5559 TCGA-BA-6873 TCGA-BB-7861 TCGA-BB-7862 TCGA-C9-A47Z 
         415         1747          113          310          536            5 
TCGA-CN-6011 TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A63W TCGA-CQ-6218 TCGA-CQ-7064 
         933          535          904          348         1253         1560 
TCGA-CV-5966 TCGA-CV-5973 TCGA-CV-6003 TCGA-CV-6961 TCGA-CV-7432 TCGA-CV-A45R 
         519         2641         1665         1959         1937         5480 
TCGA-CV-A6JY TCGA-D6-6826 TCGA-DQ-7588 TCGA-F7-A50J TCGA-IQ-A61L TCGA-KU-A66T 
         646          154         1965          585          351          552 
TCGA-MZ-A6I9 TCGA-QK-AA3K TCGA-UF-A7JS 
         254          168          413 

$`2P LOSS WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
         102          462          283         1983          276          248 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 
         722         1288         1762          520          725          623 
TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 
        1636          190          644          451           63          384 
TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 
         236          895          855          622          918          850 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A6DL 
         351          216          182         1976          314          623 
TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 
         142          187         2878          278          140          133 
TCGA-BB-4228 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 
         558          423          687          638         1153          428 
TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 
         436         1955          624            4          799          721 
TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 
        1157          142         1230         1151          392          817 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 
         993          642         1250          395          625         1960 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 
        1330          811         1268         1988         1007         1045 
TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 
         173         1980         1081         1977         1980         1966 
TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6012 
        1966         1975          683          290          630          629 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 
         628          594          629           45          432           98 
TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 
        1970          202         1110          224          318          611 
TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 
         394          735          432          429           46          443 
TCGA-CN-A49A TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63Y 
         391          645          225          526          484          175 
TCGA-CN-A641 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
         367          223          298         1466         1207          654 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 
        1660         1422         1393         1399          317          341 
TCGA-CQ-5334 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 
         129         1000         1057          985         1959         1959 
TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 
        1179         1750         1007          509         1309         1274 
TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CA 
         877         1950         1353         1960          707         1963 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI 
         893          998          785          391          303          950 
TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 
        2562          358         1663         1152          799         1777 
TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 
        1521         1966         1050         1125         1971          514 
TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 
        1969          362          311          345          354          234 
TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 
         379          350          479         1956         1435         1191 
TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 
        1440         1245         1960          105         1979          759 
TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 
         889           30          972         1968         1036          796 
TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 
        1954          997         1430         1951          392          907 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 
         913          946          908          898          930          216 
TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 
         156          181         1077          911         1472         1955 
TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 
         522         1950         3295         1438          584          546 
TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5970 
        1978         2886         2327         1958         2437          406 
TCGA-CV-5971 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6433 
         701         1478         1840          215         1315          641 
TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6941 
        1899         1970         1948         1969         1952         1959 
TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6960 
        3835         1948         1969         1966         1957         1969 
TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 
        3837         1959         1970         1970         1936         1959 
TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 
        1939         1945         1987         1979         1952         1444 
TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7254 
        1095          954          797         1967         1960         1976 
TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 
        1099         1974         1948         1955         1957         1947 
TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 
        1937         1973         1972         1984         1958         1959 
TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 
        1981          851         1945         1960         1940         1946 
TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN 
        1954         1722         1977         1970         1075          906 
TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 
        1959          670          110          714          606          685 
TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 
        1950          317          321          237          828          773 
TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6827 TCGA-D6-8568 
         292          701           77          491          568          106 
TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO 
         128          539          376          483          232          435 
TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 
         424          368          389          338         1778         1081 
TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 
         516         1030          548          575          775          622 
TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 
         299          369          368          324          340         1131 
TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A61S TCGA-F7-A61V 
         490          658           15           92            3          384 
TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 
          14           13            6          407           58          133 
TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 
         414          403          206            2            5           25 
TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 
          37           55           44           24           25           11 
TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 
          49           10          111           33         1057          485 
TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J 
         122          441          588          360          412          440 
TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X 
         360          224          378          168           14           34 
TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A7D7 TCGA-P3-A5Q5 
         392           56          111          112          240          910 
TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 
        1726         1559         1120         1954          578         1917 
TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG 
        1968          400          553          357          245          218 
TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A8Z7 TCGA-QK-A8Z9 
         228          225          387          567          198          149 
TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71B 
         135          135          157         1326         1663         1319 
TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD 
        1252         1278         1043         1894          484          735 
TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ 
        1497          665          214 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                5                 2 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             5480              3837 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
              552               714 
[1] "5.0 - 5480.0 (552.0)" "2.0 - 3837.0 (714.0)"
[1] "hr=" "1.1"
D43V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  2P LOSS MUTATED         0        4         9        15         0         0
  2P LOSS WILD-TYPE      26       71        65       220        12         1
D43V3, multiclass
           clus
vv          2P LOSS MUTATED 2P LOSS WILD-TYPE
  STAGE I                 0                26
  STAGE II                4                71
  STAGE III               9                65
  STAGE IVA              15               220
  STAGE IVB               0                12
  STAGE IVC               0                 1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  2P LOSS MUTATED       1   7   8  12
  2P LOSS WILD-TYPE    46 120  86 150
D43V4, multiclass
       clus
vv      2P LOSS MUTATED 2P LOSS WILD-TYPE
  T0+T1               1                46
  T2                  7               120
  T3                  8                86
  T4                 12               150
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  2P LOSS MUTATED    12   8   8   0
  2P LOSS WILD-TYPE 158  55 144   8
D43V5, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  N0              12               158
  N1               8                55
  N2               8               144
  N3               0                 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"
                   vv
clus                 M0  M1  MX
  2P LOSS MUTATED     8   0   7
  2P LOSS WILD-TYPE 159   1  51
D43V6, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  M0               8               159
  M1               0                 1
  MX               7                51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V7, binary
                   cls
clus                  0   1
  2P LOSS MUTATED    15  17
  2P LOSS WILD-TYPE 117 339
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     15   17
  2P LOSS WILD-TYPE  117  339
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE              15               117
  MALE                17               339
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  2P LOSS MUTATED                                      32
  2P LOSS WILD-TYPE                                   445
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  2P LOSS MUTATED                                                             0
  2P LOSS WILD-TYPE                                                           1
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  2P LOSS MUTATED                                                     0
  2P LOSS WILD-TYPE                                                  10
D43V8, multiclass
                                                             clus
vv                                                            2P LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    32
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       0
                                                             clus
vv                                                            2P LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     445
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                 1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V9, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     2  30
  2P LOSS WILD-TYPE  77 379
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      2   30
  2P LOSS WILD-TYPE   77  379
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  NO                2                77
  YES              30               379
[1] 2 2
[1] FALSE
D43V10, continuous
D43V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2P LOSS MUTATED                                  0     1
  2P LOSS WILD-TYPE                                2    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2P LOSS MUTATED                           2    28
  2P LOSS WILD-TYPE                        42   387
D43V12, multiclass
                                  clus
vv                                 2P LOSS MUTATED 2P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      2                42
  WHITE                                         28               387
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V13, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     4  27
  2P LOSS WILD-TYPE  20 404
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      4   27
  2P LOSS WILD-TYPE   20  404
                        clus
vv                       2P LOSS MUTATED 2P LOSS WILD-TYPE
  HISPANIC OR LATINO                   4                20
  NOT HISPANIC OR LATINO              27               404
[1] 2 2
[1] FALSE

Clustering(44) Variable = 2Q LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                 0   1
  2Q LOSS MUTATED    29   9
  2Q LOSS WILD-TYPE 272 104
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               38               376 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                9               104 
$`2Q LOSS MUTATED`
TCGA-BA-4076 TCGA-BA-5152 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-6873 TCGA-BB-7861 
         415         1288         1747           63          113          310 
TCGA-BB-7862 TCGA-C9-A47Z TCGA-CN-4736 TCGA-CN-6018 TCGA-CN-A499 TCGA-CN-A49B 
         536            5          395           45          535          904 
TCGA-CN-A63W TCGA-CQ-5327 TCGA-CQ-7064 TCGA-CR-6472 TCGA-CR-6484 TCGA-CR-7371 
         348         1660         1560         1050          354         1979 
TCGA-CR-7399 TCGA-CR-7402 TCGA-CV-5973 TCGA-CV-6003 TCGA-CV-6961 TCGA-CV-7432 
         181          911         2641         1665         1959         1937 
TCGA-CV-A45R TCGA-CV-A6JY TCGA-D6-6826 TCGA-D6-A6EM TCGA-DQ-7593 TCGA-F7-A50J 
        5480          646          154          232          369          585 
TCGA-F7-A620 TCGA-IQ-A61L TCGA-KU-A66T TCGA-KU-A6H7 TCGA-MZ-A6I9 TCGA-QK-A8Z7 
          13          351          552          378          254          198 
TCGA-QK-AA3K TCGA-UF-A71E 
         168         1278 

$`2Q LOSS WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
         102          462          283         1983          276          248 
TCGA-BA-5151 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 
         722         1762          520          725          623         1636 
TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A4IF 
         190          644          451          384          236          895 
TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB 
         855          622          918          850          351          216 
TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 
         182         1976          314          623          142          187 
TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7863 
        2878          278          140          133          558          423 
TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 
         687          638         1153          428          436         1955 
TCGA-BB-8601 TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 
         624            4          799          721         1157          142 
TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
        1230         1151          392          817          993          642 
TCGA-CN-4735 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 
        1250          625         1960         1330          811         1268 
TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 
        1988         1007         1045          173         1980         1081 
TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 
        1977         1980         1966         1966         1975          683 
TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 
         290          630          933          629          628          594 
TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 
         629          432           98         1970          202         1110 
TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 
         224          318          611          394          735          432 
TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49A TCGA-CN-A49C TCGA-CN-A63T 
         429           46          443          391          645          225 
TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A6V1 TCGA-CN-A6V3 
         526          484          175          367          223          298 
TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 
        1466         1207          654         1422         1393         1399 
TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 
         317          341          129         1253         1000         1057 
TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7065 
         985         1959         1959         1179         1750         1007 
TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 
         509         1309         1274          877         1950         1353 
TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE 
        1960          707         1963          893          998          785 
TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 
         391          303          950         2562          358         1663 
TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 
        1152          799         1777         1521         1966         1125 
TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 
        1971          514         1969          362          311          345 
TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 
         234          379          350          479         1956         1435 
TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7372 
        1191         1440         1245         1960          105          759 
TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 
         889           30          972         1968         1036          796 
TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 
        1954          997         1430         1951          392          907 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 
         913          946          908          898          930          216 
TCGA-CR-7398 TCGA-CR-7401 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 
         156         1077         1472         1955          522         1950 
TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 
        3295         1438          584          546         1978         2886 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 
        2327         1958         2437          519          406          701 
TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6436 
        1478         1840          215         1315          641         1899 
TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6942 
        1970         1948         1969         1952         1959         3835 
TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-7090 
        1948         1969         1966         1957         1969         3837 
TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 
        1959         1970         1970         1936         1959         1939 
TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7242 
        1945         1987         1979         1952         1444         1095 
TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 
         954          797         1967         1960         1976         1099 
TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7427 
        1974         1948         1955         1957         1947         1937 
TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7440 
        1973         1972         1984         1958         1959         1981 
TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 
         851         1945         1960         1940         1946         1954 
TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO 
        1722         1977         1970         1075          906         1959 
TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 
         670          110          714          606          685         1950 
TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6517 
         317          321          237          828          773          292 
TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 
         701           77          491          568          106          128 
TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ 
         539          376          483          435          424          368 
TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 
         389          338         1778         1081          516         1030 
TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 
         548         1965          575          775          622          299 
TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 
         368          324          340         1131          490          658 
TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A623 
          15           92            3          384           14            6 
TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A 
         407           58          133          414          403          206 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 
           2            5           25           37           55           44 
TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ 
          24           25           11           49           10          111 
TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E 
          33         1057          485          122          441          588 
TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A6H8 
         360          412          440          360          224          168 
TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G 
          14           34          392           56          111          112 
TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX 
         240          910         1726         1559         1120         1954 
TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 
         578         1917         1968          400          553          357 
TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 
         245          218          228          225          387          567 
TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-UF-A718 TCGA-UF-A719 
         149          135          135          157         1326         1663 
TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD 
        1319         1252         1043         1894          484          735 
TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JS 
        1497          665          214          413 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                5                 2 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             5480              3837 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            475.0             723.5 
[1] "5.0 - 5480.0 (475.0)" "2.0 - 3837.0 (723.5)"
[1] "hr=" "1"  
D44V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  2Q LOSS MUTATED         0        5        12        19         0         0
  2Q LOSS WILD-TYPE      26       70        62       216        12         1
D44V3, multiclass
           clus
vv          2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  STAGE I                 0                26
  STAGE II                5                70
  STAGE III              12                62
  STAGE IVA              19               216
  STAGE IVB               0                12
  STAGE IVC               0                 1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  2Q LOSS MUTATED       2   9  12  14
  2Q LOSS WILD-TYPE    45 118  82 148
D44V4, multiclass
       clus
vv      2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  T0+T1               2                45
  T2                  9               118
  T3                 12                82
  T4                 14               148
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  2Q LOSS MUTATED    13  11  12   0
  2Q LOSS WILD-TYPE 157  52 140   8
D44V5, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  N0              13               157
  N1              11                52
  N2              12               140
  N3               0                 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"
                   vv
clus                 M0  M1  MX
  2Q LOSS MUTATED    16   0   6
  2Q LOSS WILD-TYPE 151   1  52
D44V6, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  M0              16               151
  M1               0                 1
  MX               6                52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V7, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    20  24
  2Q LOSS WILD-TYPE 112 332
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     20   24
  2Q LOSS WILD-TYPE  112  332
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE              20               112
  MALE                24               332
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  2Q LOSS MUTATED                                      42
  2Q LOSS WILD-TYPE                                   435
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  2Q LOSS MUTATED                                                             0
  2Q LOSS WILD-TYPE                                                           1
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  2Q LOSS MUTATED                                                     2
  2Q LOSS WILD-TYPE                                                   8
D44V8, multiclass
                                                             clus
vv                                                            2Q LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    42
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       2
                                                             clus
vv                                                            2Q LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     435
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                 1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V9, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     2  42
  2Q LOSS WILD-TYPE  77 367
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      2   42
  2Q LOSS WILD-TYPE   77  367
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  NO                2                77
  YES              42               367
[1] 2 2
[1] FALSE
D44V10, continuous
D44V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2Q LOSS MUTATED                                  0     3
  2Q LOSS WILD-TYPE                                2     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2Q LOSS MUTATED                           3    37
  2Q LOSS WILD-TYPE                        41   378
D44V12, multiclass
                                  clus
vv                                 2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          3                 8
  BLACK OR AFRICAN AMERICAN                      3                41
  WHITE                                         37               378
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V13, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     4  37
  2Q LOSS WILD-TYPE  20 394
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      4   37
  2Q LOSS WILD-TYPE   20  394
                        clus
vv                       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   4                20
  NOT HISPANIC OR LATINO              37               394
[1] 2 2
[1] FALSE

Clustering(45) Variable = 3P LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                 0   1
  3P LOSS MUTATED   166  78
  3P LOSS WILD-TYPE 135  35
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              244               170 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               78                35 
$`3P LOSS MUTATED`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-5149 TCGA-BA-5555 
         102          462          283          415          248          520 
TCGA-BA-5558 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-7269 
        1636          644          451           63          384          236 
TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DL 
         918          850          351          216          182          623 
TCGA-BA-A8YP TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-7862 TCGA-BB-7864 TCGA-BB-7870 
         142          278          133          536          687         1153 
TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A47Z TCGA-CN-4725 
         428          436         1955          624            5         1157 
TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 
         142         1151          392         1250          395          625 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 
        1960         1330          811         1988         1007         1045 
TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 
         173         1980         1081         1977         1980         1966 
TCGA-CN-5367 TCGA-CN-5373 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6016 
        1966          683          630          933          629          594 
TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6024 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6996 
          45          432          224          611          394          432 
TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A63T 
         429           46          443          391          904          225 
TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A641 TCGA-CN-A6V3 TCGA-CQ-5330 TCGA-CQ-5332 
         526          348          367          298         1393          317 
TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 
        1253         1000          985         1959         1959         1179 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4C6 
        1560         1007          509         1274         1950         1353 
TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE 
        1960          707         1963          893          998          785 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5250 TCGA-CR-6473 TCGA-CR-6477 
         950         2562          358          799         1125          514 
TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6482 TCGA-CR-6491 TCGA-CR-6493 TCGA-CR-7364 
        1969          362          345          350         1956         1435 
TCGA-CR-7367 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 
        1440         1960          105         1979          759          889 
TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7383 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7390 
        1968         1036         1954         1430         1951          907 
TCGA-CR-7398 TCGA-CR-7401 TCGA-CR-7402 TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5434 
         156         1077          911         1955         1950         3295 
TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5444 
        1438          584          546         1978         2886         2437 
TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5978 TCGA-CV-5979 
         519          406         2641         1478          215         1315 
TCGA-CV-6003 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6941 
        1665         1970         1948         1969         1952         1959 
TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7091 
        1969         1966         1957         1969         1959         1959 
TCGA-CV-7095 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7180 
        1970         1936         1959         1939         1945         1987 
TCGA-CV-7242 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7254 TCGA-CV-7410 TCGA-CV-7418 
        1095          797         1967         1976         1948         1955 
TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7434 
        1957         1947         1973         1972         1937         1958 
TCGA-CV-7435 TCGA-CV-A45R TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A6JE 
        1959         5480         1940         1946         1954         1075 
TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JZ TCGA-CV-A6K1 TCGA-CX-7082 TCGA-CX-7086 
         670          110          714          685          317          237 
TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6825 TCGA-D6-6826 
         828          773          292          701          491          154 
TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4ZB TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ 
         106          128          376          435          424          368 
TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 
         389          338          516         1030          548         1965 
TCGA-DQ-7589 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-A50G 
         575          622          299         1131          490           15 
TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61W TCGA-F7-A620 TCGA-H7-8502 
          92          585            3           14           13          133 
TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-8224 TCGA-HD-8635 
         414          403            2            5           55           25 
TCGA-HD-A633 TCGA-HD-A6HZ TCGA-IQ-7630 TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J 
          49          111          485          360          412          440 
TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66T TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67D 
         351          360          552           14           34           56 
TCGA-P3-A5QA TCGA-P3-A6T4 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IH TCGA-QK-A6V9 
        1726         1968          553          357          228          567 
TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K 
         198          149          135          135          157          168 
TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JC 
        1326         1663         1319         1278         1043          484 
TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JS 
         735         1497          665          413 

$`3P LOSS WILD-TYPE`
TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 
        1983          276          722         1288         1762          725 
TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6873 TCGA-BA-A4IF TCGA-BA-A4IG 
         623         1747          190          113          895          855 
TCGA-BA-A4IH TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4225 
         622         1976          314          187         2878          140 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7863 TCGA-BB-7866 TCGA-C9-A480 TCGA-CN-4722 
         558          310          423          638            4          799 
TCGA-CN-4723 TCGA-CN-4727 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4741 
         721         1230          817          993          642         1268 
TCGA-CN-5370 TCGA-CN-5374 TCGA-CN-6013 TCGA-CN-6017 TCGA-CN-6020 TCGA-CN-6021 
        1975          290          628          629           98         1970 
TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6988 TCGA-CN-6994 TCGA-CN-A499 TCGA-CN-A49C 
         202         1110          318          735          535          645 
TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A6V1 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
         484          175          223         1466         1207          654 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6223 
        1660         1422         1399          341          129         1057 
TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5248 
        1750         1309          877          391          303         1663 
TCGA-CR-5249 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6474 
        1152         1777         1521         1966         1050         1971 
TCGA-CR-6481 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6492 TCGA-CR-7365 
         311          354          234          379          479         1191 
TCGA-CR-7368 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7389 
        1245           30          972          796          997          392 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 
         913          946          908          898          930          216 
TCGA-CR-7399 TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5971 
         181         1472          522         2327         1958          701 
TCGA-CV-5977 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-7090 
        1840          641         1899         3835         1948         3837 
TCGA-CV-7097 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7243 TCGA-CV-7250 
        1970         1979         1952         1444          954         1960 
TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7427 TCGA-CV-7433 TCGA-CV-7440 TCGA-CV-A45O 
        1099         1974         1937         1984         1981          851 
TCGA-CV-A45Q TCGA-CV-A45Y TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JN 
        1945         1960         1722         1977         1970          906 
TCGA-CV-A6JO TCGA-CV-A6JY TCGA-CV-A6K0 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-D6-6824 
        1959          646          606         1950          321           77 
TCGA-D6-6827 TCGA-D6-A4Z9 TCGA-D6-A6EK TCGA-D6-A6EM TCGA-DQ-5624 TCGA-DQ-5625 
         568          539          483          232         1778         1081 
TCGA-DQ-7590 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-8489 
         775          369          368          324          340          658 
TCGA-F7-A61V TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-A76A TCGA-HD-7754 
         384            6          407           58          206           25 
TCGA-HD-7917 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-A4C1 TCGA-HD-A634 TCGA-HD-A6I0 
          37           44           24           11           10           33 
TCGA-HL-7533 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-KU-A66S TCGA-KU-A6H7 
        1057          122          441          588          224          378 
TCGA-KU-A6H8 TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-MZ-A7D7 
         168          392          111          112          254          240 
TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 
         910         1559         1120         1954          578         1917 
TCGA-P3-A6T8 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6II TCGA-QK-A6IJ TCGA-UF-A71D 
         400          245          218          225          387         1252 
TCGA-UF-A7JA TCGA-UF-A7JJ 
        1894          214 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                2                 4 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             5480              3837 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              694               711 
[1] "2.0 - 5480.0 (694.0)" "4.0 - 3837.0 (711.0)"
[1] "hr=" "1.4"
D45V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  3P LOSS MUTATED        15       40        44       146         9         0
  3P LOSS WILD-TYPE      11       35        30        89         3         1
D45V3, multiclass
           clus
vv          3P LOSS MUTATED 3P LOSS WILD-TYPE
  STAGE I                15                11
  STAGE II               40                35
  STAGE III              44                30
  STAGE IVA             146                89
  STAGE IVB               9                 3
  STAGE IVC               0                 1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  3P LOSS MUTATED      25  67  64 101
  3P LOSS WILD-TYPE    22  60  30  61
D45V4, multiclass
       clus
vv      3P LOSS MUTATED 3P LOSS WILD-TYPE
  T0+T1              25                22
  T2                 67                60
  T3                 64                30
  T4                101                61
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  3P LOSS MUTATED    98  34 102   5
  3P LOSS WILD-TYPE  72  29  50   3
D45V5, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  N0              98                72
  N1              34                29
  N2             102                50
  N3               5                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1  MX
  3P LOSS MUTATED   101   0  27
  3P LOSS WILD-TYPE  66   1  31
D45V6, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  M0             101                66
  M1               0                 1
  MX              27                31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V7, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    63 220
  3P LOSS WILD-TYPE  69 136
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     63  220
  3P LOSS WILD-TYPE   69  136
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE              63                69
  MALE               220               136
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  3P LOSS MUTATED                                     278
  3P LOSS WILD-TYPE                                   199
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  3P LOSS MUTATED                                                             1
  3P LOSS WILD-TYPE                                                           0
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  3P LOSS MUTATED                                                     4
  3P LOSS WILD-TYPE                                                   6
D45V8, multiclass
                                                             clus
vv                                                            3P LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                   278
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       4
                                                             clus
vv                                                            3P LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     199
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                 0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V9, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    50 233
  3P LOSS WILD-TYPE  29 176
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     50  233
  3P LOSS WILD-TYPE   29  176
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  NO               50                29
  YES             233               176
[1] 2 2
[1] FALSE
D45V10, continuous
D45V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3P LOSS MUTATED                                  1     6
  3P LOSS WILD-TYPE                                1     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3P LOSS MUTATED                          35   231
  3P LOSS WILD-TYPE                         9   184
D45V12, multiclass
                                  clus
vv                                 3P LOSS MUTATED 3P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 1
  ASIAN                                          6                 5
  BLACK OR AFRICAN AMERICAN                     35                 9
  WHITE                                        231               184
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V13, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    15 243
  3P LOSS WILD-TYPE   9 188
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     15  243
  3P LOSS WILD-TYPE    9  188
                        clus
vv                       3P LOSS MUTATED 3P LOSS WILD-TYPE
  HISPANIC OR LATINO                  15                 9
  NOT HISPANIC OR LATINO             243               188
[1] 2 2
[1] FALSE

Clustering(46) Variable = 3Q LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                 0   1
  3Q LOSS MUTATED    29  19
  3Q LOSS WILD-TYPE 272  94
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               48               366 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               19                94 
$`3Q LOSS MUTATED`
TCGA-BA-4076 TCGA-BA-5555 TCGA-BA-5558 TCGA-BA-6871 TCGA-BA-A6DB TCGA-BA-A6DL 
         415          520         1636           63          216          623 
TCGA-BB-7870 TCGA-CN-4735 TCGA-CN-4738 TCGA-CN-6010 TCGA-CN-6018 TCGA-CN-6997 
        1153         1250         1960          630           45          429 
TCGA-CN-A63U TCGA-CN-A63W TCGA-CQ-5332 TCGA-CQ-6224 TCGA-CQ-7065 TCGA-CQ-A4CD 
         526          348          317          985         1007          998 
TCGA-CR-6473 TCGA-CR-6493 TCGA-CR-7373 TCGA-CR-7383 TCGA-CR-7390 TCGA-CR-7398 
        1125         1956          889         1954          907          156 
TCGA-CR-7401 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5966 TCGA-CV-5976 TCGA-CV-6441 
        1077         3295         1438          519         1478         1970 
TCGA-CV-6952 TCGA-CV-6961 TCGA-CV-7100 TCGA-CV-7418 TCGA-CV-7428 TCGA-CV-7430 
        1966         1959         1959         1955         1973         1972 
TCGA-CV-A6JE TCGA-D6-6826 TCGA-DQ-7588 TCGA-F7-A620 TCGA-H7-A6C5 TCGA-HD-7753 
        1075          154         1965           13          403            5 
TCGA-IQ-A61L TCGA-MT-A51W TCGA-MT-A51X TCGA-QK-A6IH TCGA-QK-A8ZB TCGA-QK-AA3K 
         351           14           34          228          135          168 

$`3Q LOSS WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
         102          462          283         1983          276          248 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5559 
         722         1288         1762          725          623         1747 
TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 
         190          644          451          384          113          236 
TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA 
         895          855          622          918          850          351 
TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 
         182         1976          314          142          187         2878 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 
         278          140          133          558          310          536 
TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 
         423          687          638          428          436         1955 
TCGA-BB-8601 TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 
         624            5            4          799          721         1157 
TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 
         142         1230         1151          392          817          993 
TCGA-CN-4733 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 
         642          395          625         1330          811         1268 
TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 
        1988         1007         1045          173         1980         1081 
TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 
        1977         1980         1966         1966         1975          683 
TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 
         290          933          629          628          594          629 
TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
         432           98         1970          202         1110          224 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6998 
         318          611          394          735          432           46 
TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T 
         443          535          391          904          645          225 
TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 
         484          175          367          223          298         1466 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 
        1207          654         1660         1422         1393         1399 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6227 
         341          129         1253         1000         1057         1959 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7067 TCGA-CQ-7068 
        1959         1179         1750         1560          509         1309 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
        1274          877         1950         1353         1960          707 
TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI 
        1963          893          785          391          303          950 
TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 
        2562          358         1663         1152          799         1777 
TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 
        1521         1966         1050         1971          514         1969 
TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 
         362          311          345          354          234          379 
TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 
         350          479         1435         1191         1440         1245 
TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7374 TCGA-CR-7376 
        1960          105         1979          759           30          972 
TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 
        1968         1036          796          997         1430         1951 
TCGA-CR-7389 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 
         392          913          946          908          898          930 
TCGA-CR-7397 TCGA-CR-7399 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 
         216          181          911         1472         1955          522 
TCGA-CV-5432 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 
        1950          584          546         1978         2886         2327 
TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5977 
        1958         2437          406          701         2641         1840 
TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6934 
         215         1315         1665          641         1899         1948 
TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 
        1969         1952         1959         3835         1948         1969 
TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 
        1957         1969         3837         1959         1970         1970 
TCGA-CV-7099 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 
        1936         1939         1945         1987         1979         1952 
TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 
        1444         1095          954          797         1967         1960 
TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7422 TCGA-CV-7424 
        1976         1099         1974         1948         1957         1947 
TCGA-CV-7427 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7440 
        1937         1937         1984         1958         1959         1981 
TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 
         851         1945         5480         1960         1940         1946 
TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JN TCGA-CV-A6JO 
        1954         1722         1977         1970          906         1959 
TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 
         670          110          646          714          606          685 
TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 
        1950          317          321          237          828          773 
TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6827 TCGA-D6-8568 
         292          701           77          491          568          106 
TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO 
         128          539          376          483          232          435 
TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 
         424          368          389          338         1778         1081 
TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 
         516         1030          548          575          775          622 
TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 
         299          369          368          324          340         1131 
TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S 
         490          658           15           92          585            3 
TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 
         384           14            6          407           58          133 
TCGA-H7-A6C4 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 
         414          206            2           25           37           55 
TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 
          44           24           25           11           49           10 
TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 
         111           33         1057          485          122          441 
TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61O TCGA-KU-A66S 
         588          360          412          440          360          224 
TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F 
         552          378          168          392           56          111 
TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE 
         112          254          240          910         1726         1559 
TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-P3-A6T8 
        1120         1954          578         1917         1968          400 
TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6II TCGA-QK-A6IJ 
         553          357          245          218          225          387 
TCGA-QK-A6V9 TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-AA3J TCGA-UF-A718 
         567          198          149          135          157         1326 
TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA 
        1663         1319         1252         1278         1043         1894 
TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JS 
         484          735         1497          665          214          413 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                5                 2 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             3295              5480 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
              898               694 
[1] "5.0 - 3295.0 (898.0)" "2.0 - 5480.0 (694.0)"
[1] "hr=" "1.5"
D46V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  3Q LOSS MUTATED         5        6         5        34         2         0
  3Q LOSS WILD-TYPE      21       69        69       201        10         1
D46V3, multiclass
           clus
vv          3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  STAGE I                 5                21
  STAGE II                6                69
  STAGE III               5                69
  STAGE IVA              34               201
  STAGE IVB               2                10
  STAGE IVC               0                 1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  3Q LOSS MUTATED       8   9  12  24
  3Q LOSS WILD-TYPE    39 118  82 138
D46V4, multiclass
       clus
vv      3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  T0+T1               8                39
  T2                  9               118
  T3                 12                82
  T4                 24               138
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  3Q LOSS MUTATED    27   4  22   0
  3Q LOSS WILD-TYPE 143  59 130   8
D46V5, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  N0              27               143
  N1               4                59
  N2              22               130
  N3               0                 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"
                   vv
clus                 M0  M1  MX
  3Q LOSS MUTATED    17   0   3
  3Q LOSS WILD-TYPE 150   1  55
D46V6, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  M0              17               150
  M1               0                 1
  MX               3                55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V7, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    13  46
  3Q LOSS WILD-TYPE 119 310
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     13   46
  3Q LOSS WILD-TYPE  119  310
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE              13               119
  MALE                46               310
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  3Q LOSS MUTATED                                      59
  3Q LOSS WILD-TYPE                                   418
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  3Q LOSS MUTATED                                                             0
  3Q LOSS WILD-TYPE                                                           1
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  3Q LOSS MUTATED                                                     0
  3Q LOSS WILD-TYPE                                                  10
D46V8, multiclass
                                                             clus
vv                                                            3Q LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    59
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       0
                                                             clus
vv                                                            3Q LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     418
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                 1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V9, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     8  51
  3Q LOSS WILD-TYPE  71 358
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      8   51
  3Q LOSS WILD-TYPE   71  358
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  NO                8                71
  YES              51               358
[1] 2 2
[1] FALSE
D46V10, continuous
D46V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3Q LOSS MUTATED                                  0     1
  3Q LOSS WILD-TYPE                                2    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3Q LOSS MUTATED                          10    48
  3Q LOSS WILD-TYPE                        34   367
D46V12, multiclass
                                  clus
vv                                 3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                     10                34
  WHITE                                         48               367
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V13, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     2  55
  3Q LOSS WILD-TYPE  22 376
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      2   55
  3Q LOSS WILD-TYPE   22  376
                        clus
vv                       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                22
  NOT HISPANIC OR LATINO              55               376
[1] 2 2
[1] FALSE

Clustering(47) Variable = 4P LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                 0   1
  4P LOSS MUTATED   113  45
  4P LOSS WILD-TYPE 188  68
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              158               256 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               45                68 
$`4P LOSS MUTATED`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
         462          283          415         1983          276          248 
TCGA-BA-5555 TCGA-BA-5557 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-A4IF TCGA-BA-A4IG 
         520          623          451           63          895          855 
TCGA-BA-A6D8 TCGA-BA-A6DB TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4223 TCGA-BB-4224 
         850          216          623          142         2878          278 
TCGA-BB-7861 TCGA-BB-7871 TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A47Z TCGA-C9-A480 
         310          428         1955          624            5            4 
TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 
         721         1157          142         1151          392          817 
TCGA-CN-4735 TCGA-CN-4739 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5360 TCGA-CN-5363 
        1250         1330         1988         1007         1081         1977 
TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6018 TCGA-CN-6019 
         290          630          933          629           45          432 
TCGA-CN-6021 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6997 TCGA-CN-6998 
        1970          611          394          735          429           46 
TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63W 
         443          535          904          225          526          348 
TCGA-CN-A641 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6223 TCGA-CQ-6228 TCGA-CQ-7064 
         367          298         1466         1057         1959         1560 
TCGA-CQ-7067 TCGA-CQ-7072 TCGA-CQ-A4C9 TCGA-CQ-A4CD TCGA-CQ-A4CI TCGA-CR-5248 
         509         1950          707          998          950         1663 
TCGA-CR-6472 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-7365 TCGA-CR-7367 
        1050          234          379          350         1191         1440 
TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 
        1960          105         1979          759          889           30 
TCGA-CR-7383 TCGA-CR-7388 TCGA-CR-7390 TCGA-CR-7398 TCGA-CR-7404 TCGA-CV-5431 
        1954         1951          907          156         1472          522 
TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5440 TCGA-CV-5444 
        1950         3295         1438          584         1978         2437 
TCGA-CV-5978 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6941 TCGA-CV-6942 
         215         1970         1948         1969         1959         3835 
TCGA-CV-6961 TCGA-CV-7091 TCGA-CV-7097 TCGA-CV-7101 TCGA-CV-7235 TCGA-CV-7238 
        1959         1959         1970         1939         1952         1444 
TCGA-CV-7242 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7261 TCGA-CV-7418 TCGA-CV-7422 
        1095          797         1967         1099         1955         1957 
TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7435 TCGA-CV-7440 TCGA-CX-7082 TCGA-CX-7219 
        1972         1937         1959         1981          317          828 
TCGA-D6-6516 TCGA-D6-6823 TCGA-D6-A4Z9 TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP 
         773          701          539          232          435          424 
TCGA-D6-A74Q TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-F7-8298 TCGA-F7-A50G 
         338          516         1965          575          490           15 
TCGA-F7-A61S TCGA-F7-A61V TCGA-H7-8502 TCGA-H7-A6C5 TCGA-HD-7753 TCGA-HD-7917 
           3          384          133          403            5           37 
TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A633 TCGA-HD-A6HZ TCGA-IQ-A61E TCGA-IQ-A61G 
          55           44           49          111          588          360 
TCGA-IQ-A61H TCGA-IQ-A61J TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5QA 
         412          440          112          254          240         1726 
TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T8 TCGA-QK-A8Z7 TCGA-QK-A8ZA TCGA-QK-AA3J 
        1120         1954          400          198          135          157 
TCGA-QK-AA3K TCGA-UF-A71B TCGA-UF-A7J9 TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF 
         168         1319         1043          484          735         1497 
TCGA-UF-A7JH TCGA-UF-A7JS 
         665          413 

$`4P LOSS WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5558 
         102          722         1288         1762          725         1636 
TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 
        1747          190          644          384          113          236 
TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6DA TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DJ 
         622          918          351          182         1976          314 
TCGA-BB-4217 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7862 TCGA-BB-7863 
         187          140          133          558          536          423 
TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7872 TCGA-CN-4722 TCGA-CN-4727 
         687          638         1153          436          799         1230 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4740 
         993          642          395          625         1960          811 
TCGA-CN-4741 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5365 TCGA-CN-5366 
        1268         1045          173         1980         1980         1966 
TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 
        1966         1975          683          628          594          629 
TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6996 
          98          202         1110          224          318          432 
TCGA-CN-A49A TCGA-CN-A49C TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A6V1 TCGA-CQ-5324 
         391          645          484          175          223         1207 
TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 
         654         1660         1422         1393         1399          317 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6224 TCGA-CQ-6227 
         341          129         1253         1000          985         1959 
TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 
        1179         1750         1007         1309         1274          877 
TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CE TCGA-CQ-A4CG 
        1353         1960         1963          893          785          391 
TCGA-CQ-A4CH TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 
         303         2562          358         1152          799         1777 
TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 
        1521         1966         1125         1971          514         1969 
TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6492 TCGA-CR-6493 
         362          311          345          354          479         1956 
TCGA-CR-7364 TCGA-CR-7368 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 
        1435         1245          972         1968         1036          796 
TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7389 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
         997         1430          392          913          946          908 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 
         898          930          216          181         1077          911 
TCGA-CV-5430 TCGA-CV-5439 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5966 
        1955          546         2886         2327         1958          519 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5979 
         406          701         2641         1478         1840         1315 
TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6936 TCGA-CV-6943 TCGA-CV-6945 
        1665          641         1899         1952         1948         1969 
TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-7090 TCGA-CV-7095 TCGA-CV-7099 
        1966         1957         1969         3837         1970         1936 
TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7243 TCGA-CV-7250 
        1959         1945         1987         1979          954         1960 
TCGA-CV-7254 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7428 
        1976         1974         1948         1947         1937         1973 
TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45Y 
        1984         1958          851         1945         5480         1960 
TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD 
        1940         1946         1954         1722         1977         1970 
TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY 
        1075          906         1959          670          110          646 
TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 
         714          606          685         1950          321          237 
TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 
         292           77          491          154          568          106 
TCGA-D6-8569 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-DQ-5624 
         128          376          483          368          389         1778 
TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 
        1081         1030          548          775          622          299 
TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 
         369          368          324          340         1131          658 
TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-7774 
          92          585           14           13            6          407 
TCGA-H7-8501 TCGA-H7-A6C4 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-8634 
          58          414          206            2           25           24 
TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 
          25           11           10           33         1057          485 
TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T 
         122          441          351          360          224          552 
TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D 
         378          168           14           34          392           56 
TCGA-MT-A67F TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T4 
         111          910         1559          578         1917         1968 
TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II 
         553          357          245          218          228          225 
TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A8Z9 TCGA-QK-A8ZB TCGA-UF-A718 TCGA-UF-A719 
         387          567          149          135         1326         1663 
TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7JA TCGA-UF-A7JJ 
        1252         1278         1894          214 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                3                 2 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             3835              5480 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            629.5             723.5 
[1] "3.0 - 3835.0 (629.5)" "2.0 - 5480.0 (723.5)"
[1] "hr=" "1"  
D47V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  4P LOSS MUTATED        13       24        30        92         5         1
  4P LOSS WILD-TYPE      13       51        44       143         7         0
D47V3, multiclass
           clus
vv          4P LOSS MUTATED 4P LOSS WILD-TYPE
  STAGE I                13                13
  STAGE II               24                51
  STAGE III              30                44
  STAGE IVA              92               143
  STAGE IVB               5                 7
  STAGE IVC               1                 0
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  4P LOSS MUTATED      20  42  46  59
  4P LOSS WILD-TYPE    27  85  48 103
D47V4, multiclass
       clus
vv      4P LOSS MUTATED 4P LOSS WILD-TYPE
  T0+T1              20                27
  T2                 42                85
  T3                 46                48
  T4                 59               103
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  4P LOSS MUTATED    63  24  64   5
  4P LOSS WILD-TYPE 107  39  88   3
D47V5, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  N0              63               107
  N1              24                39
  N2              64                88
  N3               5                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1  MX
  4P LOSS MUTATED    54   1  26
  4P LOSS WILD-TYPE 113   0  32
D47V6, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  M0              54               113
  M1               1                 0
  MX              26                32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V7, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    44 139
  4P LOSS WILD-TYPE  88 217
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     44  139
  4P LOSS WILD-TYPE   88  217
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE              44                88
  MALE               139               217
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  4P LOSS MUTATED                                     178
  4P LOSS WILD-TYPE                                   299
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  4P LOSS MUTATED                                                             0
  4P LOSS WILD-TYPE                                                           1
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  4P LOSS MUTATED                                                     5
  4P LOSS WILD-TYPE                                                   5
D47V8, multiclass
                                                             clus
vv                                                            4P LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                   178
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       5
                                                             clus
vv                                                            4P LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     299
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                 1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         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"
D47V9, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    30 153
  4P LOSS WILD-TYPE  49 256
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     30  153
  4P LOSS WILD-TYPE   49  256
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  NO               30                49
  YES             153               256
[1] 2 2
[1] FALSE
D47V10, continuous
D47V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4P LOSS MUTATED                                  0     2
  4P LOSS WILD-TYPE                                2     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4P LOSS MUTATED                          22   152
  4P LOSS WILD-TYPE                        22   263
D47V12, multiclass
                                  clus
vv                                 4P LOSS MUTATED 4P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          2                 9
  BLACK OR AFRICAN AMERICAN                     22                22
  WHITE                                        152               263
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V13, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    11 160
  4P LOSS WILD-TYPE  13 271
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     11  160
  4P LOSS WILD-TYPE   13  271
                        clus
vv                       4P LOSS MUTATED 4P LOSS WILD-TYPE
  HISPANIC OR LATINO                  11                13
  NOT HISPANIC OR LATINO             160               271
[1] 2 2
[1] FALSE

Clustering(48) Variable = 4Q LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                 0   1
  4Q LOSS MUTATED    89  34
  4Q LOSS WILD-TYPE 212  79
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              123               291 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               34                79 
$`4Q LOSS MUTATED`
TCGA-BA-4075 TCGA-BA-4078 TCGA-BA-5555 TCGA-BA-5557 TCGA-BA-6870 TCGA-BA-6873 
         283          276          520          623          451          113 
TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A6D8 TCGA-BA-A6DB TCGA-BA-A8YP TCGA-BB-4227 
         895          855          850          216          142          133 
TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A47Z TCGA-C9-A480 
        1153          428         1955          624            5            4 
TCGA-CN-4725 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4735 TCGA-CN-4737 TCGA-CN-4739 
        1157         1151          392         1250          625         1330 
TCGA-CN-4742 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 
        1988         1980         1081          630          933          629 
TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6021 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6997 
          45          432         1970          611          735          429 
TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63U 
          46          443          535          904          225          526 
TCGA-CN-A63W TCGA-CQ-5323 TCGA-CQ-6224 TCGA-CQ-6228 TCGA-CQ-7064 TCGA-CQ-7067 
         348         1466          985         1959         1560          509 
TCGA-CQ-7072 TCGA-CQ-A4C9 TCGA-CQ-A4CI TCGA-CR-5248 TCGA-CR-6472 TCGA-CR-6484 
        1950          707          950         1663         1050          354 
TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7370 TCGA-CR-7371 
         234          379         1191         1440          105         1979 
TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7383 TCGA-CR-7392 TCGA-CR-7398 
         759          889           30         1954          946          156 
TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5439 
        1472          522         1950         3295         1438          546 
TCGA-CV-5440 TCGA-CV-5444 TCGA-CV-5976 TCGA-CV-6003 TCGA-CV-6441 TCGA-CV-6935 
        1978         2437         1478         1665         1970         1969 
TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6954 TCGA-CV-7091 TCGA-CV-7097 TCGA-CV-7101 
        1959         3835         1957         1959         1970         1939 
TCGA-CV-7180 TCGA-CV-7248 TCGA-CV-7261 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 
        1987         1967         1099         1955         1957         1947 
TCGA-CV-7430 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A460 TCGA-CX-7086 TCGA-CX-7219 
        1972         1959         1981         1946          237          828 
TCGA-D6-6823 TCGA-D6-A6EM TCGA-D6-A6EP TCGA-D6-A74Q TCGA-DQ-5629 TCGA-DQ-7588 
         701          232          424          338          516         1965 
TCGA-DQ-7589 TCGA-DQ-7592 TCGA-F7-A50G TCGA-F7-A61S TCGA-H7-A6C5 TCGA-HD-8634 
         575          299           15            3          403           24 
TCGA-HD-A6HZ TCGA-IQ-A61H TCGA-IQ-A61J TCGA-MT-A67G TCGA-P3-A5QA TCGA-P3-A6SX 
         111          412          440          112         1726         1954 
TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A8Z7 TCGA-QK-A8ZA TCGA-QK-AA3K TCGA-UF-A7JC 
         245          218          198          135          168          484 
TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH 
         735         1497          665 

$`4Q LOSS WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-5151 
         102          462          415         1983          248          722 
TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 
        1288         1762          725         1636         1747          190 
TCGA-BA-6869 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A4IH TCGA-BA-A4II 
         644           63          384          236          622          918 
TCGA-BA-A6DA TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BB-4217 
         351          182         1976          314          623          187 
TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 
        2878          278          140          558          310          536 
TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7872 TCGA-CN-4722 TCGA-CN-4723 
         423          687          638          436          799          721 
TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4736 
         142         1230          817          993          642          395 
TCGA-CN-4738 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 
        1960          811         1268         1007         1045          173 
TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 
        1977         1980         1966         1966         1975          683 
TCGA-CN-5374 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6020 TCGA-CN-6022 
         290          628          594          629           98          202 
TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6992 TCGA-CN-6996 TCGA-CN-A49A 
        1110          224          318          394          432          391 
TCGA-CN-A49C TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A6V1 TCGA-CN-A6V3 
         645          484          175          367          223          298 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 
        1207          654         1660         1422         1393         1399 
TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 
         317          341          129         1253         1000         1057 
TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7069 
        1959         1179         1750         1007         1309         1274 
TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD 
         877         1353         1960         1963          893          998 
TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5249 
         785          391          303         2562          358         1152 
TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 
         799         1777         1521         1966         1125         1971 
TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6491 
         514         1969          362          311          345          350 
TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7376 
         479         1956         1435         1245         1960          972 
TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 
        1968         1036          796          997         1430         1951 
TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 
         392          907          913          908          898          930 
TCGA-CR-7397 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CV-5430 TCGA-CV-5436 
         216          181         1077          911         1955          584 
TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 
        2886         2327         1958          519          406          701 
TCGA-CV-5973 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6436 
        2641         1840          215         1315          641         1899 
TCGA-CV-6934 TCGA-CV-6936 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-6960 
        1948         1952         1948         1969         1966         1969 
TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7095 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 
        1959         3837         1970         1936         1959         1945 
TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 
        1979         1952         1444         1095          954          797 
TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7427 TCGA-CV-7428 
        1960         1976         1974         1948         1937         1973 
TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A45R 
        1937         1984         1958          851         1945         5480 
TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD 
        1960         1940         1954         1722         1977         1970 
TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY 
        1075          906         1959          670          110          646 
TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 
         714          606          685         1950          317          321 
TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 
         773          292           77          491          154          568 
TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EO 
         106          128          539          376          483          435 
TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 
         368          389         1778         1081         1030          548 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
         775          622          369          368          324          340 
TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61V 
        1131          490          658           92          585          384 
TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 
          14           13            6          407           58          133 
TCGA-H7-A6C4 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 
         414          206            2            5           25           37 
TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 
          55           44           25           11           49           10 
TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E 
          33         1057          485          122          441          588 
TCGA-IQ-A61G TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 
         360          351          360          224          552          378 
TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F 
         168           14           34          392           56          111 
TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6T0 
         254          240          910         1559         1120          578 
TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IH 
        1917         1968          400          553          357          228 
TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A8Z9 TCGA-QK-A8ZB TCGA-QK-AA3J 
         225          387          567          149          135          157 
TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 
        1326         1663         1319         1252         1278         1043 
TCGA-UF-A7JA TCGA-UF-A7JJ TCGA-UF-A7JS 
        1894          214          413 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                3                 2 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             3835              5480 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              735               683 
[1] "3.0 - 3835.0 (735.0)" "2.0 - 5480.0 (683.0)"
[1] "hr=" "1.2"
D48V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  4Q LOSS MUTATED         9       18        28        68         1         1
  4Q LOSS WILD-TYPE      17       57        46       167        11         0
D48V3, multiclass
           clus
vv          4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  STAGE I                 9                17
  STAGE II               18                57
  STAGE III              28                46
  STAGE IVA              68               167
  STAGE IVB               1                11
  STAGE IVC               1                 0
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  4Q LOSS MUTATED      14  32  37  43
  4Q LOSS WILD-TYPE    33  95  57 119
D48V4, multiclass
       clus
vv      4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  T0+T1              14                33
  T2                 32                95
  T3                 37                57
  T4                 43               119
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  4Q LOSS MUTATED    41  22  50   1
  4Q LOSS WILD-TYPE 129  41 102   7
D48V5, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  N0              41               129
  N1              22                41
  N2              50               102
  N3               1                 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"
                   vv
clus                 M0  M1  MX
  4Q LOSS MUTATED    40   1  19
  4Q LOSS WILD-TYPE 127   0  39
D48V6, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  M0              40               127
  M1               1                 0
  MX              19                39
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V7, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    37 104
  4Q LOSS WILD-TYPE  95 252
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     37  104
  4Q LOSS WILD-TYPE   95  252
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE              37                95
  MALE               104               252
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  4Q LOSS MUTATED                                     139
  4Q LOSS WILD-TYPE                                   338
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  4Q LOSS MUTATED                                                             0
  4Q LOSS WILD-TYPE                                                           1
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  4Q LOSS MUTATED                                                     2
  4Q LOSS WILD-TYPE                                                   8
D48V8, multiclass
                                                             clus
vv                                                            4Q LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                   139
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       2
                                                             clus
vv                                                            4Q LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     338
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                 1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V9, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    29 112
  4Q LOSS WILD-TYPE  50 297
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     29  112
  4Q LOSS WILD-TYPE   50  297
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  NO               29                50
  YES             112               297
[1] 2 2
[1] FALSE
D48V10, continuous
D48V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4Q LOSS MUTATED                                  1     4
  4Q LOSS WILD-TYPE                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4Q LOSS MUTATED                          19   110
  4Q LOSS WILD-TYPE                        25   305
D48V12, multiclass
                                  clus
vv                                 4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 1
  ASIAN                                          4                 7
  BLACK OR AFRICAN AMERICAN                     19                25
  WHITE                                        110               305
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V13, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED     9 124
  4Q LOSS WILD-TYPE  15 307
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      9  124
  4Q LOSS WILD-TYPE   15  307
                        clus
vv                       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   9                15
  NOT HISPANIC OR LATINO             124               307
[1] 2 2
[1] FALSE

Clustering(49) Variable = 5P LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                 0   1
  5P LOSS MUTATED    30   6
  5P LOSS WILD-TYPE 271 107
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               36               378 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                6               107 
$`5P LOSS MUTATED`
TCGA-BA-6871 TCGA-BA-A6DA TCGA-BA-A8YP TCGA-BB-4224 TCGA-BB-7871 TCGA-CN-5355 
          63          351          142          278          428         1007 
TCGA-CN-5356 TCGA-CN-6988 TCGA-CN-A499 TCGA-CN-A63U TCGA-CQ-5332 TCGA-CQ-7069 
        1045          318          535          526          317         1274 
TCGA-CQ-A4C9 TCGA-CQ-A4CE TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7372 TCGA-CV-5432 
         707          785         1956         1435          759         1950 
TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-7242 TCGA-CV-7248 
        1478         1840         1315         1665         1095         1967 
TCGA-CV-7435 TCGA-D6-A6EQ TCGA-F7-A50G TCGA-IQ-A61G TCGA-IQ-A61H TCGA-QK-A6IH 
        1959          368           15          360          412          228 
TCGA-QK-AA3J TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JH 
         157         1278         1043          484          735          665 

$`5P LOSS WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 
         102          462          283          415         1983          276 
TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 
         248          722         1288         1762          520          725 
TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 
         623         1636         1747          190          644          451 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH 
         384          113          236          895          855          622 
TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DJ 
         918          850          216          182         1976          314 
TCGA-BA-A6DL TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 
         623          187         2878          140          133          558 
TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 
         310          536          423          687          638         1153 
TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 
         436         1955          624            5            4          799 
TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 
         721         1157          142         1230         1151          392 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 
         817          993          642         1250          395          625 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5358 
        1960         1330          811         1268         1988          173 
TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 
        1980         1081         1977         1980         1966         1966 
TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 
        1975          683          290          630          933          629 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 
         628          594          629           45          432           98 
TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6989 TCGA-CN-6992 
        1970          202         1110          224          611          394 
TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49A 
         735          432          429           46          443          391 
TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y 
         904          645          225          484          348          175 
TCGA-CN-A641 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
         367          223          298         1466         1207          654 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 
        1660         1422         1393         1399          341          129 
TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 
        1253         1000         1057          985         1959         1959 
TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 
        1179         1750         1560         1007          509         1309 
TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CA TCGA-CQ-A4CB 
         877         1950         1353         1960         1963          893 
TCGA-CQ-A4CD TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 
         998          391          303          950         2562          358 
TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 
        1663         1152          799         1777         1521         1966 
TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 
        1050         1125         1971          514         1969          362 
TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 
         311          345          354          234          379          350 
TCGA-CR-6492 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 
         479         1191         1440         1245         1960          105 
TCGA-CR-7371 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 
        1979          889           30          972         1968         1036 
TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 
         796         1954          997         1430         1951          392 
TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 
         907          913          946          908          898          930 
TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 
         216          156          181         1077          911         1472 
TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 
        1955          522         3295         1438          584          546 
TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 
        1978         2886         2327         1958         2437          519 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5978 TCGA-CV-6433 TCGA-CV-6436 
         406          701         2641          215          641         1899 
TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6942 
        1970         1948         1969         1952         1959         3835 
TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 
        1948         1969         1966         1957         1969         1959 
TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 
        3837         1959         1970         1970         1936         1959 
TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 
        1939         1945         1987         1979         1952         1444 
TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7406 
         954          797         1960         1976         1099         1974 
TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7428 
        1948         1955         1957         1947         1937         1973 
TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7440 TCGA-CV-A45O 
        1972         1937         1984         1958         1981          851 
TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 
        1945         5480         1960         1940         1946         1954 
TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO 
        1722         1977         1970         1075          906         1959 
TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 
         670          110          646          714          606          685 
TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 
        1950          317          321          237          828          773 
TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 
         292          701           77          491          154          568 
TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM 
         106          128          539          376          483          232 
TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 
         435          424          389          338         1778         1081 
TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 
         516         1030          548         1965          575          775 
TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
         622          299          369          368          324          340 
TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S 
        1131          490          658           92          585            3 
TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8501 
         384           14           13            6          407           58 
TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 
         133          414          403          206            2            5 
TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 
          25           37           55           44           24           25 
TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 
          11           49           10          111           33         1057 
TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61J TCGA-IQ-A61L 
         485          122          441          588          440          351 
TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W 
         360          224          552          378          168           14 
TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 
          34          392           56          111          112          254 
TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX 
         240          910         1726         1559         1120         1954 
TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 
         578         1917         1968          400          553          357 
TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A8Z7 
         245          218          225          387          567          198 
TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3K TCGA-UF-A718 TCGA-UF-A719 
         149          135          135          168         1326         1663 
TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A7JA TCGA-UF-A7JF TCGA-UF-A7JJ TCGA-UF-A7JS 
        1319         1252         1894         1497          214          413 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               15                 2 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             1967              5480 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
              721               694 
[1] "15.0 - 1967.0 (721.0)" "2.0 - 5480.0 (694.0)" 
[1] "hr=" "1.2"
D49V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  5P LOSS MUTATED         3        7         9        26         2         0
  5P LOSS WILD-TYPE      23       68        65       209        10         1
D49V3, multiclass
           clus
vv          5P LOSS MUTATED 5P LOSS WILD-TYPE
  STAGE I                 3                23
  STAGE II                7                68
  STAGE III               9                65
  STAGE IVA              26               209
  STAGE IVB               2                10
  STAGE IVC               0                 1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  5P LOSS MUTATED       3  12  12  20
  5P LOSS WILD-TYPE    44 115  82 142
D49V4, multiclass
       clus
vv      5P LOSS MUTATED 5P LOSS WILD-TYPE
  T0+T1               3                44
  T2                 12               115
  T3                 12                82
  T4                 20               142
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  5P LOSS MUTATED    16   6  20   1
  5P LOSS WILD-TYPE 154  57 132   7
D49V5, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  N0              16               154
  N1               6                57
  N2              20               132
  N3               1                 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"
                   vv
clus                 M0  M1  MX
  5P LOSS MUTATED    16   0   6
  5P LOSS WILD-TYPE 151   1  52
D49V6, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  M0              16               151
  M1               0                 1
  MX               6                52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V7, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    14  34
  5P LOSS WILD-TYPE 118 322
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     14   34
  5P LOSS WILD-TYPE  118  322
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE              14               118
  MALE                34               322
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  5P LOSS MUTATED                                      46
  5P LOSS WILD-TYPE                                   431
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  5P LOSS MUTATED                                                             0
  5P LOSS WILD-TYPE                                                           1
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  5P LOSS MUTATED                                                     2
  5P LOSS WILD-TYPE                                                   8
D49V8, multiclass
                                                             clus
vv                                                            5P LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    46
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       2
                                                             clus
vv                                                            5P LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     431
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                 1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V9, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     2  46
  5P LOSS WILD-TYPE  77 363
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      2   46
  5P LOSS WILD-TYPE   77  363
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  NO                2                77
  YES              46               363
[1] 2 2
[1] FALSE
D49V10, continuous
D49V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5P LOSS MUTATED                                  0     0
  5P LOSS WILD-TYPE                                2    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5P LOSS MUTATED                           7    38
  5P LOSS WILD-TYPE                        37   377
D49V12, multiclass
                                  clus
vv                                 5P LOSS MUTATED 5P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      7                37
  WHITE                                         38               377
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V13, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     3  36
  5P LOSS WILD-TYPE  21 395
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      3   36
  5P LOSS WILD-TYPE   21  395
                        clus
vv                       5P LOSS MUTATED 5P LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                21
  NOT HISPANIC OR LATINO              36               395
[1] 2 2
[1] FALSE

Clustering(50) Variable = 5Q LOSS MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                 0   1
  5Q LOSS MUTATED   105  28
  5Q LOSS WILD-TYPE 196  85
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              133               281 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               28                85 
$`5Q LOSS MUTATED`
TCGA-BA-4075 TCGA-BA-4078 TCGA-BA-5555 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 
         283          276          520           63          384          113 
TCGA-BA-7269 TCGA-BA-A4IG TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE 
         236          855          850          351          216          182 
TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4224 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-8596 
         142          187          278         1153          428         1955 
TCGA-BB-8601 TCGA-C9-A47Z TCGA-CN-4725 TCGA-CN-4727 TCGA-CN-4729 TCGA-CN-4730 
         624            5         1157         1230          392          817 
TCGA-CN-4731 TCGA-CN-4737 TCGA-CN-4739 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 
         993          625         1330         1988         1007         1045 
TCGA-CN-5360 TCGA-CN-5366 TCGA-CN-6010 TCGA-CN-6012 TCGA-CN-6019 TCGA-CN-6024 
        1081         1966          630          629          432          224 
TCGA-CN-6988 TCGA-CN-6992 TCGA-CN-A499 TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A641 
         318          394          535          526          348          367 
TCGA-CQ-5332 TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 
         317         1959         1179         1560         1007         1274 
TCGA-CQ-7072 TCGA-CQ-A4C9 TCGA-CQ-A4CE TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5247 
        1950          707          785          303          950          358 
TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6488 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 
        1971          514          379         1956         1435         1191 
TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7379 
        1245         1960          105         1979          759         1036 
TCGA-CR-7390 TCGA-CR-7398 TCGA-CR-7404 TCGA-CV-5432 TCGA-CV-5435 TCGA-CV-5440 
         907          156         1472         1950         1438         1978 
TCGA-CV-5441 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 
        2886         2641         1478         1840          215         1315 
TCGA-CV-6003 TCGA-CV-6960 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7101 
        1665         1969         3837         1959         1970         1939 
TCGA-CV-7180 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7248 TCGA-CV-7254 TCGA-CV-7261 
        1987         1095          954         1967         1976         1099 
TCGA-CV-7424 TCGA-CV-7435 TCGA-CV-A45R TCGA-CV-A45Z TCGA-CV-A6JE TCGA-CX-7082 
        1947         1959         5480         1940         1075          317 
TCGA-CX-7086 TCGA-D6-6823 TCGA-D6-A6EQ TCGA-D6-A74Q TCGA-DQ-5631 TCGA-DQ-7588 
         237          701          368          338          548         1965 
TCGA-DQ-7589 TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-F7-7848 TCGA-F7-A50G 
         575          299          368          324         1131           15 
TCGA-F7-A61W TCGA-H7-A6C4 TCGA-HD-7753 TCGA-HD-7917 TCGA-IQ-A61G TCGA-IQ-A61H 
          14          414            5           37          360          412 
TCGA-KU-A66T TCGA-MT-A67D TCGA-P3-A6SX TCGA-QK-A652 TCGA-QK-A6IH TCGA-QK-A6IJ 
         552           56         1954          357          228          387 
TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-UF-A71B TCGA-UF-A71D 
         198          149          135          157         1319         1252 
TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF 
        1278         1043         1894          484          735         1497 
TCGA-UF-A7JH 
         665 

$`5Q LOSS WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-5151 
         102          462          415         1983          248          722 
TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 
        1288         1762          725          623         1636         1747 
TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A4II 
         190          644          451          895          622          918 
TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-4227 
        1976          314          623         2878          140          133 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 
         558          310          536          423          687          638 
TCGA-BB-7872 TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4728 
         436            4          799          721          142         1151 
TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4740 TCGA-CN-4741 
         642         1250          395         1960          811         1268 
TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5367 TCGA-CN-5370 
         173         1980         1977         1980         1966         1975 
TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 
         683          290          933          628          594          629 
TCGA-CN-6018 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6989 
          45           98         1970          202         1110          611 
TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49A 
         735          432          429           46          443          391 
TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A6V1 
         904          645          225          484          175          223 
TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 
         298         1466         1207          654         1660         1422 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 
        1393         1399          341          129         1253         1000 
TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6228 TCGA-CQ-7063 TCGA-CQ-7067 TCGA-CQ-7068 
        1057          985         1959         1750          509         1309 
TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD 
         877         1353         1960         1963          893          998 
TCGA-CQ-A4CG TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 
         391         2562         1663         1152          799         1777 
TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6478 TCGA-CR-6480 
        1521         1966         1050         1125         1969          362 
TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6491 TCGA-CR-6492 
         311          345          354          234          350          479 
TCGA-CR-7367 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7382 
        1440          889           30          972         1968          796 
TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7391 
        1954          997         1430         1951          392          913 
TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7399 
         946          908          898          930          216          181 
TCGA-CR-7401 TCGA-CR-7402 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5434 TCGA-CV-5436 
        1077          911         1955          522         3295          584 
TCGA-CV-5439 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 
         546         2327         1958         2437          519          406 
TCGA-CV-5971 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 
         701          641         1899         1970         1948         1969 
TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6952 
        1952         1959         3835         1948         1969         1966 
TCGA-CV-6954 TCGA-CV-6961 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 
        1957         1959         1970         1936         1959         1945 
TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7245 TCGA-CV-7250 TCGA-CV-7406 
        1979         1952         1444          797         1960         1974 
TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 
        1948         1955         1957         1937         1973         1972 
TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q 
        1937         1984         1958         1981          851         1945 
TCGA-CV-A45Y TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD 
        1960         1946         1954         1722         1977         1970 
TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ 
         906         1959          670          110          646          714 
TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7219 TCGA-D6-6516 
         606          685         1950          321          828          773 
TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 
         292           77          491          154          568          106 
TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO 
         128          539          376          483          232          435 
TCGA-D6-A6EP TCGA-D6-A6ES TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 
         424          389         1778         1081          516         1030 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7593 TCGA-DQ-7596 TCGA-F7-8298 TCGA-F7-8489 
         775          622          369          340          490          658 
TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A620 TCGA-F7-A623 
          92          585            3          384           13            6 
TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 
         407           58          133          403          206            2 
TCGA-HD-7754 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 
          25           55           44           24           25           11 
TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 
          49           10          111           33         1057          485 
TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61J TCGA-IQ-A61L TCGA-IQ-A61O 
         122          441          588          440          351          360 
TCGA-KU-A66S TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A 
         224          378          168           14           34          392 
TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QA 
         111          112          254          240          910         1726 
TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-P3-A6T8 
        1559         1120          578         1917         1968          400 
TCGA-QK-A64Z TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6II TCGA-QK-A6V9 TCGA-QK-A8ZA 
         553          245          218          225          567          135 
TCGA-QK-AA3K TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A7JJ TCGA-UF-A7JS 
         168         1326         1663          214          413 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                5                 2 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             5480              3835 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              759               683 
[1] "5.0 - 5480.0 (759.0)" "2.0 - 3835.0 (683.0)"
[1] "hr=" "1.5"
D50V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  5Q LOSS MUTATED         6       26        29        77         3         0
  5Q LOSS WILD-TYPE      20       49        45       158         9         1
D50V3, multiclass
           clus
vv          5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  STAGE I                 6                20
  STAGE II               26                49
  STAGE III              29                45
  STAGE IVA              77               158
  STAGE IVB               3                 9
  STAGE IVC               0                 1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  5Q LOSS MUTATED       9  45  29  59
  5Q LOSS WILD-TYPE    38  82  65 103
D50V4, multiclass
       clus
vv      5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  T0+T1               9                38
  T2                 45                82
  T3                 29                65
  T4                 59               103
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  5Q LOSS MUTATED    51  24  52   2
  5Q LOSS WILD-TYPE 119  39 100   6
D50V5, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  N0              51               119
  N1              24                39
  N2              52               100
  N3               2                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1  MX
  5Q LOSS MUTATED    56   0  15
  5Q LOSS WILD-TYPE 111   1  43
D50V6, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  M0              56               111
  M1               0                 1
  MX              15                43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V7, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    36 120
  5Q LOSS WILD-TYPE  96 236
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     36  120
  5Q LOSS WILD-TYPE   96  236
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE              36                96
  MALE               120               236
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  5Q LOSS MUTATED                                     152
  5Q LOSS WILD-TYPE                                   325
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  5Q LOSS MUTATED                                                             0
  5Q LOSS WILD-TYPE                                                           1
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  5Q LOSS MUTATED                                                     4
  5Q LOSS WILD-TYPE                                                   6
D50V8, multiclass
                                                             clus
vv                                                            5Q LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                   152
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       4
                                                             clus
vv                                                            5Q LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     325
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                 1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V9, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    25 131
  5Q LOSS WILD-TYPE  54 278
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     25  131
  5Q LOSS WILD-TYPE   54  278
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  NO               25                54
  YES             131               278
[1] 2 2
[1] FALSE
D50V10, continuous
D50V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5Q LOSS MUTATED                                  1     5
  5Q LOSS WILD-TYPE                                1     6
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5Q LOSS MUTATED                          20   125
  5Q LOSS WILD-TYPE                        24   290
D50V12, multiclass
                                  clus
vv                                 5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 1
  ASIAN                                          5                 6
  BLACK OR AFRICAN AMERICAN                     20                24
  WHITE                                        125               290
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V13, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED     7 134
  5Q LOSS WILD-TYPE  17 297
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      7  134
  5Q LOSS WILD-TYPE   17  297
                        clus
vv                       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   7                17
  NOT HISPANIC OR LATINO             134               297
[1] 2 2
[1] FALSE

Clustering(51) Variable = 6P LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                 0   1
  6P LOSS MUTATED    37  17
  6P LOSS WILD-TYPE 264  96
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               54               360 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               17                96 
$`6P LOSS MUTATED`
TCGA-BA-5152 TCGA-BA-5559 TCGA-BB-4225 TCGA-BB-7862 TCGA-CN-4725 TCGA-CN-4728 
        1288         1747          140          536         1157         1151 
TCGA-CN-4729 TCGA-CN-4735 TCGA-CN-4740 TCGA-CN-5359 TCGA-CN-6010 TCGA-CN-6024 
         392         1250          811         1980          630          224 
TCGA-CN-6994 TCGA-CN-6997 TCGA-CN-A63T TCGA-CQ-5332 TCGA-CQ-6223 TCGA-CQ-A4C9 
         735          429          225          317         1057          707 
TCGA-CR-6488 TCGA-CR-6493 TCGA-CR-7365 TCGA-CR-7371 TCGA-CR-7373 TCGA-CR-7399 
         379         1956         1191         1979          889          181 
TCGA-CR-7404 TCGA-CV-5434 TCGA-CV-5436 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-6441 
        1472         3295          584         1958         2437         1970 
TCGA-CV-6960 TCGA-CV-7095 TCGA-CV-7101 TCGA-CV-7248 TCGA-CV-7254 TCGA-CV-7418 
        1969         1970         1939         1967         1976         1955 
TCGA-CV-A6JT TCGA-D6-6823 TCGA-D6-6826 TCGA-D6-A6EQ TCGA-D6-A74Q TCGA-DQ-5624 
         670          701          154          368          338         1778 
TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7591 TCGA-F7-A623 TCGA-HD-A6HZ TCGA-IQ-A61G 
        1965          575          622            6          111          360 
TCGA-MT-A67G TCGA-MZ-A7D7 TCGA-P3-A5QA TCGA-P3-A6T0 TCGA-UF-A71E TCGA-UF-A7JF 
         112          240         1726          578         1278         1497 

$`6P LOSS WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 
         102          462          283          415         1983          276 
TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 
         248          722         1762          520          725          623 
TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 
        1636          190          644          451           63          384 
TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II 
         113          236          895          855          622          918 
TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DJ 
         850          351          216          182         1976          314 
TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4227 
         623          142          187         2878          278          133 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 
         558          310          423          687          638         1153 
TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A47Z TCGA-C9-A480 
         428          436         1955          624            5            4 
TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4730 TCGA-CN-4731 
         799          721          142         1230          817          993 
TCGA-CN-4733 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4741 
         642          395          625         1960         1330         1268 
TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5363 
        1988         1007         1045          173         1081         1977 
TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 
        1980         1966         1966         1975          683          290 
TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 
         933          629          628          594          629           45 
TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6988 
         432           98         1970          202         1110          318 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A499 
         611          394          432           46          443          535 
TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W 
         391          904          645          526          484          348 
TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-5324 
         175          367          223          298         1466         1207 
TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 
         654         1660         1422         1393         1399          341 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 
         129         1253         1000          985         1959         1959 
TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 
        1179         1750         1560         1007          509         1309 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CA 
        1274          877         1950         1353         1960         1963 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI 
         893          998          785          391          303          950 
TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 
        2562          358         1663         1152          799         1777 
TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 
        1521         1966         1050         1125         1971          514 
TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 
        1969          362          311          345          354          234 
TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-7364 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 
         350          479         1435         1440         1245         1960 
TCGA-CR-7370 TCGA-CR-7372 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 
         105          759           30          972         1968         1036 
TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 
         796         1954          997         1430         1951          392 
TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 
         907          913          946          908          898          930 
TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7401 TCGA-CR-7402 TCGA-CV-5430 TCGA-CV-5431 
         216          156         1077          911         1955          522 
TCGA-CV-5432 TCGA-CV-5435 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 
        1950         1438          546         1978         2886         2327 
TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 
         519          406          701         2641         1478         1840 
TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6934 
         215         1315         1665          641         1899         1948 
TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 
        1969         1952         1959         3835         1948         1969 
TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7097 
        1966         1957         1959         3837         1959         1970 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 
        1936         1959         1945         1987         1979         1952 
TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7250 TCGA-CV-7261 
        1444         1095          954          797         1960         1099 
TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7428 
        1974         1948         1957         1947         1937         1973 
TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7440 
        1972         1937         1984         1958         1959         1981 
TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 
         851         1945         5480         1960         1940         1946 
TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN 
        1954         1722         1977         1970         1075          906 
TCGA-CV-A6JO TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 
        1959          110          646          714          606          685 
TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 
        1950          317          321          237          828          773 
TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 
         292           77          491          568          106          128 
TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP 
         539          376          483          232          435          424 
TCGA-D6-A6ES TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7590 
         389         1081          516         1030          548          775 
TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 
         299          369          368          324          340         1131 
TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S 
         490          658           15           92          585            3 
TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 
         384           14           13          407           58          133 
TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 
         414          403          206            2            5           25 
TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 
          37           55           44           24           25           11 
TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 
          49           10           33         1057          485          122 
TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61L TCGA-IQ-A61O 
         441          588          412          440          351          360 
TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X 
         224          552          378          168           14           34 
TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QE 
         392           56          111          254          910         1559 
TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A64Z 
        1120         1954         1917         1968          400          553 
TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ 
         357          245          218          228          225          387 
TCGA-QK-A6V9 TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J 
         567          198          149          135          135          157 
TCGA-QK-AA3K TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A7J9 
         168         1326         1663         1319         1252         1043 
TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JS 
        1894          484          735          665          214          413 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                6                 2 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             3295              5480 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
              850               674 
[1] "6.0 - 3295.0 (850.0)" "2.0 - 5480.0 (674.0)"
[1] "hr=" "1.1"
D51V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  6P LOSS MUTATED         1        9        11        36         0         0
  6P LOSS WILD-TYPE      25       66        63       199        12         1
D51V3, multiclass
           clus
vv          6P LOSS MUTATED 6P LOSS WILD-TYPE
  STAGE I                 1                25
  STAGE II                9                66
  STAGE III              11                63
  STAGE IVA              36               199
  STAGE IVB               0                12
  STAGE IVC               0                 1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  6P LOSS MUTATED       4  14  16  23
  6P LOSS WILD-TYPE    43 113  78 139
D51V4, multiclass
       clus
vv      6P LOSS MUTATED 6P LOSS WILD-TYPE
  T0+T1               4                43
  T2                 14               113
  T3                 16                78
  T4                 23               139
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  6P LOSS MUTATED    19   8  23   0
  6P LOSS WILD-TYPE 151  55 129   8
D51V5, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  N0              19               151
  N1               8                55
  N2              23               129
  N3               0                 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"
                   vv
clus                 M0  M1  MX
  6P LOSS MUTATED    17   0   9
  6P LOSS WILD-TYPE 150   1  49
D51V6, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  M0              17               150
  M1               0                 1
  MX               9                49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V7, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    14  50
  6P LOSS WILD-TYPE 118 306
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     14   50
  6P LOSS WILD-TYPE  118  306
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE              14               118
  MALE                50               306
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  6P LOSS MUTATED                                      63
  6P LOSS WILD-TYPE                                   414
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  6P LOSS MUTATED                                                             0
  6P LOSS WILD-TYPE                                                           1
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  6P LOSS MUTATED                                                     1
  6P LOSS WILD-TYPE                                                   9
D51V8, multiclass
                                                             clus
vv                                                            6P LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    63
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       1
                                                             clus
vv                                                            6P LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     414
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                 1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V9, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    12  52
  6P LOSS WILD-TYPE  67 357
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     12   52
  6P LOSS WILD-TYPE   67  357
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  NO               12                67
  YES              52               357
[1] 2 2
[1] FALSE
D51V10, continuous
D51V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6P LOSS MUTATED                                  0     0
  6P LOSS WILD-TYPE                                2    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6P LOSS MUTATED                          10    50
  6P LOSS WILD-TYPE                        34   365
D51V12, multiclass
                                  clus
vv                                 6P LOSS MUTATED 6P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                     10                34
  WHITE                                         50               365
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V13, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     6  51
  6P LOSS WILD-TYPE  18 380
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      6   51
  6P LOSS WILD-TYPE   18  380
                        clus
vv                       6P LOSS MUTATED 6P LOSS WILD-TYPE
  HISPANIC OR LATINO                   6                18
  NOT HISPANIC OR LATINO              51               380
[1] 2 2
[1] FALSE

Clustering(52) Variable = 6Q LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                 0   1
  6Q LOSS MUTATED    40  13
  6Q LOSS WILD-TYPE 261 100
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               53               361 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               13               100 
$`6Q LOSS MUTATED`
TCGA-BA-5152 TCGA-BA-5555 TCGA-BA-5559 TCGA-BB-4225 TCGA-CN-4725 TCGA-CN-4728 
        1288          520         1747          140         1157         1151 
TCGA-CN-4729 TCGA-CN-4740 TCGA-CN-5359 TCGA-CN-6010 TCGA-CN-6024 TCGA-CN-6988 
         392          811         1980          630          224          318 
TCGA-CN-6994 TCGA-CN-A641 TCGA-CQ-6223 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CR-5248 
         735          367         1057         1960          707         1663 
TCGA-CR-6473 TCGA-CR-6491 TCGA-CR-7365 TCGA-CR-7373 TCGA-CR-7399 TCGA-CR-7404 
        1125          350         1191          889          181         1472 
TCGA-CV-5434 TCGA-CV-5440 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-6441 TCGA-CV-6954 
        3295         1978         1958         2437         1970         1957 
TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7101 TCGA-CV-7235 TCGA-CV-7254 TCGA-D6-6823 
        1959         1970         1939         1952         1976          701 
TCGA-D6-6826 TCGA-DQ-5624 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7591 
         154         1778          548         1965          575          622 
TCGA-F7-A50G TCGA-F7-A623 TCGA-HD-A633 TCGA-HD-A6HZ TCGA-IQ-A61G TCGA-MT-A67G 
          15            6           49          111          360          112 
TCGA-MZ-A7D7 TCGA-P3-A6SW TCGA-P3-A6T0 TCGA-UF-A7JF TCGA-UF-A7JH 
         240         1120          578         1497          665 

$`6Q LOSS WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 
         102          462          283          415         1983          276 
TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 
         248          722         1762          725          623         1636 
TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 
         190          644          451           63          384          113 
TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 
         236          895          855          622          918          850 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A6DL 
         351          216          182         1976          314          623 
TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-4228 
         142          187         2878          278          133          558 
TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 
         310          536          423          687          638         1153 
TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A47Z TCGA-C9-A480 
         428          436         1955          624            5            4 
TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4730 TCGA-CN-4731 
         799          721          142         1230          817          993 
TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 
         642         1250          395          625         1960         1330 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5360 
        1268         1988         1007         1045          173         1081 
TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 
        1977         1980         1966         1966         1975          683 
TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 
         290          933          629          628          594          629 
TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 
          45          432           98         1970          202         1110 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 
         611          394          432          429           46          443 
TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U 
         535          391          904          645          225          526 
TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 
         484          348          175          223          298         1466 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 
        1207          654         1660         1422         1393         1399 
TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6224 
         317          341          129         1253         1000          985 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 
        1959         1959         1179         1750         1560         1007 
TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 
         509         1309         1274          877         1950         1353 
TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH 
        1963          893          998          785          391          303 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 
         950         2562          358         1152          799         1777 
TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 
        1521         1966         1050         1971          514         1969 
TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 
         362          311          345          354          234          379 
TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 
         479         1956         1435         1440         1245         1960 
TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 
         105         1979          759           30          972         1968 
TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 
        1036          796         1954          997         1430         1951 
TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 
         392          907          913          946          908          898 
TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7401 TCGA-CR-7402 TCGA-CV-5430 
         930          216          156         1077          911         1955 
TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5441 
         522         1950         1438          584          546         2886 
TCGA-CV-5442 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 
        2327          519          406          701         2641         1478 
TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 
        1840          215         1315         1665          641         1899 
TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 
        1948         1969         1952         1959         3835         1948 
TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7097 
        1969         1966         1969         1959         3837         1970 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7238 
        1936         1959         1945         1987         1979         1444 
TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7261 
        1095          954          797         1967         1960         1099 
TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7427 
        1974         1948         1955         1957         1947         1937 
TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 
        1973         1972         1937         1984         1958         1959 
TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45Y TCGA-CV-A45Z 
        1981          851         1945         5480         1960         1940 
TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE 
        1946         1954         1722         1977         1970         1075 
TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ 
         906         1959          670          110          646          714 
TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 
         606          685         1950          317          321          237 
TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6827 
         828          773          292           77          491          568 
TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM 
         106          128          539          376          483          232 
TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5625 
         435          424          368          389          338         1081 
TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-7590 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 
         516         1030          775          299          369          368 
TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50I 
         324          340         1131          490          658           92 
TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-H7-7774 
         585            3          384           14           13          407 
TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 
          58          133          414          403          206            2 
TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 
           5           25           37           55           44           24 
TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 
          25           11           10           33         1057          485 
TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61L 
         122          441          588          412          440          351 
TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W 
         360          224          552          378          168           14 
TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MZ-A6I9 TCGA-P3-A5Q5 
          34          392           56          111          254          910 
TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SX TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-P3-A6T8 
        1726         1559         1954         1917         1968          400 
TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II 
         553          357          245          218          228          225 
TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB 
         387          567          198          149          135          135 
TCGA-QK-AA3J TCGA-QK-AA3K TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71D 
         157          168         1326         1663         1319         1252 
TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JJ 
        1278         1043         1894          484          735          214 
TCGA-UF-A7JS 
         413 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                6                 2 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             3295              5480 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              889               670 
[1] "6.0 - 3295.0 (889.0)" "2.0 - 5480.0 (670.0)"
[1] "hr=" "1.5"
D52V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  6Q LOSS MUTATED         1        8        10        32         1         0
  6Q LOSS WILD-TYPE      25       67        64       203        11         1
D52V3, multiclass
           clus
vv          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  STAGE I                 1                25
  STAGE II                8                67
  STAGE III              10                64
  STAGE IVA              32               203
  STAGE IVB               1                11
  STAGE IVC               0                 1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  6Q LOSS MUTATED       4  13  11  24
  6Q LOSS WILD-TYPE    43 114  83 138
D52V4, multiclass
       clus
vv      6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T0+T1               4                43
  T2                 13               114
  T3                 11                83
  T4                 24               138
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  6Q LOSS MUTATED    17   8  20   1
  6Q LOSS WILD-TYPE 153  55 132   7
D52V5, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  N0              17               153
  N1               8                55
  N2              20               132
  N3               1                 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"
                   vv
clus                 M0  M1  MX
  6Q LOSS MUTATED    15   0   9
  6Q LOSS WILD-TYPE 152   1  49
D52V6, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  M0              15               152
  M1               0                 1
  MX               9                49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V7, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    12  50
  6Q LOSS WILD-TYPE 120 306
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     12   50
  6Q LOSS WILD-TYPE  120  306
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE              12               120
  MALE                50               306
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  6Q LOSS MUTATED                                      61
  6Q LOSS WILD-TYPE                                   416
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  6Q LOSS MUTATED                                                             0
  6Q LOSS WILD-TYPE                                                           1
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  6Q LOSS MUTATED                                                     1
  6Q LOSS WILD-TYPE                                                   9
D52V8, multiclass
                                                             clus
vv                                                            6Q LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    61
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       1
                                                             clus
vv                                                            6Q LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     416
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                 1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V9, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    12  50
  6Q LOSS WILD-TYPE  67 359
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     12   50
  6Q LOSS WILD-TYPE   67  359
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  NO               12                67
  YES              50               359
[1] 2 2
[1] FALSE
D52V10, continuous
D52V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6Q LOSS MUTATED                                  0     0
  6Q LOSS WILD-TYPE                                2    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6Q LOSS MUTATED                          10    50
  6Q LOSS WILD-TYPE                        34   365
D52V12, multiclass
                                  clus
vv                                 6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                     10                34
  WHITE                                         50               365
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V13, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED     3  53
  6Q LOSS WILD-TYPE  21 378
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      3   53
  6Q LOSS WILD-TYPE   21  378
                        clus
vv                       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                21
  NOT HISPANIC OR LATINO              53               378
[1] 2 2
[1] FALSE

Clustering(53) Variable = 7P LOSS MUTATION ANALYSIS
D53V1, survival
                   sevent
clus2                 0   1
  7P LOSS MUTATED    19   6
  7P LOSS WILD-TYPE 282 107
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               25               389 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                6               107 
$`7P LOSS MUTATED`
TCGA-BA-5559 TCGA-BA-A4IG TCGA-BA-A6DE TCGA-CN-5374 TCGA-CN-6992 TCGA-CN-6998 
        1747          855          182          290          394           46 
TCGA-CN-A49B TCGA-CN-A63U TCGA-CN-A63W TCGA-CR-6473 TCGA-CV-5435 TCGA-CV-6003 
         904          526          348         1125         1438         1665 
TCGA-CV-7242 TCGA-CV-7430 TCGA-CV-7433 TCGA-CX-7082 TCGA-D6-A6EQ TCGA-F7-A50G 
        1095         1972         1984          317          368           15 
TCGA-F7-A623 TCGA-HD-A6HZ TCGA-KU-A6H7 TCGA-MZ-A6I9 TCGA-QK-A6IH TCGA-QK-AA3J 
           6          111          378          254          228          157 
TCGA-UF-A719 
        1663 

$`7P LOSS WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 
         102          462          283          415         1983          276 
TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 
         248          722         1288         1762          520          725 
TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 
         623         1636          190          644          451           63 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A4II 
         384          113          236          895          622          918 
TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A6DL 
         850          351          216         1976          314          623 
TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 
         142          187         2878          278          140          133 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 
         558          310          536          423          687          638 
TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A47Z 
        1153          428          436         1955          624            5 
TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 
           4          799          721         1157          142         1230 
TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 
        1151          392          817          993          642         1250 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 
         395          625         1960         1330          811         1268 
TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 
        1988         1007         1045          173         1980         1081 
TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 
        1977         1980         1966         1966         1975          683 
TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 
         630          933          629          628          594          629 
TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 
          45          432           98         1970          202         1110 
TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 
         224          318          611          735          432          429 
TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63V 
         443          535          391          645          225          484 
TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-5324 
         175          367          223          298         1466         1207 
TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 
         654         1660         1422         1393         1399          317 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 
         341          129         1253         1000         1057          985 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 
        1959         1959         1179         1750         1560         1007 
TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 
         509         1309         1274          877         1950         1353 
TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE 
        1960          707         1963          893          998          785 
TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 
         391          303          950         2562          358         1663 
TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 
        1152          799         1777         1521         1966         1050 
TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 
        1971          514         1969          362          311          345 
TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 
         354          234          379          350          479         1956 
TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 
        1435         1191         1440         1245         1960          105 
TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 
        1979          759          889           30          972         1968 
TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 
        1036          796         1954          997         1430         1951 
TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 
         392          907          913          946          908          898 
TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 
         930          216          156          181         1077          911 
TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5436 
        1472         1955          522         1950         3295          584 
TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 
         546         1978         2886         2327         1958         2437 
TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 
         519          406          701         2641         1478         1840 
TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 
         215         1315          641         1899         1970         1948 
TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 
        1969         1952         1959         3835         1948         1969 
TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 
        1966         1957         1969         1959         3837         1959 
TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 
        1970         1970         1936         1959         1939         1945 
TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7243 TCGA-CV-7245 
        1987         1979         1952         1444          954          797 
TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 
        1967         1960         1976         1099         1974         1948 
TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7432 
        1955         1957         1947         1937         1973         1937 
TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A45R 
        1958         1959         1981          851         1945         5480 
TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A468 
        1960         1940         1946         1954         1722         1977 
TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU 
        1970         1075          906         1959          670          110 
TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 
         646          714          606          685         1950          321 
TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 
         237          828          773          292          701           77 
TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 
         491          154          568          106          128          539 
TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6ES 
         376          483          232          435          424          389 
TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 
         338         1778         1081          516         1030          548 
TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 
        1965          575          775          622          299          369 
TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 
         368          324          340         1131          490          658 
TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 
          92          585            3          384           14           13 
TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A 
         407           58          133          414          403          206 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 
           2            5           25           37           55           44 
TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6I0 
          24           25           11           49           10           33 
TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G 
        1057          485          122          441          588          360 
TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T 
         412          440          351          360          224          552 
TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F 
         168           14           34          392           56          111 
TCGA-MT-A67G TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW 
         112          240          910         1726         1559         1120 
TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A64Z 
        1954          578         1917         1968          400          553 
TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 
         357          245          218          225          387          567 
TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3K TCGA-UF-A718 
         198          149          135          135          168         1326 
TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC 
        1319         1252         1278         1043         1894          484 
TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JS 
         735         1497          665          214          413 

  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                6                 2 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
             1984              5480 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
              378               714 
[1] "6.0 - 1984.0 (378.0)" "2.0 - 5480.0 (714.0)"
[1] "hr=" "1.2"
D53V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  7P LOSS MUTATED         1        3         4        13         1         1
  7P LOSS WILD-TYPE      25       72        70       222        11         0
D53V3, multiclass
           clus
vv          7P LOSS MUTATED 7P LOSS WILD-TYPE
  STAGE I                 1                25
  STAGE II                3                72
  STAGE III               4                70
  STAGE IVA              13               222
  STAGE IVB               1                11
  STAGE IVC               1                 0
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  7P LOSS MUTATED       3   8   6   7
  7P LOSS WILD-TYPE    44 119  88 155
D53V4, multiclass
       clus
vv      7P LOSS MUTATED 7P LOSS WILD-TYPE
  T0+T1               3                44
  T2                  8               119
  T3                  6                88
  T4                  7               155
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  7P LOSS MUTATED     5   6  12   0
  7P LOSS WILD-TYPE 165  57 140   8
D53V5, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  N0               5               165
  N1               6                57
  N2              12               140
  N3               0                 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"
                   vv
clus                 M0  M1  MX
  7P LOSS MUTATED     9   1   5
  7P LOSS WILD-TYPE 158   0  53
D53V6, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  M0               9               158
  M1               1                 0
  MX               5                53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V7, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     9  19
  7P LOSS WILD-TYPE 123 337
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      9   19
  7P LOSS WILD-TYPE  123  337
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  FEMALE               9               123
  MALE                19               337
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  7P LOSS MUTATED                                      27
  7P LOSS WILD-TYPE                                   450
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  7P LOSS MUTATED                                                             0
  7P LOSS WILD-TYPE                                                           1
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  7P LOSS MUTATED                                                     1
  7P LOSS WILD-TYPE                                                   9
D53V8, multiclass
                                                             clus
vv                                                            7P LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    27
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       1
                                                             clus
vv                                                            7P LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     450
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                 1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V9, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     3  25
  7P LOSS WILD-TYPE  76 384
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      3   25
  7P LOSS WILD-TYPE   76  384
     clus
vv    7P LOSS MUTATED 7P LOSS WILD-TYPE
  NO                3                76
  YES              25               384
[1] 2 2
[1] FALSE
D53V10, continuous
D53V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7P LOSS MUTATED                                  0     0
  7P LOSS WILD-TYPE                                2    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7P LOSS MUTATED                           2    25
  7P LOSS WILD-TYPE                        42   390
D53V12, multiclass
                                  clus
vv                                 7P LOSS MUTATED 7P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      2                42
  WHITE                                         25               390
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V13, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     1  26
  7P LOSS WILD-TYPE  23 405
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      1   26
  7P LOSS WILD-TYPE   23  405
                        clus
vv                       7P LOSS MUTATED 7P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                23
  NOT HISPANIC OR LATINO              26               405
[1] 2 2
[1] FALSE

Clustering(54) Variable = 7Q LOSS MUTATION ANALYSIS
D54V1, survival
                   sevent
clus2                 0   1
  7Q LOSS MUTATED    25  10
  7Q LOSS WILD-TYPE 276 103
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               35               379 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               10               103 
$`7Q LOSS MUTATED`
TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-5152 TCGA-BA-5559 TCGA-BA-A4IH TCGA-BA-A6DE 
         462          415         1288         1747          622          182 
TCGA-BB-4224 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4737 TCGA-CN-5359 TCGA-CN-5374 
         278          817          993          625         1980          290 
TCGA-CN-6998 TCGA-CN-A49B TCGA-CN-A63U TCGA-CN-A63W TCGA-CR-6474 TCGA-CR-7374 
          46          904          526          348         1971           30 
TCGA-CR-7398 TCGA-CV-5444 TCGA-CV-6003 TCGA-CV-6954 TCGA-CV-7180 TCGA-CV-7433 
         156         2437         1665         1957         1987         1984 
TCGA-CX-7082 TCGA-D6-6823 TCGA-F7-8489 TCGA-F7-A50G TCGA-HD-A6HZ TCGA-IQ-7632 
         317          701          658           15          111          441 
TCGA-KU-A66T TCGA-KU-A6H7 TCGA-MZ-A6I9 TCGA-P3-A5QE TCGA-QK-A8Z9 
         552          378          254         1559          149 

$`7Q LOSS WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 
         102          283         1983          276          248          722 
TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6868 
        1762          520          725          623         1636          190 
TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 
         644          451           63          384          113          236 
TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB 
         895          855          918          850          351          216 
TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 
        1976          314          623          142          187         2878 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 
         140          133          558          310          536          423 
TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 
         687          638         1153          428          436         1955 
TCGA-BB-8601 TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 
         624            5            4          799          721         1157 
TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4733 TCGA-CN-4735 
         142         1230         1151          392          642         1250 
TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 
         395         1960         1330          811         1268         1988 
TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 
        1007         1045          173         1081         1977         1980 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6010 TCGA-CN-6011 
        1966         1966         1975          683          630          933 
TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 
         629          628          594          629           45          432 
TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 
          98         1970          202         1110          224          318 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-A498 
         611          394          735          432          429          443 
TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63Y 
         535          391          645          225          484          175 
TCGA-CN-A641 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
         367          223          298         1466         1207          654 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 
        1660         1422         1393         1399          317          341 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 
         129         1253         1000         1057          985         1959 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 
        1959         1179         1750         1560         1007          509 
TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 
        1309         1274          877         1950         1353         1960 
TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG 
         707         1963          893          998          785          391 
TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 
         303          950         2562          358         1663         1152 
TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 
         799         1777         1521         1966         1050         1125 
TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 
         514         1969          362          311          345          354 
TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 
         234          379          350          479         1956         1435 
TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 
        1191         1440         1245         1960          105         1979 
TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 
         759          889          972         1968         1036          796 
TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 
        1954          997         1430         1951          392          907 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 
         913          946          908          898          930          216 
TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 
         181         1077          911         1472         1955          522 
TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 
        1950         3295         1438          584          546         1978 
TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 
        2886         2327         1958          519          406          701 
TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6433 
        2641         1478         1840          215         1315          641 
TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6941 
        1899         1970         1948         1969         1952         1959 
TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-6960 TCGA-CV-6961 
        3835         1948         1969         1966         1969         1959 
TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 
        3837         1959         1970         1970         1936         1959 
TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7242 
        1939         1945         1979         1952         1444         1095 
TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 
         954          797         1967         1960         1976         1099 
TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7427 
        1974         1948         1955         1957         1947         1937 
TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7440 
        1973         1972         1937         1958         1959         1981 
TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 
         851         1945         5480         1960         1940         1946 
TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN 
        1954         1722         1977         1970         1075          906 
TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 
        1959          670          110          646          714          606 
TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 
         685         1950          321          237          828          773 
TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 
         292           77          491          154          568          106 
TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO 
         128          539          376          483          232          435 
TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 
         424          368          389          338         1778         1081 
TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 
         516         1030          548         1965          575          775 
TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
         622          299          369          368          324          340 
TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V 
        1131          490           92          585            3          384 
TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 
          14           13            6          407           58          133 
TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 
         414          403          206            2            5           25 
TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 
          37           55           44           24           25           11 
TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 
          49           10           33         1057          485          122 
TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61L TCGA-IQ-A61O 
         588          360          412          440          351          360 
TCGA-KU-A66S TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D 
         224          168           14           34          392           56 
TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A6SW 
         111          112          240          910         1726         1120 
TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A64Z 
        1954          578         1917         1968          400          553 
TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ 
         357          245          218          228          225          387 
TCGA-QK-A6V9 TCGA-QK-A8Z7 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K 
         567          198          135          135          157          168 
TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 
        1326         1663         1319         1252         1278         1043 
TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ 
        1894          484          735         1497          665          214 
TCGA-UF-A7JS 
         413 

  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               15                 2 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
             2437              5480 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
              552               722 
[1] "15.0 - 2437.0 (552.0)" "2.0 - 5480.0 (722.0)" 
[1] "hr=" "1.2"
D54V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  7Q LOSS MUTATED         1        5         6        22         0         0
  7Q LOSS WILD-TYPE      25       70        68       213        12         1
D54V3, multiclass
           clus
vv          7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  STAGE I                 1                25
  STAGE II                5                70
  STAGE III               6                68
  STAGE IVA              22               213
  STAGE IVB               0                12
  STAGE IVC               0                 1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  7Q LOSS MUTATED       1  16   5  12
  7Q LOSS WILD-TYPE    46 111  89 150
D54V4, multiclass
       clus
vv      7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  T0+T1               1                46
  T2                 16               111
  T3                  5                89
  T4                 12               150
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  7Q LOSS MUTATED     8   8  15   0
  7Q LOSS WILD-TYPE 162  55 137   8
D54V5, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  N0               8               162
  N1               8                55
  N2              15               137
  N3               0                 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"
                   vv
clus                 M0  M1  MX
  7Q LOSS MUTATED    12   0   6
  7Q LOSS WILD-TYPE 155   1  52
D54V6, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  M0              12               155
  M1               0                 1
  MX               6                52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V7, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED    12  27
  7Q LOSS WILD-TYPE 120 329
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED     12   27
  7Q LOSS WILD-TYPE  120  329
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  FEMALE              12               120
  MALE                27               329
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  7Q LOSS MUTATED                                      37
  7Q LOSS WILD-TYPE                                   440
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  7Q LOSS MUTATED                                                             0
  7Q LOSS WILD-TYPE                                                           1
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  7Q LOSS MUTATED                                                     2
  7Q LOSS WILD-TYPE                                                   8
D54V8, multiclass
                                                             clus
vv                                                            7Q LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    37
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       2
                                                             clus
vv                                                            7Q LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     440
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                 1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V9, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     7  32
  7Q LOSS WILD-TYPE  72 377
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      7   32
  7Q LOSS WILD-TYPE   72  377
     clus
vv    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  NO                7                72
  YES              32               377
[1] 2 2
[1] FALSE
D54V10, continuous
D54V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7Q LOSS MUTATED                                  0     0
  7Q LOSS WILD-TYPE                                2    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7Q LOSS MUTATED                           3    36
  7Q LOSS WILD-TYPE                        41   379
D54V12, multiclass
                                  clus
vv                                 7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      3                41
  WHITE                                         36               379
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V13, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     1  37
  7Q LOSS WILD-TYPE  23 394
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      1   37
  7Q LOSS WILD-TYPE   23  394
                        clus
vv                       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                23
  NOT HISPANIC OR LATINO              37               394
[1] 2 2
[1] FALSE

Clustering(55) Variable = 8P LOSS MUTATION ANALYSIS
D55V1, survival
                   sevent
clus2                 0   1
  8P LOSS MUTATED    97  45
  8P LOSS WILD-TYPE 204  68
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              142               272 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               45                68 
$`8P LOSS MUTATED`
TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5558 TCGA-BA-6870 
         462          415          248          722         1636          451 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A6D8 TCGA-BA-A6DE TCGA-BB-4227 
         384          113          236          850          182          133 
TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7871 TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4725 
         536          423          428            5            4         1157 
TCGA-CN-4726 TCGA-CN-4736 TCGA-CN-4742 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 
         142          395         1988         1081         1977         1980 
TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6013 
        1966         1975          683          290          933          628 
TCGA-CN-6016 TCGA-CN-6020 TCGA-CN-6992 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-A498 
         594           98          394          432          429          443 
TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A641 TCGA-CQ-5332 TCGA-CQ-5334 TCGA-CQ-6227 
         391          904          367          317          129         1959 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 
        1959         1179         1750         1560         1007          509 
TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4CB TCGA-CR-5247 TCGA-CR-6471 
        1274         1950         1353          893          358         1966 
TCGA-CR-6474 TCGA-CR-6484 TCGA-CR-6488 TCGA-CR-7364 TCGA-CR-7369 TCGA-CR-7372 
        1971          354          379         1435         1960          759 
TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7377 TCGA-CR-7388 TCGA-CR-7399 TCGA-CR-7401 
         889           30         1968         1951          181         1077 
TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5441 TCGA-CV-5966 TCGA-CV-5973 TCGA-CV-6436 
        1950         3295         2886          519         2641         1899 
TCGA-CV-6935 TCGA-CV-6942 TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-7090 
        1969         3835         1966         1957         1969         3837 
TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7248 
        1959         1945         1952         1444         1095         1967 
TCGA-CV-7261 TCGA-CV-7422 TCGA-CV-7427 TCGA-CV-7434 TCGA-CV-7440 TCGA-CV-A460 
        1099         1957         1937         1958         1981         1946 
TCGA-CV-A464 TCGA-CV-A6JD TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JZ TCGA-CX-7219 
        1722         1970         1959          670          714          828 
TCGA-D6-6517 TCGA-D6-6825 TCGA-D6-A4Z9 TCGA-D6-A6EM TCGA-D6-A6ES TCGA-DQ-5624 
         292          491          539          232          389         1778 
TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7589 TCGA-DQ-7592 TCGA-F7-8298 
        1081         1030          548          575          299          490 
TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61W TCGA-F7-A620 TCGA-H7-8501 TCGA-H7-8502 
          92          585           14           13           58          133 
TCGA-HD-7753 TCGA-HD-8224 TCGA-HD-8635 TCGA-HD-A633 TCGA-IQ-7630 TCGA-IQ-A61E 
           5           55           25           49          485          588 
TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61L TCGA-KU-A66T TCGA-MT-A51X 
         360          412          440          351          552           34 
TCGA-MZ-A6I9 TCGA-P3-A5QA TCGA-P3-A6SX TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 
         254         1726         1954          400          553          357 
TCGA-QK-A6IH TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K 
         228          149          135          135          157          168 
TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JD 
        1252         1278         1043          735 

$`8P LOSS WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5152 TCGA-BA-5153 
         102          283         1983          276         1288         1762 
TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 
         520          725          623         1747          190          644 
TCGA-BA-6871 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6DA 
          63          895          855          622          918          351 
TCGA-BA-A6DB TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 
         216         1976          314          623          142          187 
TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7864 
        2878          278          140          558          310          687 
TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-CN-4722 
         638         1153          436         1955          624          799 
TCGA-CN-4723 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 
         721         1230         1151          392          817          993 
TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 
         642         1250          625         1960         1330          811 
TCGA-CN-4741 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5366 
        1268         1007         1045          173         1980         1966 
TCGA-CN-6010 TCGA-CN-6012 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6021 
         630          629          629           45          432         1970 
TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 
         202         1110          224          318          611          735 
TCGA-CN-6998 TCGA-CN-A499 TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V 
          46          535          645          225          526          484 
TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-5324 
         348          175          223          298         1466         1207 
TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 
         654         1660         1422         1393         1399          341 
TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-7068 TCGA-CQ-7071 
        1253         1000         1057          985         1309          877 
TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG 
        1960          707         1963          998          785          391 
TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 
         303          950         2562         1663         1152          799 
TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6477 TCGA-CR-6478 
        1777         1521         1050         1125          514         1969 
TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6491 TCGA-CR-6492 
         362          311          345          234          350          479 
TCGA-CR-6493 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7370 TCGA-CR-7371 
        1956         1191         1440         1245          105         1979 
TCGA-CR-7376 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 
         972         1036          796         1954          997         1430 
TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 
         392          907          913          946          908          898 
TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 
         930          216          156          911         1472         1955 
TCGA-CV-5431 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5442 
         522         1438          584          546         1978         2327 
TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5976 TCGA-CV-5977 
        1958         2437          406          701         1478         1840 
TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6441 TCGA-CV-6934 
         215         1315         1665          641         1970         1948 
TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6961 TCGA-CV-7091 
        1952         1959         1948         1969         1959         1959 
TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7101 TCGA-CV-7180 TCGA-CV-7183 
        1970         1970         1936         1939         1987         1979 
TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7406 TCGA-CV-7410 
         954          797         1960         1976         1974         1948 
TCGA-CV-7418 TCGA-CV-7424 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 
        1955         1947         1973         1972         1937         1984 
TCGA-CV-7435 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45Y TCGA-CV-A45Z 
        1959          851         1945         5480         1960         1940 
TCGA-CV-A461 TCGA-CV-A468 TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JU TCGA-CV-A6JY 
        1954         1977         1075          906          110          646 
TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 
         606          685         1950          317          321          237 
TCGA-D6-6516 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 
         773          701           77          154          568          106 
TCGA-D6-8569 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ 
         128          376          483          435          424          368 
TCGA-D6-A74Q TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7593 
         338          516         1965          775          622          369 
TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G 
         368          324          340         1131          658           15 
TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-A6C4 TCGA-H7-A6C5 
           3          384            6          407          414          403 
TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8314 TCGA-HD-8634 
         206            2           25           37           44           24 
TCGA-HD-A4C1 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7631 
          11           10          111           33         1057          122 
TCGA-IQ-7632 TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W 
         441          360          224          378          168           14 
TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A7D7 TCGA-P3-A5Q5 
         392           56          111          112          240          910 
TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-QK-A6IF 
        1559         1120          578         1917         1968          245 
TCGA-QK-A6IG TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A8Z7 TCGA-UF-A718 
         218          225          387          567          198         1326 
TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JF TCGA-UF-A7JH 
        1663         1319         1894          484         1497          665 
TCGA-UF-A7JJ TCGA-UF-A7JS 
         214          413 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                4                 2 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             3837              5480 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              611               723 
[1] "4.0 - 3837.0 (611.0)" "2.0 - 5480.0 (723.0)"
[1] "hr=" "1.1"
D55V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  8P LOSS MUTATED        11       25        32        84         5         1
  8P LOSS WILD-TYPE      15       50        42       151         7         0
D55V3, multiclass
           clus
vv          8P LOSS MUTATED 8P LOSS WILD-TYPE
  STAGE I                11                15
  STAGE II               25                50
  STAGE III              32                42
  STAGE IVA              84               151
  STAGE IVB               5                 7
  STAGE IVC               1                 0
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  8P LOSS MUTATED      19  40  42  58
  8P LOSS WILD-TYPE    28  87  52 104
D55V4, multiclass
       clus
vv      8P LOSS MUTATED 8P LOSS WILD-TYPE
  T0+T1              19                28
  T2                 40                87
  T3                 42                52
  T4                 58               104
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  8P LOSS MUTATED    57  25  60   2
  8P LOSS WILD-TYPE 113  38  92   6
D55V5, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  N0              57               113
  N1              25                38
  N2              60                92
  N3               2                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1  MX
  8P LOSS MUTATED    62   1  22
  8P LOSS WILD-TYPE 105   0  36
D55V6, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  M0              62               105
  M1               1                 0
  MX              22                36
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V7, binary
                   cls
clus                  0   1
  8P LOSS MUTATED    56 119
  8P LOSS WILD-TYPE  76 237
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     56  119
  8P LOSS WILD-TYPE   76  237
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE              56                76
  MALE               119               237
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  8P LOSS MUTATED                                     173
  8P LOSS WILD-TYPE                                   304
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  8P LOSS MUTATED                                                             0
  8P LOSS WILD-TYPE                                                           1
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  8P LOSS MUTATED                                                     2
  8P LOSS WILD-TYPE                                                   8
D55V8, multiclass
                                                             clus
vv                                                            8P LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                   173
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       2
                                                             clus
vv                                                            8P LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     304
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                 1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V9, binary
                   cls
clus                  0   1
  8P LOSS MUTATED    29 146
  8P LOSS WILD-TYPE  50 263
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     29  146
  8P LOSS WILD-TYPE   50  263
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  NO               29                50
  YES             146               263
[1] 2 2
[1] FALSE
D55V10, continuous
D55V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8P LOSS MUTATED                                  1     6
  8P LOSS WILD-TYPE                                1     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8P LOSS MUTATED                          19   143
  8P LOSS WILD-TYPE                        25   272
D55V12, multiclass
                                  clus
vv                                 8P LOSS MUTATED 8P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 1
  ASIAN                                          6                 5
  BLACK OR AFRICAN AMERICAN                     19                25
  WHITE                                        143               272
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V13, binary
                   cls
clus                  0   1
  8P LOSS MUTATED    10 152
  8P LOSS WILD-TYPE  14 279
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     10  152
  8P LOSS WILD-TYPE   14  279
                        clus
vv                       8P LOSS MUTATED 8P LOSS WILD-TYPE
  HISPANIC OR LATINO                  10                14
  NOT HISPANIC OR LATINO             152               279
[1] 2 2
[1] FALSE

Clustering(56) Variable = 8Q LOSS MUTATION ANALYSIS
D56V1, survival
                   sevent
clus2                 0   1
  8Q LOSS MUTATED    15   7
  8Q LOSS WILD-TYPE 286 106
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               22               392 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                7               106 
$`8Q LOSS MUTATED`
TCGA-BA-4076 TCGA-BA-A6D8 TCGA-CN-4726 TCGA-CN-5360 TCGA-CN-5367 TCGA-CN-6011 
         415          850          142         1081         1966          933 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-A641 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CR-6471 
         628          594          367         1750         1560         1966 
TCGA-CV-7242 TCGA-CV-7261 TCGA-CV-7440 TCGA-CV-A6JD TCGA-CV-A6JT TCGA-D6-A6EM 
        1095         1099         1981         1970          670          232 
TCGA-H7-8502 TCGA-IQ-7630 TCGA-MZ-A6I9 TCGA-QK-AA3J 
         133          485          254          157 

$`8Q LOSS WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
         102          462          283         1983          276          248 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 
         722         1288         1762          520          725          623 
TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 
        1636         1747          190          644          451           63 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH 
         384          113          236          895          855          622 
TCGA-BA-A4II TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DJ 
         918          351          216          182         1976          314 
TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 
         623          142          187         2878          278          140 
TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 
         133          558          310          536          423          687 
TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 
         638         1153          428          436         1955          624 
TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4727 
           5            4          799          721         1157         1230 
TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 
        1151          392          817          993          642         1250 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 
         395          625         1960         1330          811         1268 
TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5363 
        1988         1007         1045          173         1980         1977 
TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 
        1980         1966         1975          683          290          630 
TCGA-CN-6012 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 
         629          629           45          432           98         1970 
TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 
         202         1110          224          318          611          394 
TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A499 
         735          432          429           46          443          535 
TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V 
         391          904          645          225          526          484 
TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-5324 
         348          175          223          298         1466         1207 
TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 
         654         1660         1422         1393         1399          317 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 
         341          129         1253         1000         1057          985 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 
        1959         1959         1179         1007          509         1309 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
        1274          877         1950         1353         1960          707 
TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH 
        1963          893          998          785          391          303 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 
         950         2562          358         1663         1152          799 
TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 
        1777         1521         1050         1125         1971          514 
TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 
        1969          362          311          345          354          234 
TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 
         379          350          479         1956         1435         1191 
TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 
        1440         1245         1960          105         1979          759 
TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 
         889           30          972         1968         1036          796 
TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 
        1954          997         1430         1951          392          907 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 
         913          946          908          898          930          216 
TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 
         156          181         1077          911         1472         1955 
TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 
         522         1950         3295         1438          584          546 
TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 
        1978         2886         2327         1958         2437          519 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 
         406          701         2641         1478         1840          215 
TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 
        1315         1665          641         1899         1970         1948 
TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 
        1969         1952         1959         3835         1948         1969 
TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 
        1966         1957         1969         1959         3837         1959 
TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 
        1970         1970         1936         1959         1939         1945 
TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7243 TCGA-CV-7245 
        1987         1979         1952         1444          954          797 
TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 
        1967         1960         1976         1974         1948         1955 
TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 
        1957         1947         1937         1973         1972         1937 
TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A45R 
        1984         1958         1959          851         1945         5480 
TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A468 
        1960         1940         1946         1954         1722         1977 
TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ 
        1075          906         1959          110          646          714 
TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 
         606          685         1950          317          321          237 
TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 
         828          773          292          701           77          491 
TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB 
         154          568          106          128          539          376 
TCGA-D6-A6EK TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q 
         483          435          424          368          389          338 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 
        1778         1081          516         1030          548         1965 
TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 
         575          775          622          299          369          368 
TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G 
         324          340         1131          490          658           15 
TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 
          92          585            3          384           14           13 
TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A 
           6          407           58          414          403          206 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 
           2            5           25           37           55           44 
TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ 
          24           25           11           49           10          111 
TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G 
          33         1057          122          441          588          360 
TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T 
         412          440          351          360          224          552 
TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D 
         378          168           14           34          392           56 
TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE 
         111          112          240          910         1726         1559 
TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-P3-A6T8 
        1120         1954          578         1917         1968          400 
TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II 
         553          357          245          218          228          225 
TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB 
         387          567          198          149          135          135 
TCGA-QK-AA3K TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E 
         168         1326         1663         1319         1252         1278 
TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH 
        1043         1894          484          735         1497          665 
TCGA-UF-A7JJ TCGA-UF-A7JS 
         214          413 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
              133                 2 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             1981              5480 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
              760               701 
[1] "133.0 - 1981.0 (760.0)" "2.0 - 5480.0 (701.0)"  
[1] "hr=" "1.2"
D56V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  8Q LOSS MUTATED         2        6         4        13         0         0
  8Q LOSS WILD-TYPE      24       69        70       222        12         1
D56V3, multiclass
           clus
vv          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  STAGE I                 2                24
  STAGE II                6                69
  STAGE III               4                70
  STAGE IVA              13               222
  STAGE IVB               0                12
  STAGE IVC               0                 1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  8Q LOSS MUTATED       2   6   6  11
  8Q LOSS WILD-TYPE    45 121  88 151
D56V4, multiclass
       clus
vv      8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  T0+T1               2                45
  T2                  6               121
  T3                  6                88
  T4                 11               151
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  8Q LOSS MUTATED     9   5   8   0
  8Q LOSS WILD-TYPE 161  58 144   8
D56V5, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  N0               9               161
  N1               5                58
  N2               8               144
  N3               0                 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"
                   vv
clus                 M0  M1  MX
  8Q LOSS MUTATED    12   0   3
  8Q LOSS WILD-TYPE 155   1  55
D56V6, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  M0              12               155
  M1               0                 1
  MX               3                55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V7, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     6  22
  8Q LOSS WILD-TYPE 126 334
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      6   22
  8Q LOSS WILD-TYPE  126  334
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE               6               126
  MALE                22               334
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  8Q LOSS MUTATED                                      27
  8Q LOSS WILD-TYPE                                   450
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  8Q LOSS MUTATED                                                             0
  8Q LOSS WILD-TYPE                                                           1
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  8Q LOSS MUTATED                                                     1
  8Q LOSS WILD-TYPE                                                   9
D56V8, multiclass
                                                             clus
vv                                                            8Q LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    27
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       1
                                                             clus
vv                                                            8Q LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     450
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                 1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V9, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     6  22
  8Q LOSS WILD-TYPE  73 387
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      6   22
  8Q LOSS WILD-TYPE   73  387
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  NO                6                73
  YES              22               387
[1] 2 2
[1] FALSE
D56V10, continuous
D56V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8Q LOSS MUTATED                                  0     0
  8Q LOSS WILD-TYPE                                2    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8Q LOSS MUTATED                           2    25
  8Q LOSS WILD-TYPE                        42   390
D56V12, multiclass
                                  clus
vv                                 8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      2                42
  WHITE                                         25               390
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V13, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     2  25
  8Q LOSS WILD-TYPE  22 406
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      2   25
  8Q LOSS WILD-TYPE   22  406
                        clus
vv                       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                22
  NOT HISPANIC OR LATINO              25               406
[1] 2 2
[1] FALSE

Clustering(57) Variable = 9P LOSS MUTATION ANALYSIS
D57V1, survival
                   sevent
clus2                 0   1
  9P LOSS MUTATED   106  46
  9P LOSS WILD-TYPE 195  67
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              152               262 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               46                67 
$`9P LOSS MUTATED`
TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5555 TCGA-BA-6868 TCGA-BA-6869 
         462          415          276          520          190          644 
TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A6D8 
         451           63          384          236          895          850 
TCGA-BA-A6DE TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4224 TCGA-BB-7862 TCGA-BB-7872 
         182          623          142          278          536          436 
TCGA-BB-8601 TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4729 TCGA-CN-4730 
         624          721          142         1230          392          817 
TCGA-CN-4731 TCGA-CN-4735 TCGA-CN-4737 TCGA-CN-4740 TCGA-CN-5360 TCGA-CN-5373 
         993         1250          625          811         1081          683 
TCGA-CN-6018 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 
          45           98         1970          224          318          611 
TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A63W TCGA-CN-A641 TCGA-CQ-5325 TCGA-CQ-5332 
         394          429          348          367          654          317 
TCGA-CQ-6221 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 
        1000         1959         1959         1560         1007          509 
TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4CB TCGA-CR-5247 TCGA-CR-6472 TCGA-CR-6474 
        1274         1950          893          358         1050         1971 
TCGA-CR-6477 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7368 
         514          379          350         1435         1191         1245 
TCGA-CR-7372 TCGA-CR-7374 TCGA-CR-7383 TCGA-CR-7388 TCGA-CR-7390 TCGA-CR-7398 
         759           30         1954         1951          907          156 
TCGA-CR-7401 TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 
        1077         1955         1950         1438          584          546 
TCGA-CV-5444 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5979 TCGA-CV-6441 TCGA-CV-6934 
        2437         2641         1478         1315         1970         1948 
TCGA-CV-6945 TCGA-CV-6960 TCGA-CV-7091 TCGA-CV-7097 TCGA-CV-7101 TCGA-CV-7180 
        1969         1969         1959         1970         1939         1987 
TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7422 TCGA-CV-7430 TCGA-CV-7432 
        1095          954          797         1957         1972         1937 
TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45Y TCGA-CV-A460 TCGA-CV-A461 
        1958         1959         1981         1960         1946         1954 
TCGA-CV-A464 TCGA-CV-A6JU TCGA-CX-7082 TCGA-CX-7086 TCGA-D6-6823 TCGA-D6-6826 
        1722          110          317          237          701          154 
TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EO TCGA-D6-A6EP 
         106          128          539          376          435          424 
TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5629 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7595 
         389          338          516          548         1965          324 
TCGA-F7-7848 TCGA-F7-A50I TCGA-F7-A61W TCGA-F7-A623 TCGA-H7-A6C5 TCGA-HD-7753 
        1131           92           14            6          403            5 
TCGA-HD-7754 TCGA-HD-8635 TCGA-HD-A633 TCGA-HD-A6HZ TCGA-IQ-7630 TCGA-IQ-A61G 
          25           25           49          111          485          360 
TCGA-IQ-A61J TCGA-KU-A66T TCGA-MT-A51X TCGA-MT-A67D TCGA-MZ-A7D7 TCGA-P3-A6SX 
         440          552           34           56          240         1954 
TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A6IH TCGA-QK-A6IJ TCGA-QK-A8Z7 
        1968          400          553          228          387          198 
TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71B 
         135          135          157         1326         1663         1319 
TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7JA TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH 
        1252         1278         1894          735         1497          665 
TCGA-UF-A7JJ TCGA-UF-A7JS 
         214          413 

$`9P LOSS WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 
         102          283         1983          248          722         1288 
TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6873 
        1762          725          623         1636         1747          113 
TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DG 
         855          622          918          351          216         1976 
TCGA-BA-A6DJ TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 
         314          187         2878          140          133          558 
TCGA-BB-7861 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 
         310          423          687          638         1153          428 
TCGA-BB-8596 TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4725 TCGA-CN-4728 
        1955            5            4          799         1157         1151 
TCGA-CN-4733 TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4741 TCGA-CN-4742 
         642          395         1960         1330         1268         1988 
TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5363 TCGA-CN-5365 
        1007         1045          173         1980         1977         1980 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 
        1966         1966         1975          290          630          933 
TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6022 
         629          628          594          629          432          202 
TCGA-CN-6023 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A499 
        1110          735          432           46          443          535 
TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V 
         391          904          645          225          526          484 
TCGA-CN-A63Y TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5327 
         175          223          298         1466         1207         1660 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 
        1422         1393         1399          341          129         1253 
TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-7071 
        1057          985         1179         1750         1309          877 
TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CD TCGA-CQ-A4CE 
        1353         1960          707         1963          998          785 
TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 
         391          303          950         2562         1663         1152 
TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6478 
         799         1777         1521         1966         1125         1969 
TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6492 
         362          311          345          354          234          479 
TCGA-CR-6493 TCGA-CR-7367 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7373 
        1956         1440         1960          105         1979          889 
TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7386 
         972         1968         1036          796          997         1430 
TCGA-CR-7389 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 
         392          913          946          908          898          930 
TCGA-CR-7397 TCGA-CR-7399 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5434 
         216          181          911         1472          522         3295 
TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5966 TCGA-CV-5970 
        1978         2886         2327         1958          519          406 
TCGA-CV-5971 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 
         701         1840          215         1665          641         1899 
TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6952 
        1969         1952         1959         3835         1948         1966 
TCGA-CV-6954 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7095 TCGA-CV-7099 TCGA-CV-7100 
        1957         1959         3837         1970         1936         1959 
TCGA-CV-7102 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7248 TCGA-CV-7250 
        1945         1979         1952         1444         1967         1960 
TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7424 
        1976         1099         1974         1948         1955         1947 
TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7433 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A45R 
        1937         1973         1984          851         1945         5480 
TCGA-CV-A45Z TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO 
        1940         1977         1970         1075          906         1959 
TCGA-CV-A6JT TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 
         670          646          714          606          685         1950 
TCGA-CX-7085 TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 
         321          828          773          292           77          491 
TCGA-D6-6827 TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EQ TCGA-DQ-5624 TCGA-DQ-5625 
         568          483          232          368         1778         1081 
TCGA-DQ-5630 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 
        1030          575          775          622          299          369 
TCGA-DQ-7594 TCGA-DQ-7596 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50J 
         368          340          490          658           15          585 
TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A620 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 
           3          384           13          407           58          133 
TCGA-H7-A6C4 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 
         414          206            2           37           55           44 
TCGA-HD-8634 TCGA-HD-A4C1 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7631 
          24           11           10           33         1057          122 
TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61H TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S 
         441          588          412          351          360          224 
TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G 
         378          168           14          392          111          112 
TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6T0 
         254          910         1726         1559         1120          578 
TCGA-P3-A6T2 TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6II TCGA-QK-A6V9 
        1917          357          245          218          225          567 
TCGA-QK-A8Z9 TCGA-QK-AA3K TCGA-UF-A7J9 TCGA-UF-A7JC 
         149          168         1043          484 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                5                 2 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             2641              5480 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              617               780 
[1] "5.0 - 2641.0 (617.0)" "2.0 - 5480.0 (780.0)"
[1] "hr=" "1.6"
D57V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  9P LOSS MUTATED        10       25        25        89         4         1
  9P LOSS WILD-TYPE      16       50        49       146         8         0
D57V3, multiclass
           clus
vv          9P LOSS MUTATED 9P LOSS WILD-TYPE
  STAGE I                10                16
  STAGE II               25                50
  STAGE III              25                49
  STAGE IVA              89               146
  STAGE IVB               4                 8
  STAGE IVC               1                 0
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  9P LOSS MUTATED      17  46  31  62
  9P LOSS WILD-TYPE    30  81  63 100
D57V4, multiclass
       clus
vv      9P LOSS MUTATED 9P LOSS WILD-TYPE
  T0+T1              17                30
  T2                 46                81
  T3                 31                63
  T4                 62               100
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  9P LOSS MUTATED    64  24  57   2
  9P LOSS WILD-TYPE 106  39  95   6
D57V5, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  N0              64               106
  N1              24                39
  N2              57                95
  N3               2                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1  MX
  9P LOSS MUTATED    59   1  17
  9P LOSS WILD-TYPE 108   0  41
D57V6, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  M0              59               108
  M1               1                 0
  MX              17                41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V7, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    41 134
  9P LOSS WILD-TYPE  91 222
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     41  134
  9P LOSS WILD-TYPE   91  222
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE              41                91
  MALE               134               222
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  9P LOSS MUTATED                                     172
  9P LOSS WILD-TYPE                                   305
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  9P LOSS MUTATED                                                             0
  9P LOSS WILD-TYPE                                                           1
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  9P LOSS MUTATED                                                     3
  9P LOSS WILD-TYPE                                                   7
D57V8, multiclass
                                                             clus
vv                                                            9P LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                   172
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       3
                                                             clus
vv                                                            9P LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     305
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                 1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V9, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    28 147
  9P LOSS WILD-TYPE  51 262
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     28  147
  9P LOSS WILD-TYPE   51  262
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  NO               28                51
  YES             147               262
[1] 2 2
[1] FALSE
D57V10, continuous
D57V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9P LOSS MUTATED                                  1     3
  9P LOSS WILD-TYPE                                1     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9P LOSS MUTATED                          22   144
  9P LOSS WILD-TYPE                        22   271
D57V12, multiclass
                                  clus
vv                                 9P LOSS MUTATED 9P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 1
  ASIAN                                          3                 8
  BLACK OR AFRICAN AMERICAN                     22                22
  WHITE                                        144               271
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V13, binary
                   cls
clus                  0   1
  9P LOSS MUTATED     8 148
  9P LOSS WILD-TYPE  16 283
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      8  148
  9P LOSS WILD-TYPE   16  283
                        clus
vv                       9P LOSS MUTATED 9P LOSS WILD-TYPE
  HISPANIC OR LATINO                   8                16
  NOT HISPANIC OR LATINO             148               283
[1] 2 2
[1] FALSE

Clustering(58) Variable = 9Q LOSS MUTATION ANALYSIS
D58V1, survival
                   sevent
clus2                 0   1
  9Q LOSS MUTATED    48  22
  9Q LOSS WILD-TYPE 253  91
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               70               344 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               22                91 
$`9Q LOSS MUTATED`
TCGA-BA-4074 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A6D8 
         462          451           63          236          895          850 
TCGA-BB-8601 TCGA-CN-4737 TCGA-CN-4740 TCGA-CN-6018 TCGA-CN-6020 TCGA-CN-6024 
         624          625          811           45           98          224 
TCGA-CN-A63W TCGA-CQ-6221 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-7067 TCGA-CQ-7069 
         348         1000         1959         1959          509         1274 
TCGA-CQ-7072 TCGA-CR-5247 TCGA-CR-6472 TCGA-CR-6474 TCGA-CR-7364 TCGA-CR-7365 
        1950          358         1050         1971         1435         1191 
TCGA-CR-7372 TCGA-CR-7374 TCGA-CR-7390 TCGA-CV-5430 TCGA-CV-5435 TCGA-CV-5436 
         759           30          907         1955         1438          584 
TCGA-CV-5441 TCGA-CV-5973 TCGA-CV-5979 TCGA-CV-6441 TCGA-CV-6945 TCGA-CV-7091 
        2886         2641         1315         1970         1969         1959 
TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7101 TCGA-CV-7180 TCGA-CV-7243 TCGA-CV-7430 
        1970         1970         1939         1987          954         1972 
TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A464 TCGA-CV-A6JU TCGA-CX-7082 TCGA-D6-6823 
        1959         1981         1722          110          317          701 
TCGA-D6-A6EP TCGA-DQ-5631 TCGA-F7-7848 TCGA-F7-A50I TCGA-F7-A623 TCGA-H7-A6C5 
         424          548         1131           92            6          403 
TCGA-HD-7753 TCGA-HD-8635 TCGA-HD-A6HZ TCGA-IQ-A61G TCGA-IQ-A61J TCGA-KU-A66T 
           5           25          111          360          440          552 
TCGA-MT-A67D TCGA-QK-A6IJ TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-UF-A719 TCGA-UF-A71B 
          56          387          135          135         1663         1319 
TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ 
         735         1497          665          214 

$`9Q LOSS WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
         102          283          415         1983          276          248 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 
         722         1288         1762          520          725          623 
TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6872 TCGA-BA-6873 
        1636         1747          190          644          384          113 
TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE 
         855          622          918          351          216          182 
TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 
        1976          314          623          142          187         2878 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 
         278          140          133          558          310          536 
TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 
         423          687          638         1153          428          436 
TCGA-BB-8596 TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 
        1955            5            4          799          721         1157 
TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 
         142         1230         1151          392          817          993 
TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4741 
         642         1250          395         1960         1330         1268 
TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 
        1988         1007         1045          173         1980         1081 
TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 
        1977         1980         1966         1966         1975          683 
TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 
         290          630          933          629          628          594 
TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6988 
         629          432         1970          202         1110          318 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 
         611          394          735          432          429           46 
TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T 
         443          535          391          904          645          225 
TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A6V1 TCGA-CN-A6V3 
         526          484          175          367          223          298 
TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 
        1466         1207          654         1660         1422         1393 
TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6223 
        1399          317          341          129         1253         1057 
TCGA-CQ-6224 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7068 
         985         1179         1750         1560         1007         1309 
TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB 
         877         1353         1960          707         1963          893 
TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 
         998          785          391          303          950         2562 
TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 
        1663         1152          799         1777         1521         1966 
TCGA-CR-6473 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 
        1125          514         1969          362          311          345 
TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 
         354          234          379          350          479         1956 
TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7373 
        1440         1245         1960          105         1979          889 
TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 
         972         1968         1036          796         1954          997 
TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
        1430         1951          392          913          946          908 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 
         898          930          216          156          181         1077 
TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5439 
         911         1472          522         1950         3295          546 
TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 
        1978         2327         1958         2437          519          406 
TCGA-CV-5971 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-6003 TCGA-CV-6433 
         701         1478         1840          215         1665          641 
TCGA-CV-6436 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6942 
        1899         1948         1969         1952         1959         3835 
TCGA-CV-6943 TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 
        1948         1966         1957         1969         1959         3837 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 
        1936         1959         1945         1979         1952         1444 
TCGA-CV-7242 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 
        1095          797         1967         1960         1976         1099 
TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7427 
        1974         1948         1955         1957         1947         1937 
TCGA-CV-7428 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-A45O TCGA-CV-A45Q 
        1973         1937         1984         1958          851         1945 
TCGA-CV-A45R TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A468 
        5480         1960         1940         1946         1954         1977 
TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JY 
        1970         1075          906         1959          670          646 
TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 
         714          606          685         1950          321          237 
TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 
         828          773          292           77          491          154 
TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK 
         568          106          128          539          376          483 
TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 
         232          435          368          389          338         1778 
TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 
        1081          516         1030         1965          575          775 
TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
         622          299          369          368          324          340 
TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V 
         490          658           15          585            3          384 
TCGA-F7-A61W TCGA-F7-A620 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 
          14           13          407           58          133          414 
TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 
         206            2           25           37           55           44 
TCGA-HD-8634 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 
          24           11           49           10           33         1057 
TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61H TCGA-IQ-A61L 
         485          122          441          588          412          351 
TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X 
         360          224          378          168           14           34 
TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 
         392          111          112          254          240          910 
TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 
        1726         1559         1120         1954          578         1917 
TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG 
        1968          400          553          357          245          218 
TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6V9 TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-QK-AA3J 
         228          225          567          198          149          157 
TCGA-QK-AA3K TCGA-UF-A718 TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA 
         168         1326         1252         1278         1043         1894 
TCGA-UF-A7JC TCGA-UF-A7JS 
         484          413 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                5                 2 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             2886              5480 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              747               686 
[1] "5.0 - 2886.0 (747.0)" "2.0 - 5480.0 (686.0)"
[1] "hr=" "1"  
D58V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  9Q LOSS MUTATED         4       14        14        38         1         1
  9Q LOSS WILD-TYPE      22       61        60       197        11         0
D58V3, multiclass
           clus
vv          9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  STAGE I                 4                22
  STAGE II               14                61
  STAGE III              14                60
  STAGE IVA              38               197
  STAGE IVB               1                11
  STAGE IVC               1                 0
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  9Q LOSS MUTATED       7  28  12  26
  9Q LOSS WILD-TYPE    40  99  82 136
D58V4, multiclass
       clus
vv      9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T0+T1               7                40
  T2                 28                99
  T3                 12                82
  T4                 26               136
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  9Q LOSS MUTATED    29  12  25   0
  9Q LOSS WILD-TYPE 141  51 127   8
D58V5, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  N0              29               141
  N1              12                51
  N2              25               127
  N3               0                 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"
                   vv
clus                 M0  M1  MX
  9Q LOSS MUTATED    28   1  10
  9Q LOSS WILD-TYPE 139   0  48
D58V6, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  M0              28               139
  M1               1                 0
  MX              10                48
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V7, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    20  61
  9Q LOSS WILD-TYPE 112 295
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     20   61
  9Q LOSS WILD-TYPE  112  295
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE              20               112
  MALE                61               295
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  9Q LOSS MUTATED                                      81
  9Q LOSS WILD-TYPE                                   396
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  9Q LOSS MUTATED                                                             0
  9Q LOSS WILD-TYPE                                                           1
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  9Q LOSS MUTATED                                                     0
  9Q LOSS WILD-TYPE                                                  10
D58V8, multiclass
                                                             clus
vv                                                            9Q LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    81
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       0
                                                             clus
vv                                                            9Q LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     396
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                 1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V9, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    15  66
  9Q LOSS WILD-TYPE  64 343
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     15   66
  9Q LOSS WILD-TYPE   64  343
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  NO               15                64
  YES              66               343
[1] 2 2
[1] FALSE
D58V10, continuous
D58V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9Q LOSS MUTATED                                  0     0
  9Q LOSS WILD-TYPE                                2    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9Q LOSS MUTATED                          11    65
  9Q LOSS WILD-TYPE                        33   350
D58V12, multiclass
                                  clus
vv                                 9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                     11                33
  WHITE                                         65               350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V13, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED     6  65
  9Q LOSS WILD-TYPE  18 366
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      6   65
  9Q LOSS WILD-TYPE   18  366
                        clus
vv                       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   6                18
  NOT HISPANIC OR LATINO              65               366
[1] 2 2
[1] FALSE

Clustering(59) Variable = 10P LOSS MUTATION ANALYSIS
D59V1, survival
                    sevent
clus2                  0   1
  10P LOSS MUTATED    82  45
  10P LOSS WILD-TYPE 219  68
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               127                287 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                45                 68 
$`10P LOSS MUTATED`
TCGA-BA-4075 TCGA-BA-4078 TCGA-BA-5152 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6870 
         283          276         1288         1747          190          451 
TCGA-BA-6873 TCGA-BA-A4IF TCGA-BA-A6D8 TCGA-BA-A8YP TCGA-BB-7870 TCGA-BB-7872 
         113          895          850          142         1153          436 
TCGA-BB-8601 TCGA-C9-A47Z TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4737 TCGA-CN-5355 
         624            5          721         1157          625         1007 
TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6012 
        1980         1081         1977          290          933          629 
TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6996 
          45          432           98          224          318          432 
TCGA-CN-6998 TCGA-CN-A49A TCGA-CN-A63U TCGA-CN-A63W TCGA-CQ-5323 TCGA-CQ-6223 
          46          391          526          348         1466         1057 
TCGA-CQ-6224 TCGA-CQ-6228 TCGA-CQ-7064 TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4C7 
         985         1959         1560         1274         1950         1960 
TCGA-CR-6474 TCGA-CR-6484 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 
        1971          354         1191         1440         1245         1960 
TCGA-CR-7370 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7386 
         105          759          889          796         1954         1430 
TCGA-CR-7389 TCGA-CR-7398 TCGA-CV-5435 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5977 
         392          156         1438         2437          519         1840 
TCGA-CV-5979 TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6952 TCGA-CV-6954 
        1315         1952         1959         3835         1966         1957 
TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7097 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 
        1959         3837         1970         1959         1939         1945 
TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7406 TCGA-CV-7418 
        1095          954          797         1967         1974         1955 
TCGA-CV-7424 TCGA-CV-7428 TCGA-CV-7432 TCGA-CV-7434 TCGA-CV-A6JD TCGA-CV-A6JT 
        1947         1973         1937         1958         1970          670 
TCGA-CV-A6K1 TCGA-CX-7219 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6826 TCGA-D6-A4ZB 
         685          828          292          701          154          376 
TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-DQ-5629 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7590 
         424          368          516          548         1965          775 
TCGA-DQ-7593 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A61V TCGA-F7-A620 
         369          658           15           92          384           13 
TCGA-HD-8635 TCGA-HD-A633 TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J TCGA-KU-A66T 
          25           49          360          412          440          552 
TCGA-KU-A6H7 TCGA-MT-A51X TCGA-MZ-A6I9 TCGA-P3-A6SX TCGA-P3-A6T2 TCGA-P3-A6T4 
         378           34          254         1954         1917         1968 
TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A6IF TCGA-QK-A6IH TCGA-QK-A6V9 TCGA-QK-A8Z9 
         400          553          245          228          567          149 
TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3K TCGA-UF-A718 TCGA-UF-A71B TCGA-UF-A7JC 
         135          135          168         1326         1319          484 
TCGA-UF-A7JD 
         735 

$`10P LOSS WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-5151 
         102          462          415         1983          248          722 
TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6869 
        1762          520          725          623         1636          644 
TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II 
          63          384          236          855          622          918 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A6DL 
         351          216          182         1976          314          623 
TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 
         187         2878          278          140          133          558 
TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7871 
         310          536          423          687          638          428 
TCGA-BB-8596 TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 
        1955            4          799          142         1230         1151 
TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 
         392          817          993          642         1250          395 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5356 
        1960         1330          811         1268         1988         1045 
TCGA-CN-5358 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 
         173         1980         1966         1966         1975          683 
TCGA-CN-6010 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6021 TCGA-CN-6022 
         630          628          594          629         1970          202 
TCGA-CN-6023 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6997 TCGA-CN-A498 
        1110          611          394          735          429          443 
TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63Y 
         535          904          645          225          484          175 
TCGA-CN-A641 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 
         367          223          298         1207          654         1660 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 
        1422         1393         1399          317          341          129 
TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7065 
        1253         1000         1959         1179         1750         1007 
TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CA 
         509         1309          877         1353          707         1963 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI 
         893          998          785          391          303          950 
TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 
        2562          358         1663         1152          799         1777 
TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6477 TCGA-CR-6478 
        1521         1966         1050         1125          514         1969 
TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 
         362          311          345          234          379          350 
TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7371 TCGA-CR-7374 TCGA-CR-7376 
         479         1956         1435         1979           30          972 
TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7385 TCGA-CR-7388 TCGA-CR-7390 TCGA-CR-7391 
        1968         1036          997         1951          907          913 
TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7399 
         946          908          898          930          216          181 
TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 
        1077          911         1472         1955          522         1950 
TCGA-CV-5434 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 
        3295          584          546         1978         2886         2327 
TCGA-CV-5443 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5978 
        1958          406          701         2641         1478          215 
TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 
        1665          641         1899         1970         1948         1969 
TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6960 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7099 
        1948         1969         1969         1959         1970         1936 
TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7250 TCGA-CV-7254 
        1987         1979         1952         1444         1960         1976 
TCGA-CV-7261 TCGA-CV-7410 TCGA-CV-7422 TCGA-CV-7427 TCGA-CV-7430 TCGA-CV-7433 
        1099         1948         1957         1937         1972         1984 
TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45Y 
        1959         1981          851         1945         5480         1960 
TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JE 
        1940         1946         1954         1722         1977         1075 
TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 
         906         1959          110          646          714          606 
TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-D6-6516 TCGA-D6-6824 
        1950          317          321          237          773           77 
TCGA-D6-6825 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A6EK 
         491          568          106          128          539          483 
TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 
         232          435          389          338         1778         1081 
TCGA-DQ-5630 TCGA-DQ-7589 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7595 
        1030          575          622          299          368          324 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61W 
         340         1131          490          585            3           14 
TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 
           6          407           58          133          414          403 
TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 
         206            2            5           25           37           55 
TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-A4C1 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 
          44           24           11           10          111           33 
TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61L 
        1057          485          122          441          588          351 
TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A67A TCGA-MT-A67D 
         360          224          168           14          392           56 
TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE 
         111          112          240          910         1726         1559 
TCGA-P3-A6SW TCGA-P3-A6T0 TCGA-QK-A652 TCGA-QK-A6IG TCGA-QK-A6II TCGA-QK-A6IJ 
        1120          578          357          218          225          387 
TCGA-QK-A8Z7 TCGA-QK-AA3J TCGA-UF-A719 TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 
         198          157         1663         1252         1278         1043 
TCGA-UF-A7JA TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JS 
        1894         1497          665          214          413 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 5                  2 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              3837               5480 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               735                683 
[1] "5.0 - 3837.0 (735.0)" "2.0 - 5480.0 (683.0)"
[1] "hr=" "1.5"
D59V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  10P LOSS MUTATED         5       22        20        81         5         0
  10P LOSS WILD-TYPE      21       53        54       154         7         1
D59V3, multiclass
           clus
vv          10P LOSS MUTATED 10P LOSS WILD-TYPE
  STAGE I                  5                 21
  STAGE II                22                 53
  STAGE III               20                 54
  STAGE IVA               81                154
  STAGE IVB                5                  7
  STAGE IVC                0                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  10P LOSS MUTATED       8  39  27  59
  10P LOSS WILD-TYPE    39  88  67 103
D59V4, multiclass
       clus
vv      10P LOSS MUTATED 10P LOSS WILD-TYPE
  T0+T1                8                 39
  T2                  39                 88
  T3                  27                 67
  T4                  59                103
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  10P LOSS MUTATED    47  20  53   2
  10P LOSS WILD-TYPE 123  43  99   6
D59V5, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  N0               47                123
  N1               20                 43
  N2               53                 99
  N3                2                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  10P LOSS MUTATED    52   0  19
  10P LOSS WILD-TYPE 115   1  39
D59V6, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  M0               52                115
  M1                0                  1
  MX               19                 39
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V7, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    32 117
  10P LOSS WILD-TYPE 100 239
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     32  117
  10P LOSS WILD-TYPE  100  239
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE               32                100
  MALE                117                239
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  10P LOSS MUTATED                                     149
  10P LOSS WILD-TYPE                                   328
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  10P LOSS MUTATED                                                             0
  10P LOSS WILD-TYPE                                                           1
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  10P LOSS MUTATED                                                     0
  10P LOSS WILD-TYPE                                                  10
D59V8, multiclass
                                                             clus
vv                                                            10P LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    149
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        0
                                                             clus
vv                                                            10P LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      328
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                  1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V9, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    28 121
  10P LOSS WILD-TYPE  51 288
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     28  121
  10P LOSS WILD-TYPE   51  288
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  NO                28                 51
  YES              121                288
[1] 2 2
[1] FALSE
D59V10, continuous
D59V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10P LOSS MUTATED                                  0     4
  10P LOSS WILD-TYPE                                2     7
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10P LOSS MUTATED                          22   120
  10P LOSS WILD-TYPE                        22   295
D59V12, multiclass
                                  clus
vv                                 10P LOSS MUTATED 10P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           4                  7
  BLACK OR AFRICAN AMERICAN                      22                 22
  WHITE                                         120                295
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V13, binary
                    cls
clus                   0   1
  10P LOSS MUTATED     7 131
  10P LOSS WILD-TYPE  17 300
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      7  131
  10P LOSS WILD-TYPE   17  300
                        clus
vv                       10P LOSS MUTATED 10P LOSS WILD-TYPE
  HISPANIC OR LATINO                    7                 17
  NOT HISPANIC OR LATINO              131                300
[1] 2 2
[1] FALSE

Clustering(60) Variable = 10Q LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                  0   1
  10Q LOSS MUTATED    60  31
  10Q LOSS WILD-TYPE 241  82
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                91                323 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                31                 82 
$`10Q LOSS MUTATED`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4078 TCGA-BA-5152 TCGA-BA-5555 TCGA-BA-5559 
         462          283          276         1288          520         1747 
TCGA-BA-A6D8 TCGA-BA-A8YP TCGA-BB-7870 TCGA-BB-8601 TCGA-C9-A47Z TCGA-CN-4725 
         850          142         1153          624            5         1157 
TCGA-CN-5355 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5374 TCGA-CN-6012 TCGA-CN-6018 
        1007         1980         1081          290          629           45 
TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6024 TCGA-CN-6998 TCGA-CN-A49A TCGA-CN-A63U 
         432           98          224           46          391          526 
TCGA-CQ-5332 TCGA-CQ-6224 TCGA-CQ-6228 TCGA-CQ-7064 TCGA-CQ-7072 TCGA-CR-6470 
         317          985         1959         1560         1950         1521 
TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6484 TCGA-CR-7365 TCGA-CR-7368 TCGA-CR-7369 
        1971          514          354         1191         1245         1960 
TCGA-CR-7370 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7383 TCGA-CR-7386 TCGA-CR-7389 
         105          759          889         1954         1430          392 
TCGA-CR-7398 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5977 
         156          522         1950         3295         1438         1840 
TCGA-CV-5979 TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7097 
        1315         1952         1959         1959         3837         1970 
TCGA-CV-7101 TCGA-CV-7242 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7406 TCGA-CV-7418 
        1939         1095          797         1967         1974         1955 
TCGA-CV-7424 TCGA-CV-7432 TCGA-D6-6823 TCGA-D6-A4ZB TCGA-D6-A6EP TCGA-D6-A6EQ 
        1947         1937          701          376          424          368 
TCGA-D6-A6ES TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7593 
         389          548         1965          575          775          369 
TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J TCGA-KU-A66T TCGA-KU-A6H7 TCGA-MT-A51X 
         360          412          440          552          378           34 
TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-QK-A6IH TCGA-QK-A6V9 
         254          240          578         1917          228          567 
TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-AA3K TCGA-UF-A718 TCGA-UF-A71B TCGA-UF-A7J9 
         149          135          168         1326         1319         1043 
TCGA-UF-A7JC 
         484 

$`10Q LOSS WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5153 
         102          415         1983          248          722         1762 
TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 
         725          623         1636          190          644          451 
TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG 
          63          384          113          236          895          855 
TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DG 
         622          918          351          216          182         1976 
TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 
         314          623          187         2878          278          140 
TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 
         133          558          310          536          423          687 
TCGA-BB-7866 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-C9-A480 TCGA-CN-4722 
         638          428          436         1955            4          799 
TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 
         721          142         1230         1151          392          817 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 
         993          642         1250          395          625         1960 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5358 
        1330          811         1268         1988         1045          173 
TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 
        1977         1980         1966         1966         1975          683 
TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6021 
         630          933          628          594          629         1970 
TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 
         202         1110          318          611          394          735 
TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A49C 
         432          429          443          535          904          645 
TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A6V1 
         225          484          348          175          367          223 
TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 
         298         1466         1207          654         1660         1422 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 
        1393         1399          341          129         1253         1000 
TCGA-CQ-6223 TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7065 TCGA-CQ-7067 
        1057         1959         1179         1750         1007          509 
TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
        1309         1274          877         1353         1960          707 
TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH 
        1963          893          998          785          391          303 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 
         950         2562          358         1663         1152          799 
TCGA-CR-6467 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6478 TCGA-CR-6480 
        1777         1966         1050         1125         1969          362 
TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 
         311          345          234          379          350          479 
TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7367 TCGA-CR-7371 TCGA-CR-7374 TCGA-CR-7376 
        1956         1435         1440         1979           30          972 
TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7388 TCGA-CR-7390 
        1968         1036          796          997         1951          907 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 
         913          946          908          898          930          216 
TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5436 
         181         1077          911         1472         1955          584 
TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 
         546         1978         2886         2327         1958         2437 
TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5978 
         519          406          701         2641         1478          215 
TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 
        1665          641         1899         1970         1948         1969 
TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6960 
        3835         1948         1969         1966         1957         1969 
TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7180 
        1959         1970         1936         1959         1945         1987 
TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7243 TCGA-CV-7250 TCGA-CV-7254 
        1979         1952         1444          954         1960         1976 
TCGA-CV-7261 TCGA-CV-7410 TCGA-CV-7422 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 
        1099         1948         1957         1937         1973         1972 
TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q 
        1984         1958         1959         1981          851         1945 
TCGA-CV-A45R TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A464 
        5480         1960         1940         1946         1954         1722 
TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT 
        1977         1970         1075          906         1959          670 
TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 
         110          646          714          606          685         1950 
TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6517 
         317          321          237          828          773          292 
TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 
          77          491          154          568          106          128 
TCGA-D6-A4Z9 TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A74Q TCGA-DQ-5624 
         539          483          232          435          338         1778 
TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7594 
        1081          516         1030          622          299          368 
TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G 
         324          340         1131          490          658           15 
TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 
          92          585            3          384           14           13 
TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 
           6          407           58          133          414          403 
TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 
         206            2            5           25           37           55 
TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 
          44           24           25           11           49           10 
TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 
         111           33         1057          485          122          441 
TCGA-IQ-A61E TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A6H8 TCGA-MT-A51W 
         588          351          360          224          168           14 
TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-P3-A5Q5 TCGA-P3-A5QA 
         392           56          111          112          910         1726 
TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A64Z 
        1559         1120         1954         1968          400          553 
TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A8Z7 
         357          245          218          225          387          198 
TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-UF-A719 TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7JA 
         135          157         1663         1252         1278         1894 
TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JS 
         735         1497          665          214          413 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 5                  2 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              3837               5480 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               701                701 
[1] "5.0 - 3837.0 (701.0)" "2.0 - 5480.0 (701.0)"
[1] "hr=" "1.5"
D60V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  10Q LOSS MUTATED         3       17        13        56         3         0
  10Q LOSS WILD-TYPE      23       58        61       179         9         1
D60V3, multiclass
           clus
vv          10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  STAGE I                  3                 23
  STAGE II                17                 58
  STAGE III               13                 61
  STAGE IVA               56                179
  STAGE IVB                3                  9
  STAGE IVC                0                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  10Q LOSS MUTATED       5  28  23  36
  10Q LOSS WILD-TYPE    42  99  71 126
D60V4, multiclass
       clus
vv      10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T0+T1                5                 42
  T2                  28                 99
  T3                  23                 71
  T4                  36                126
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  10Q LOSS MUTATED    36   8  39   1
  10Q LOSS WILD-TYPE 134  55 113   7
D60V5, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  N0               36                134
  N1                8                 55
  N2               39                113
  N3                1                  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"
                    vv
clus                  M0  M1  MX
  10Q LOSS MUTATED    40   0  12
  10Q LOSS WILD-TYPE 127   1  46
D60V6, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  M0               40                127
  M1                0                  1
  MX               12                 46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V7, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    20  84
  10Q LOSS WILD-TYPE 112 272
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     20   84
  10Q LOSS WILD-TYPE  112  272
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE               20                112
  MALE                 84                272
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  10Q LOSS MUTATED                                     104
  10Q LOSS WILD-TYPE                                   373
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  10Q LOSS MUTATED                                                             0
  10Q LOSS WILD-TYPE                                                           1
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  10Q LOSS MUTATED                                                     0
  10Q LOSS WILD-TYPE                                                  10
D60V8, multiclass
                                                             clus
vv                                                            10Q LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    104
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        0
                                                             clus
vv                                                            10Q LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      373
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                  1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V9, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    21  83
  10Q LOSS WILD-TYPE  58 326
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     21   83
  10Q LOSS WILD-TYPE   58  326
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  NO                21                 58
  YES               83                326
[1] 2 2
[1] FALSE
D60V10, continuous
D60V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10Q LOSS MUTATED                                  0     3
  10Q LOSS WILD-TYPE                                2     8
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10Q LOSS MUTATED                          16    85
  10Q LOSS WILD-TYPE                        28   330
D60V12, multiclass
                                  clus
vv                                 10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           3                  8
  BLACK OR AFRICAN AMERICAN                      16                 28
  WHITE                                          85                330
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V13, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     6  91
  10Q LOSS WILD-TYPE  18 340
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      6   91
  10Q LOSS WILD-TYPE   18  340
                        clus
vv                       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    6                 18
  NOT HISPANIC OR LATINO               91                340
[1] 2 2
[1] FALSE

Clustering(61) Variable = 11P LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                  0   1
  11P LOSS MUTATED    85  36
  11P LOSS WILD-TYPE 216  77
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               121                293 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                36                 77 
$`11P LOSS MUTATED`
TCGA-BA-4074 TCGA-BA-4078 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 
         462          276           63          384          113          236 
TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6DE TCGA-BB-4227 TCGA-BB-7870 
         855          622          918          182          133         1153 
TCGA-BB-8596 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4735 TCGA-CN-4739 TCGA-CN-4740 
        1955         1151          392         1250         1330          811 
TCGA-CN-5356 TCGA-CN-5359 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5374 
        1045         1980         1977         1980         1966          290 
TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6988 TCGA-CN-6989 
         933          629           98         1970          318          611 
TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49A TCGA-CN-A49C 
         394          735           46          443          391          645 
TCGA-CN-A63U TCGA-CN-A63Y TCGA-CQ-5332 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-A4CB 
         526          175          317         1959         1959          893 
TCGA-CQ-A4CI TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6481 
         950          358         1663          514         1969          311 
TCGA-CR-7370 TCGA-CR-7374 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7388 TCGA-CR-7399 
         105           30         1954          997         1951          181 
TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5977 
        1472          522         1950          546         1978         1840 
TCGA-CV-5978 TCGA-CV-6441 TCGA-CV-6936 TCGA-CV-6942 TCGA-CV-6945 TCGA-CV-7091 
         215         1970         1952         3835         1969         1959 
TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7235 TCGA-CV-7245 
        1970         1970         1939         1945         1952          797 
TCGA-CV-7430 TCGA-CV-7433 TCGA-CV-7435 TCGA-CV-A45R TCGA-CV-A45Y TCGA-CV-A6JU 
        1972         1984         1959         5480         1960          110 
TCGA-CX-7082 TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6ES TCGA-DQ-5624 
         317          106          539          376          389         1778 
TCGA-DQ-5629 TCGA-DQ-7589 TCGA-DQ-7594 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 
         516          575          368          340         1131          490 
TCGA-F7-A50I TCGA-F7-A623 TCGA-H7-A6C4 TCGA-HD-7753 TCGA-HD-7917 TCGA-HD-8635 
          92            6          414            5           37           25 
TCGA-HD-A6HZ TCGA-IQ-A61G TCGA-IQ-A61J TCGA-KU-A66T TCGA-MT-A51W TCGA-MT-A67D 
         111          360          440          552           14           56 
TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A6SW TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A6IH 
         112          254         1120         1968          400          228 
TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-AA3J TCGA-QK-AA3K TCGA-UF-A718 
         198          149          135          157          168         1326 
TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7JA TCGA-UF-A7JH 
        1663         1319         1252         1278         1894          665 
TCGA-UF-A7JS 
         413 

$`11P LOSS WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-5151 
         102          283          415         1983          248          722 
TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 
        1288         1762          520          725          623         1636 
TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-A4IF TCGA-BA-A6D8 
        1747          190          644          451          895          850 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP 
         351          216         1976          314          623          142 
TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4228 TCGA-BB-7861 
         187         2878          278          140          558          310 
TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7871 TCGA-BB-7872 
         536          423          687          638          428          436 
TCGA-BB-8601 TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 
         624            5            4          799          721         1157 
TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4736 
         142         1230          817          993          642          395 
TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 
         625         1960         1268         1988         1007          173 
TCGA-CN-5360 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6010 TCGA-CN-6013 
        1081         1966         1975          683          630          628 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6022 TCGA-CN-6023 
         594          629           45          432          202         1110 
TCGA-CN-6024 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A63T 
         224          432          429          535          904          225 
TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A641 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 
         484          348          367          223          298         1466 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 
        1207          654         1660         1422         1393         1399 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 
         341          129         1253         1000         1057          985 
TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 
        1179         1750         1560         1007          509         1309 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
        1274          877         1950         1353         1960          707 
TCGA-CQ-A4CA TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5243 
        1963          998          785          391          303         2562 
TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 
        1152          799         1777         1521         1966         1050 
TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6480 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 
        1125         1971          362          345          354          234 
TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 
         379          350          479         1956         1435         1191 
TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 
        1440         1245         1960         1979          759          889 
TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7386 TCGA-CR-7389 
         972         1968         1036          796         1430          392 
TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 
         907          913          946          908          898          930 
TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7401 TCGA-CR-7402 TCGA-CV-5430 TCGA-CV-5434 
         216          156         1077          911         1955         3295 
TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 
        1438          584         2886         2327         1958         2437 
TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5979 
         519          406          701         2641         1478         1315 
TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6941 
        1665          641         1899         1948         1969         1959 
TCGA-CV-6943 TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 
        1948         1966         1957         1969         1959         3837 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7238 TCGA-CV-7242 
        1936         1959         1987         1979         1444         1095 
TCGA-CV-7243 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7406 
         954         1967         1960         1976         1099         1974 
TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7428 
        1948         1955         1957         1947         1937         1973 
TCGA-CV-7432 TCGA-CV-7434 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A45Z 
        1937         1958         1981          851         1945         1940 
TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE 
        1946         1954         1722         1977         1970         1075 
TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 
         906         1959          670          646          714          606 
TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 
         685         1950          321          237          828          773 
TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 
         292          701           77          491          154          568 
TCGA-D6-8569 TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ 
         128          483          232          435          424          368 
TCGA-D6-A74Q TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7590 
         338         1081         1030          548         1965          775 
TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7595 TCGA-F7-8489 TCGA-F7-A50G 
         622          299          369          324          658           15 
TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-H7-7774 
         585            3          384           14           13          407 
TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7754 
          58          133          403          206            2           25 
TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 
          55           44           24           11           49           10 
TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E 
          33         1057          485          122          441          588 
TCGA-IQ-A61H TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A6H7 TCGA-KU-A6H8 
         412          351          360          224          378          168 
TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67F TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QA 
          34          392          111          240          910         1726 
TCGA-P3-A5QE TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-QK-A64Z TCGA-QK-A652 
        1559         1954          578         1917          553          357 
TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A8ZB 
         245          218          225          387          567          135 
TCGA-UF-A7J9 TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JJ 
        1043          484          735         1497          214 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 5                  2 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              5480               3837 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               575                725 
[1] "5.0 - 5480.0 (575.0)" "2.0 - 3837.0 (725.0)"
[1] "hr=" "1.1"
D61V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  11P LOSS MUTATED         6       14        16        68         8         0
  11P LOSS WILD-TYPE      20       61        58       167         4         1
D61V3, multiclass
           clus
vv          11P LOSS MUTATED 11P LOSS WILD-TYPE
  STAGE I                  6                 20
  STAGE II                14                 61
  STAGE III               16                 58
  STAGE IVA               68                167
  STAGE IVB                8                  4
  STAGE IVC                0                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  11P LOSS MUTATED      13  31  23  47
  11P LOSS WILD-TYPE    34  96  71 115
D61V4, multiclass
       clus
vv      11P LOSS MUTATED 11P LOSS WILD-TYPE
  T0+T1               13                 34
  T2                  31                 96
  T3                  23                 71
  T4                  47                115
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  11P LOSS MUTATED    41  14  45   5
  11P LOSS WILD-TYPE 129  49 107   3
D61V5, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  N0               41                129
  N1               14                 49
  N2               45                107
  N3                5                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  11P LOSS MUTATED    44   0  18
  11P LOSS WILD-TYPE 123   1  40
D61V6, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  M0               44                123
  M1                0                  1
  MX               18                 40
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V7, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    32 103
  11P LOSS WILD-TYPE 100 253
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     32  103
  11P LOSS WILD-TYPE  100  253
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE               32                100
  MALE                103                253
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  11P LOSS MUTATED                                     129
  11P LOSS WILD-TYPE                                   348
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  11P LOSS MUTATED                                                             0
  11P LOSS WILD-TYPE                                                           1
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  11P LOSS MUTATED                                                     6
  11P LOSS WILD-TYPE                                                   4
D61V8, multiclass
                                                             clus
vv                                                            11P LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    129
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        6
                                                             clus
vv                                                            11P LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      348
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                  1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                          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"
D61V9, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    23 112
  11P LOSS WILD-TYPE  56 297
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     23  112
  11P LOSS WILD-TYPE   56  297
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  NO                23                 56
  YES              112                297
[1] 2 2
[1] FALSE
D61V10, continuous
D61V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11P LOSS MUTATED                                  1     0
  11P LOSS WILD-TYPE                                1    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11P LOSS MUTATED                          14   115
  11P LOSS WILD-TYPE                        30   300
D61V12, multiclass
                                  clus
vv                                 11P LOSS MUTATED 11P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  1
  ASIAN                                           0                 11
  BLACK OR AFRICAN AMERICAN                      14                 30
  WHITE                                         115                300
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V13, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    10 111
  11P LOSS WILD-TYPE  14 320
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     10  111
  11P LOSS WILD-TYPE   14  320
                        clus
vv                       11P LOSS MUTATED 11P LOSS WILD-TYPE
  HISPANIC OR LATINO                   10                 14
  NOT HISPANIC OR LATINO              111                320
[1] 2 2
[1] FALSE

Clustering(62) Variable = 11Q LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                  0   1
  11Q LOSS MUTATED   102  43
  11Q LOSS WILD-TYPE 199  70
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               145                269 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                43                 70 
$`11Q LOSS MUTATED`
TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-6868 
         462          415         1983          276          248          190 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II 
         384          113          236          855          622          918 
TCGA-BA-A6DA TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-8596 TCGA-CN-4727 TCGA-CN-4728 
         351          638         1153         1955         1230         1151 
TCGA-CN-4729 TCGA-CN-4735 TCGA-CN-4739 TCGA-CN-4741 TCGA-CN-5359 TCGA-CN-5360 
         392         1250         1330         1268         1980         1081 
TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6012 
        1977         1980         1966          290          933          629 
TCGA-CN-6013 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 
         628           98         1970          611          394          735 
TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T 
          46          443          391          904          645          225 
TCGA-CN-A63Y TCGA-CN-A641 TCGA-CQ-5323 TCGA-CQ-5332 TCGA-CQ-6221 TCGA-CQ-6224 
         175          367         1466          317         1000          985 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-A4CB TCGA-CR-5243 TCGA-CR-5248 
        1959         1959         1179          893         2562         1663 
TCGA-CR-5249 TCGA-CR-6470 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6481 TCGA-CR-6487 
        1152         1521          514         1969          311          234 
TCGA-CR-7370 TCGA-CR-7374 TCGA-CR-7377 TCGA-CR-7388 TCGA-CR-7399 TCGA-CR-7404 
         105           30         1968         1951          181         1472 
TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5970 
         522         1950          546         1978         2886          406 
TCGA-CV-5977 TCGA-CV-6433 TCGA-CV-6441 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6942 
        1840          641         1970         1969         1952         3835 
TCGA-CV-6945 TCGA-CV-6961 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7101 
        1969         1959         1959         1970         1970         1939 
TCGA-CV-7102 TCGA-CV-7406 TCGA-CV-7422 TCGA-CV-7433 TCGA-CV-7435 TCGA-CV-A45R 
        1945         1974         1957         1984         1959         5480 
TCGA-CV-A45Y TCGA-CV-A460 TCGA-CV-A6JE TCGA-CX-7082 TCGA-D6-6825 TCGA-D6-A4Z9 
        1960         1946         1075          317          491          539 
TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 
         389          338         1778         1965          575          775 
TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-A50G 
         369          368          340         1131          490           15 
TCGA-F7-A50I TCGA-F7-A623 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A 
          92            6          133          414          403          206 
TCGA-HD-7753 TCGA-HD-8314 TCGA-HD-A6HZ TCGA-HL-7533 TCGA-IQ-A61G TCGA-IQ-A61H 
           5           44          111         1057          360          412 
TCGA-IQ-A61J TCGA-KU-A66T TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67D TCGA-MT-A67G 
         440          552           14           34           56          112 
TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T4 TCGA-P3-A6T8 
         254          240         1120         1954         1968          400 
TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6V9 TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-QK-A8ZA 
         218          228          567          198          149          135 
TCGA-QK-AA3J TCGA-QK-AA3K TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7JA TCGA-UF-A7JH 
         157          168         1319         1278         1894          665 
TCGA-UF-A7JS 
         413 

$`11Q LOSS WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4075 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 
         102          283          722         1288         1762          520 
TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6869 TCGA-BA-6870 
         725          623         1636         1747          644          451 
TCGA-BA-6871 TCGA-BA-A4IF TCGA-BA-A6D8 TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DG 
          63          895          850          216          182         1976 
TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 
         314          623          142          187         2878          278 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 
         140          133          558          310          536          423 
TCGA-BB-7864 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8601 TCGA-C9-A47Z TCGA-C9-A480 
         687          428          436          624            5            4 
TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4730 TCGA-CN-4731 
         799          721         1157          142          817          993 
TCGA-CN-4733 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4740 TCGA-CN-4742 
         642          395          625         1960          811         1988 
TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 
        1007         1045          173         1966         1975          683 
TCGA-CN-6010 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6022 
         630          594          629           45          432          202 
TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-A499 
        1110          224          318          432          429          535 
TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5324 
         526          484          348          223          298         1207 
TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 
         654         1660         1422         1393         1399          341 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6223 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 
         129         1253         1057         1750         1560         1007 
TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 
         509         1309         1274          877         1950         1353 
TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG 
        1960          707         1963          998          785          391 
TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5247 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6471 
         303          950          358          799         1777         1966 
TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6480 TCGA-CR-6482 TCGA-CR-6484 
        1050         1125         1971          362          345          354 
TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 
         379          350          479         1956         1435         1191 
TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 
        1440         1245         1960         1979          759          889 
TCGA-CR-7376 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 
         972         1036          796         1954          997         1430 
TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 
         392          907          913          946          908          898 
TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7401 TCGA-CR-7402 TCGA-CV-5430 
         930          216          156         1077          911         1955 
TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 
        3295         1438          584         2327         1958         2437 
TCGA-CV-5966 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5978 TCGA-CV-5979 
         519          701         2641         1478          215         1315 
TCGA-CV-6003 TCGA-CV-6436 TCGA-CV-6934 TCGA-CV-6941 TCGA-CV-6943 TCGA-CV-6952 
        1665         1899         1948         1959         1948         1966 
TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-7090 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7180 
        1957         1969         3837         1936         1959         1987 
TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 
        1979         1952         1444         1095          954          797 
TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7410 TCGA-CV-7418 
        1967         1960         1976         1099         1948         1955 
TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7434 
        1947         1937         1973         1972         1937         1958 
TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A45Z TCGA-CV-A461 TCGA-CV-A464 
        1981          851         1945         1940         1954         1722 
TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU 
        1977         1970          906         1959          670          110 
TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 
         646          714          606          685         1950          321 
TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 
         237          828          773          292          701           77 
TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4ZB TCGA-D6-A6EK 
         154          568          106          128          376          483 
TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-DQ-5625 TCGA-DQ-5629 
         232          435          424          368         1081          516 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7595 TCGA-F7-8489 
        1030          548          622          299          324          658 
TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-H7-7774 
         585            3          384           14           13          407 
TCGA-H7-8501 TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8634 
          58            2           25           37           55           24 
TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-IQ-7630 
          25           11           49           10           33          485 
TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S 
         122          441          588          351          360          224 
TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A67A TCGA-MT-A67F TCGA-P3-A5Q5 TCGA-P3-A5QA 
         378          168          392          111          910         1726 
TCGA-P3-A5QE TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF 
        1559          578         1917          553          357          245 
TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A8ZB TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71D 
         225          387          135         1326         1663         1252 
TCGA-UF-A7J9 TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JJ 
        1043          484          735         1497          214 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 5                  2 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              5480               3837 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               629                722 
[1] "5.0 - 5480.0 (629.0)" "2.0 - 3837.0 (722.0)"
[1] "hr=" "1.1"
D62V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  11Q LOSS MUTATED         8       18        18        80         6         0
  11Q LOSS WILD-TYPE      18       57        56       155         6         1
D62V3, multiclass
           clus
vv          11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  STAGE I                  8                 18
  STAGE II                18                 57
  STAGE III               18                 56
  STAGE IVA               80                155
  STAGE IVB                6                  6
  STAGE IVC                0                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  11Q LOSS MUTATED      16  36  28  52
  11Q LOSS WILD-TYPE    31  91  66 110
D62V4, multiclass
       clus
vv      11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T0+T1               16                 31
  T2                  36                 91
  T3                  28                 66
  T4                  52                110
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  11Q LOSS MUTATED    44  18  59   3
  11Q LOSS WILD-TYPE 126  45  93   5
D62V5, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  N0               44                126
  N1               18                 45
  N2               59                 93
  N3                3                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  11Q LOSS MUTATED    48   0  25
  11Q LOSS WILD-TYPE 119   1  33
D62V6, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  M0               48                119
  M1                0                  1
  MX               25                 33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V7, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    28 132
  11Q LOSS WILD-TYPE 104 224
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     28  132
  11Q LOSS WILD-TYPE  104  224
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE               28                104
  MALE                132                224
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  11Q LOSS MUTATED                                     154
  11Q LOSS WILD-TYPE                                   323
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  11Q LOSS MUTATED                                                             0
  11Q LOSS WILD-TYPE                                                           1
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  11Q LOSS MUTATED                                                     6
  11Q LOSS WILD-TYPE                                                   4
D62V8, multiclass
                                                             clus
vv                                                            11Q LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    154
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        6
                                                             clus
vv                                                            11Q LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      323
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                  1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                          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"
D62V9, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    32 128
  11Q LOSS WILD-TYPE  47 281
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     32  128
  11Q LOSS WILD-TYPE   47  281
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  NO                32                 47
  YES              128                281
[1] 2 2
[1] FALSE
D62V10, continuous
D62V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11Q LOSS MUTATED                                  1     0
  11Q LOSS WILD-TYPE                                1    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11Q LOSS MUTATED                          12   143
  11Q LOSS WILD-TYPE                        32   272
D62V12, multiclass
                                  clus
vv                                 11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  1
  ASIAN                                           0                 11
  BLACK OR AFRICAN AMERICAN                      12                 32
  WHITE                                         143                272
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V13, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    11 138
  11Q LOSS WILD-TYPE  13 293
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     11  138
  11Q LOSS WILD-TYPE   13  293
                        clus
vv                       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   11                 13
  NOT HISPANIC OR LATINO              138                293
[1] 2 2
[1] FALSE

Clustering(63) Variable = 12P LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                  0   1
  12P LOSS MUTATED    13  16
  12P LOSS WILD-TYPE 288  97
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                29                385 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                16                 97 
$`12P LOSS MUTATED`
TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 
        1983          248          190          451          384          113 
TCGA-BA-7269 TCGA-BA-A6DA TCGA-BA-A6DE TCGA-BB-8596 TCGA-CN-5355 TCGA-CN-5365 
         236          351          182         1955         1007         1980 
TCGA-CN-5374 TCGA-CR-6484 TCGA-CR-7377 TCGA-CR-7389 TCGA-CV-6441 TCGA-CV-7090 
         290          354         1968          392         1970         3837 
TCGA-CV-7100 TCGA-CV-7432 TCGA-CV-A460 TCGA-CV-A6JY TCGA-D6-6826 TCGA-D6-A6EP 
        1959         1937         1946          646          154          424 
TCGA-DQ-5631 TCGA-HD-8224 TCGA-IQ-A61E TCGA-MZ-A6I9 TCGA-UF-A719 
         548           55          588          254         1663 

$`12P LOSS WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5151 
         102          462          283          415          276          722 
TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 
        1288         1762          520          725          623         1636 
TCGA-BA-5559 TCGA-BA-6869 TCGA-BA-6871 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH 
        1747          644           63          895          855          622 
TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DB TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A6DL 
         918          850          216         1976          314          623 
TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 
         142          187         2878          278          140          133 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 
         558          310          536          423          687          638 
TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8601 TCGA-C9-A47Z TCGA-C9-A480 
        1153          428          436          624            5            4 
TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 
         799          721         1157          142         1230         1151 
TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 
         392          817          993          642         1250          395 
TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 
         625         1960         1330          811         1268         1988 
TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5366 
        1045          173         1980         1081         1977         1966 
TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 
        1966         1975          683          630          933          629 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 
         628          594          629           45          432           98 
TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 
        1970          202         1110          224          318          611 
TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 
         394          735          432          429           46          443 
TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U 
         535          391          904          645          225          526 
TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A6V1 TCGA-CN-A6V3 
         484          348          175          367          223          298 
TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 
        1466         1207          654         1660         1422         1393 
TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 
        1399          317          341          129         1253         1000 
TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 
        1057          985         1959         1959         1179         1750 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 
        1560         1007          509         1309         1274          877 
TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB 
        1950         1353         1960          707         1963          893 
TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 
         998          785          391          303          950         2562 
TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 
         358         1663         1152          799         1777         1521 
TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 
        1966         1050         1125         1971          514         1969 
TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 
         362          311          345          234          379          350 
TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 
         479         1956         1435         1191         1440         1245 
TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 
        1960          105         1979          759          889           30 
TCGA-CR-7376 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 
         972         1036          796         1954          997         1430 
TCGA-CR-7388 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 
        1951          907          913          946          908          898 
TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 
         930          216          156          181         1077          911 
TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 
        1472         1955          522         1950         3295         1438 
TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 
         584          546         1978         2886         2327         1958 
TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 
        2437          519          406          701         2641         1478 
TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 
        1840          215         1315         1665          641         1899 
TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 
        1948         1969         1952         1959         3835         1948 
TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7091 
        1969         1966         1957         1969         1959         1959 
TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7180 
        1970         1970         1936         1939         1945         1987 
TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 
        1979         1952         1444         1095          954          797 
TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 
        1967         1960         1976         1099         1974         1948 
TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 
        1955         1957         1947         1937         1973         1972 
TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q 
        1984         1958         1959         1981          851         1945 
TCGA-CV-A45R TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A468 
        5480         1960         1940         1954         1722         1977 
TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU 
        1970         1075          906         1959          670          110 
TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 
         714          606          685         1950          317          321 
TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 
         237          828          773          292          701           77 
TCGA-D6-6825 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB 
         491          568          106          128          539          376 
TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q 
         483          232          435          368          389          338 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-7588 TCGA-DQ-7589 
        1778         1081          516         1030         1965          575 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 
         775          622          299          369          368          324 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I 
         340         1131          490          658           15           92 
TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 
         585            3          384           14           13            6 
TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A 
         407           58          133          414          403          206 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8314 TCGA-HD-8634 
           2            5           25           37           44           24 
TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 
          25           11           49           10          111           33 
TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61G TCGA-IQ-A61H 
        1057          485          122          441          360          412 
TCGA-IQ-A61J TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 
         440          351          360          224          552          378 
TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F 
         168           14           34          392           56          111 
TCGA-MT-A67G TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW 
         112          240          910         1726         1559         1120 
TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A64Z 
        1954          578         1917         1968          400          553 
TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ 
         357          245          218          228          225          387 
TCGA-QK-A6V9 TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J 
         567          198          149          135          135          157 
TCGA-QK-AA3K TCGA-UF-A718 TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 
         168         1326         1319         1252         1278         1043 
TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ 
        1894          484          735         1497          665          214 
TCGA-UF-A7JS 
         413 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                55                  2 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              3837               5480 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
               451                721 
[1] "55.0 - 3837.0 (451.0)" "2.0 - 5480.0 (721.0)" 
[1] "hr=" "1.6"
D63V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  12P LOSS MUTATED         0        6         5        14         1         0
  12P LOSS WILD-TYPE      26       69        69       221        11         1
D63V3, multiclass
           clus
vv          12P LOSS MUTATED 12P LOSS WILD-TYPE
  STAGE I                  0                 26
  STAGE II                 6                 69
  STAGE III                5                 69
  STAGE IVA               14                221
  STAGE IVB                1                 11
  STAGE IVC                0                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  12P LOSS MUTATED       1   9   5  11
  12P LOSS WILD-TYPE    46 118  89 151
D63V4, multiclass
       clus
vv      12P LOSS MUTATED 12P LOSS WILD-TYPE
  T0+T1                1                 46
  T2                   9                118
  T3                   5                 89
  T4                  11                151
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  12P LOSS MUTATED    11   2   9   1
  12P LOSS WILD-TYPE 159  61 143   7
D63V5, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  N0               11                159
  N1                2                 61
  N2                9                143
  N3                1                  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"
                    vv
clus                  M0  M1  MX
  12P LOSS MUTATED    11   0   3
  12P LOSS WILD-TYPE 156   1  55
D63V6, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  M0               11                156
  M1                0                  1
  MX                3                 55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V7, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    11  22
  12P LOSS WILD-TYPE 121 334
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     11   22
  12P LOSS WILD-TYPE  121  334
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE               11                121
  MALE                 22                334
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  12P LOSS MUTATED                                      33
  12P LOSS WILD-TYPE                                   444
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  12P LOSS MUTATED                                                             0
  12P LOSS WILD-TYPE                                                           1
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  12P LOSS MUTATED                                                     0
  12P LOSS WILD-TYPE                                                  10
D63V8, multiclass
                                                             clus
vv                                                            12P LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     33
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        0
                                                             clus
vv                                                            12P LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      444
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                  1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V9, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     7  26
  12P LOSS WILD-TYPE  72 383
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      7   26
  12P LOSS WILD-TYPE   72  383
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  NO                 7                 72
  YES               26                383
[1] 2 2
[1] FALSE
D63V10, continuous
D63V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12P LOSS MUTATED                                  0     1
  12P LOSS WILD-TYPE                                2    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12P LOSS MUTATED                           5    25
  12P LOSS WILD-TYPE                        39   390
D63V12, multiclass
                                  clus
vv                                 12P LOSS MUTATED 12P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           1                 10
  BLACK OR AFRICAN AMERICAN                       5                 39
  WHITE                                          25                390
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V13, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     3  27
  12P LOSS WILD-TYPE  21 404
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      3   27
  12P LOSS WILD-TYPE   21  404
                        clus
vv                       12P LOSS MUTATED 12P LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                 21
  NOT HISPANIC OR LATINO               27                404
[1] 2 2
[1] FALSE

Clustering(64) Variable = 12Q LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                  0   1
  12Q LOSS MUTATED    17   8
  12Q LOSS WILD-TYPE 284 105
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                25                389 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 8                105 
$`12Q LOSS MUTATED`
TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IH TCGA-BA-A6DE 
         190          451          113          236          622          182 
TCGA-BB-8596 TCGA-CN-5355 TCGA-CN-5374 TCGA-CN-6024 TCGA-CN-6994 TCGA-CR-6493 
        1955         1007          290          224          735         1956 
TCGA-CR-7390 TCGA-CV-6003 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7254 TCGA-CV-7432 
         907         1665         3837         1959         1976         1937 
TCGA-CV-A6JY TCGA-CX-7219 TCGA-D6-A6EP TCGA-F7-7848 TCGA-IQ-A61G TCGA-MZ-A6I9 
         646          828          424         1131          360          254 
TCGA-UF-A719 
        1663 

$`12Q LOSS WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 
         102          462          283          415         1983          276 
TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 
         248          722         1288         1762          520          725 
TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6869 TCGA-BA-6871 TCGA-BA-6872 
         623         1636         1747          644           63          384 
TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB 
         895          855          918          850          351          216 
TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 
        1976          314          623          142          187         2878 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 
         278          140          133          558          310          536 
TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 
         423          687          638         1153          428          436 
TCGA-BB-8601 TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 
         624            5            4          799          721         1157 
TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 
         142         1230         1151          392          817          993 
TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 
         642         1250          395          625         1960         1330 
TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 
         811         1268         1988         1045          173         1980 
TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 
        1081         1977         1980         1966         1966         1975 
TCGA-CN-5373 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 
         683          630          933          629          628          594 
TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 
         629           45          432           98         1970          202 
TCGA-CN-6023 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6996 TCGA-CN-6997 
        1110          318          611          394          432          429 
TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C 
          46          443          535          391          904          645 
TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 
         225          526          484          348          175          367 
TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 
         223          298         1466         1207          654         1660 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 
        1422         1393         1399          317          341          129 
TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 
        1253         1000         1057          985         1959         1959 
TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 
        1179         1750         1560         1007          509         1309 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
        1274          877         1950         1353         1960          707 
TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH 
        1963          893          998          785          391          303 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 
         950         2562          358         1663         1152          799 
TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 
        1777         1521         1966         1050         1125         1971 
TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 
         514         1969          362          311          345          354 
TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-7364 TCGA-CR-7365 
         234          379          350          479         1435         1191 
TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 
        1440         1245         1960          105         1979          759 
TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 
         889           30          972         1968         1036          796 
TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7391 
        1954          997         1430         1951          392          913 
TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 
         946          908          898          930          216          156 
TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 
         181         1077          911         1472         1955          522 
TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 
        1950         3295         1438          584          546         1978 
TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 
        2886         2327         1958         2437          519          406 
TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 
         701         2641         1478         1840          215         1315 
TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 
         641         1899         1970         1948         1969         1952 
TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-6954 
        1959         3835         1948         1969         1966         1957 
TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 
        1969         1959         1970         1970         1936         1959 
TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 
        1939         1945         1987         1979         1952         1444 
TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7261 
        1095          954          797         1967         1960         1099 
TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7427 
        1974         1948         1955         1957         1947         1937 
TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7440 
        1973         1972         1984         1958         1959         1981 
TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 
         851         1945         5480         1960         1940         1946 
TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN 
        1954         1722         1977         1970         1075          906 
TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 
        1959          670          110          714          606          685 
TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-D6-6516 TCGA-D6-6517 
        1950          317          321          237          773          292 
TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 
         701           77          491          154          568          106 
TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO 
         128          539          376          483          232          435 
TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 
         368          389          338         1778         1081          516 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 
        1030          548         1965          575          775          622 
TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-8298 
         299          369          368          324          340          490 
TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V 
         658           15           92          585            3          384 
TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 
          14           13            6          407           58          133 
TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 
         414          403          206            2            5           25 
TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 
          37           55           44           24           25           11 
TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 
          49           10          111           33         1057          485 
TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61L 
         122          441          588          412          440          351 
TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W 
         360          224          552          378          168           14 
TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A7D7 
          34          392           56          111          112          240 
TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 
         910         1726         1559         1120         1954          578 
TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF 
        1917         1968          400          553          357          245 
TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A8Z7 
         218          228          225          387          567          198 
TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-UF-A718 
         149          135          135          157          168         1326 
TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC 
        1319         1252         1278         1043         1894          484 
TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JS 
         735         1497          665          214          413 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
               113                  2 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
              3837               5480 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
               735                701 
[1] "113.0 - 3837.0 (735.0)" "2.0 - 5480.0 (701.0)"  
[1] "hr=" "1.2"
D64V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  12Q LOSS MUTATED         1        6         3        15         0         0
  12Q LOSS WILD-TYPE      25       69        71       220        12         1
D64V3, multiclass
           clus
vv          12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  STAGE I                  1                 25
  STAGE II                 6                 69
  STAGE III                3                 71
  STAGE IVA               15                220
  STAGE IVB                0                 12
  STAGE IVC                0                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  12Q LOSS MUTATED       1  10   2  12
  12Q LOSS WILD-TYPE    46 117  92 150
D64V4, multiclass
       clus
vv      12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  T0+T1                1                 46
  T2                  10                117
  T3                   2                 92
  T4                  12                150
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  12Q LOSS MUTATED    11   4   6   0
  12Q LOSS WILD-TYPE 159  59 146   8
D64V5, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  N0               11                159
  N1                4                 59
  N2                6                146
  N3                0                  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"
                    vv
clus                  M0  M1  MX
  12Q LOSS MUTATED     9   0   3
  12Q LOSS WILD-TYPE 158   1  55
D64V6, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  M0                9                158
  M1                0                  1
  MX                3                 55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V7, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     7  22
  12Q LOSS WILD-TYPE 125 334
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      7   22
  12Q LOSS WILD-TYPE  125  334
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE                7                125
  MALE                 22                334
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  12Q LOSS MUTATED                                      28
  12Q LOSS WILD-TYPE                                   449
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  12Q LOSS MUTATED                                                             0
  12Q LOSS WILD-TYPE                                                           1
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  12Q LOSS MUTATED                                                     1
  12Q LOSS WILD-TYPE                                                   9
D64V8, multiclass
                                                             clus
vv                                                            12Q LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     28
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        1
                                                             clus
vv                                                            12Q LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      449
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                  1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                          9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V9, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     4  25
  12Q LOSS WILD-TYPE  75 384
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      4   25
  12Q LOSS WILD-TYPE   75  384
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  NO                 4                 75
  YES               25                384
[1] 2 2
[1] FALSE
D64V10, continuous
D64V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12Q LOSS MUTATED                                  0     0
  12Q LOSS WILD-TYPE                                2    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12Q LOSS MUTATED                           6    21
  12Q LOSS WILD-TYPE                        38   394
D64V12, multiclass
                                  clus
vv                                 12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                 11
  BLACK OR AFRICAN AMERICAN                       6                 38
  WHITE                                          21                394
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V13, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     3  24
  12Q LOSS WILD-TYPE  21 407
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      3   24
  12Q LOSS WILD-TYPE   21  407
                        clus
vv                       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                 21
  NOT HISPANIC OR LATINO               24                407
[1] 2 2
[1] FALSE

Clustering(65) Variable = 13Q LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                  0   1
  13Q LOSS MUTATED    98  33
  13Q LOSS WILD-TYPE 203  80
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               131                283 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                33                 80 
$`13Q LOSS MUTATED`
TCGA-BA-4074 TCGA-BA-4078 TCGA-BA-5152 TCGA-BA-5555 TCGA-BA-5559 TCGA-BA-6869 
         462          276         1288          520         1747          644 
TCGA-BA-6871 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 
          63          113          236          622          918          850 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DL TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-7862 
         351          216          623          278          133          536 
TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A47Z 
         687         1153          428         1955          624            5 
TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4730 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-5360 
         721         1157          817         1330          811         1081 
TCGA-CN-5363 TCGA-CN-5367 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 
        1977         1966          683          290          630          933 
TCGA-CN-6012 TCGA-CN-6018 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6024 TCGA-CN-6988 
         629           45           98         1970          224          318 
TCGA-CN-6994 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49C 
         735           46          443          535          391          645 
TCGA-CN-A63T TCGA-CQ-5323 TCGA-CQ-5330 TCGA-CQ-6224 TCGA-CQ-7064 TCGA-CQ-7067 
         225         1466         1393          985         1560          509 
TCGA-CQ-A4CA TCGA-CQ-A4CE TCGA-CR-5249 TCGA-CR-6472 TCGA-CR-6477 TCGA-CR-6478 
        1963          785         1152         1050          514         1969 
TCGA-CR-6481 TCGA-CR-6487 TCGA-CR-7364 TCGA-CR-7372 TCGA-CR-7374 TCGA-CR-7379 
         311          234         1435          759           30         1036 
TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7397 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5434 
        1954          997          216          911         1472         3295 
TCGA-CV-5441 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6954 
        2886         1840          215         1959         3835         1957 
TCGA-CV-7091 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7235 TCGA-CV-7242 TCGA-CV-7245 
        1959         1936         1959         1952         1095          797 
TCGA-CV-7248 TCGA-CV-7406 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7435 TCGA-CV-7440 
        1967         1974         1955         1957         1959         1981 
TCGA-CV-A45R TCGA-CV-A45Y TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A6JE TCGA-CX-7082 
        5480         1960         1954         1722         1075          317 
TCGA-CX-7219 TCGA-D6-6825 TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-D6-A6EP TCGA-DQ-5630 
         828          491          106          539          424         1030 
TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-A50G 
        1965          575          324          340         1131           15 
TCGA-F7-A50I TCGA-F7-A623 TCGA-HD-7753 TCGA-HD-7917 TCGA-HD-8635 TCGA-HD-A6HZ 
          92            6            5           37           25          111 
TCGA-IQ-A61O TCGA-KU-A66T TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A5QA TCGA-P3-A6SX 
         360          552          112          254         1726         1954 
TCGA-P3-A6T4 TCGA-QK-A6IG TCGA-QK-A6V9 TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-QK-AA3K 
        1968          218          567          198          149          168 
TCGA-UF-A718 TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JC 
        1326         1252         1278         1043          484 

$`13Q LOSS WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-5151 
         102          283          415         1983          248          722 
TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6870 
        1762          725          623         1636          190          451 
TCGA-BA-6872 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DJ 
         384          895          855          182         1976          314 
TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-4228 TCGA-BB-7861 
         142          187         2878          140          558          310 
TCGA-BB-7863 TCGA-BB-7866 TCGA-BB-7872 TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4726 
         423          638          436            4          799          142 
TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 
        1230         1151          392          993          642         1250 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 
         395          625         1960         1268         1988         1007 
TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5370 
        1045          173         1980         1980         1966         1975 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6022 TCGA-CN-6023 
         628          594          629          432          202         1110 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-A49B TCGA-CN-A63U 
         611          394          432          429          904          526 
TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A6V1 TCGA-CN-A6V3 
         484          348          175          367          223          298 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5331 TCGA-CQ-5332 
        1207          654         1660         1422         1399          317 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6227 
         341          129         1253         1000         1057         1959 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7069 
        1959         1179         1750         1007         1309         1274 
TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB 
         877         1950         1353         1960          707          893 
TCGA-CQ-A4CD TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 
         998          391          303          950         2562          358 
TCGA-CR-5248 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 
        1663          799         1777         1521         1966         1125 
TCGA-CR-6474 TCGA-CR-6480 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6488 TCGA-CR-6491 
        1971          362          345          354          379          350 
TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 
         479         1956         1191         1440         1245         1960 
TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7373 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7382 
         105         1979          889          972         1968          796 
TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 
        1430         1951          392          907          913          946 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 
         908          898          930          156          181         1077 
TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 
        1955          522         1950         1438          584          546 
TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 
        1978         2327         1958         2437          519          406 
TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 
         701         2641         1478         1315         1665          641 
TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6943 
        1899         1970         1948         1969         1952         1948 
TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7095 
        1969         1966         1969         1959         3837         1970 
TCGA-CV-7097 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7238 
        1970         1939         1945         1987         1979         1444 
TCGA-CV-7243 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7410 TCGA-CV-7424 
         954         1960         1976         1099         1948         1947 
TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 
        1937         1973         1972         1937         1984         1958 
TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A468 TCGA-CV-A6JD 
         851         1945         1940         1946         1977         1970 
TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ 
         906         1959          670          110          646          714 
TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-D6-6516 
         606          685         1950          321          237          773 
TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8569 
         292          701           77          154          568          128 
TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EQ TCGA-D6-A6ES 
         376          483          232          435          368          389 
TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5631 TCGA-DQ-7590 
         338         1778         1081          516          548          775 
TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-F7-8298 TCGA-F7-8489 
         622          299          369          368          490          658 
TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-H7-7774 
         585            3          384           14           13          407 
TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 
          58          133          414          403          206            2 
TCGA-HD-7754 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-A4C1 TCGA-HD-A633 
          25           55           44           24           11           49 
TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 
          10           33         1057          485          122          441 
TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61L TCGA-KU-A66S 
         588          360          412          440          351          224 
TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D 
         378          168           14           34          392           56 
TCGA-MT-A67F TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6T0 
         111          240          910         1559         1120          578 
TCGA-P3-A6T2 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IH 
        1917          400          553          357          245          228 
TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-UF-A719 
         225          387          135          135          157         1663 
TCGA-UF-A71B TCGA-UF-A7JA TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ 
        1319         1894          735         1497          665          214 
TCGA-UF-A7JS 
         413 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 5                  2 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              5480               3837 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               735                685 
[1] "5.0 - 5480.0 (735.0)" "2.0 - 3837.0 (685.0)"
[1] "hr=" "1.1"
D65V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  13Q LOSS MUTATED        11       18        22        75         3         1
  13Q LOSS WILD-TYPE      15       57        52       160         9         0
D65V3, multiclass
           clus
vv          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  STAGE I                 11                 15
  STAGE II                18                 57
  STAGE III               22                 52
  STAGE IVA               75                160
  STAGE IVB                3                  9
  STAGE IVC                1                  0
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  13Q LOSS MUTATED      16  39  26  51
  13Q LOSS WILD-TYPE    31  88  68 111
D65V4, multiclass
       clus
vv      13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T0+T1               16                 31
  T2                  39                 88
  T3                  26                 68
  T4                  51                111
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  13Q LOSS MUTATED    50  19  50   2
  13Q LOSS WILD-TYPE 120  44 102   6
D65V5, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  N0               50                120
  N1               19                 44
  N2               50                102
  N3                2                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  13Q LOSS MUTATED    51   1  18
  13Q LOSS WILD-TYPE 116   0  40
D65V6, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  M0               51                116
  M1                1                  0
  MX               18                 40
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V7, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    39 115
  13Q LOSS WILD-TYPE  93 241
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     39  115
  13Q LOSS WILD-TYPE   93  241
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE               39                 93
  MALE                115                241
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  13Q LOSS MUTATED                                     150
  13Q LOSS WILD-TYPE                                   327
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  13Q LOSS MUTATED                                                             1
  13Q LOSS WILD-TYPE                                                           0
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  13Q LOSS MUTATED                                                     3
  13Q LOSS WILD-TYPE                                                   7
D65V8, multiclass
                                                             clus
vv                                                            13Q LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    150
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        3
                                                             clus
vv                                                            13Q LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      327
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                  0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                          7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V9, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    24 130
  13Q LOSS WILD-TYPE  55 279
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     24  130
  13Q LOSS WILD-TYPE   55  279
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO                24                 55
  YES              130                279
[1] 2 2
[1] FALSE
D65V10, continuous
D65V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  13Q LOSS MUTATED                                  1     1
  13Q LOSS WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  13Q LOSS MUTATED                          19   128
  13Q LOSS WILD-TYPE                        25   287
D65V12, multiclass
                                  clus
vv                                 13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  1
  ASIAN                                           1                 10
  BLACK OR AFRICAN AMERICAN                      19                 25
  WHITE                                         128                287
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V13, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     9 128
  13Q LOSS WILD-TYPE  15 303
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      9  128
  13Q LOSS WILD-TYPE   15  303
                        clus
vv                       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    9                 15
  NOT HISPANIC OR LATINO              128                303
[1] 2 2
[1] FALSE

Clustering(66) Variable = 14Q LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                  0   1
  14Q LOSS MUTATED    30  16
  14Q LOSS WILD-TYPE 271  97
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                46                368 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                16                 97 
$`14Q LOSS MUTATED`
TCGA-4P-AA8J TCGA-BA-4078 TCGA-BA-5152 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 
         102          276         1288          644          451           63 
TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A8YP TCGA-BB-7862 TCGA-CN-6019 TCGA-CN-6020 
         622          850          142          536          432           98 
TCGA-CN-6992 TCGA-CN-A63U TCGA-CQ-5332 TCGA-CQ-6221 TCGA-CR-5247 TCGA-CR-6470 
         394          526          317         1000          358         1521 
TCGA-CR-6472 TCGA-CR-7365 TCGA-CR-7398 TCGA-CV-5966 TCGA-CV-6935 TCGA-CV-7406 
        1050         1191          156          519         1969         1974 
TCGA-CV-7422 TCGA-CV-7435 TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A6JY TCGA-CV-A6K1 
        1957         1959         1940         1946          646          685 
TCGA-D6-6826 TCGA-D6-8569 TCGA-D6-A6EM TCGA-DQ-5631 TCGA-DQ-7590 TCGA-F7-7848 
         154          128          232          548          775         1131 
TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-8224 TCGA-MZ-A6I9 TCGA-P3-A6T0 TCGA-QK-A8Z7 
         403          206           55          254          578          198 
TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA 
        1252         1278         1043         1894 

$`14Q LOSS WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-5151 
         462          283          415         1983          248          722 
TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 
        1762          520          725          623         1636         1747 
TCGA-BA-6868 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG 
         190          384          113          236          895          855 
TCGA-BA-A4II TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DJ 
         918          351          216          182         1976          314 
TCGA-BA-A6DL TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 
         623          187         2878          278          140          133 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 
         558          310          423          687          638         1153 
TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A47Z TCGA-C9-A480 
         428          436         1955          624            5            4 
TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 
         799          721         1157          142         1230         1151 
TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 
         392          817          993          642         1250          395 
TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 
         625         1960         1330          811         1268         1988 
TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 
        1007         1045          173         1980         1081         1977 
TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 
        1980         1966         1966         1975          683          290 
TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 
         630          933          629          628          594          629 
TCGA-CN-6018 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 
          45         1970          202         1110          224          318 
TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 
         611          735          432          429           46          443 
TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63V 
         535          391          904          645          225          484 
TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 
         348          175          367          223          298         1466 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 
        1207          654         1660         1422         1393         1399 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 
         341          129         1253         1057          985         1959 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 
        1959         1179         1750         1560         1007          509 
TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 
        1309         1274          877         1950         1353         1960 
TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG 
         707         1963          893          998          785          391 
TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 
         303          950         2562         1663         1152          799 
TCGA-CR-6467 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 
        1777         1966         1125         1971          514         1969 
TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 
         362          311          345          354          234          379 
TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7367 TCGA-CR-7368 
         350          479         1956         1435         1440         1245 
TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 
        1960          105         1979          759          889           30 
TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 
         972         1968         1036          796         1954          997 
TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 
        1430         1951          392          907          913          946 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7399 TCGA-CR-7401 
         908          898          930          216          181         1077 
TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 
         911         1472         1955          522         1950         3295 
TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 
        1438          584          546         1978         2886         2327 
TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 
        1958         2437          406          701         2641         1478 
TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 
        1840          215         1315         1665          641         1899 
TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 
        1970         1948         1952         1959         3835         1948 
TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 
        1969         1966         1957         1969         1959         3837 
TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 
        1959         1970         1970         1936         1959         1939 
TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7242 
        1945         1987         1979         1952         1444         1095 
TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 
         954          797         1967         1960         1976         1099 
TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 
        1948         1955         1947         1937         1973         1972 
TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q 
        1937         1984         1958         1981          851         1945 
TCGA-CV-A45R TCGA-CV-A45Y TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD 
        5480         1960         1954         1722         1977         1970 
TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JZ 
        1075          906         1959          670          110          714 
TCGA-CV-A6K0 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 
         606         1950          317          321          237          828 
TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6827 
         773          292          701           77          491          568 
TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EO TCGA-D6-A6EP 
         106          539          376          483          435          424 
TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 
         368          389          338         1778         1081          516 
TCGA-DQ-5630 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 
        1030         1965          575          622          299          369 
TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G 
         368          324          340          490          658           15 
TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 
          92          585            3          384           14           13 
TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-HD-7229 
           6          407           58          133          414            2 
TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 
           5           25           37           44           24           25 
TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 
          11           49           10          111           33         1057 
TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H 
         485          122          441          588          360          412 
TCGA-IQ-A61J TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 
         440          351          360          224          552          378 
TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F 
         168           14           34          392           56          111 
TCGA-MT-A67G TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW 
         112          240          910         1726         1559         1120 
TCGA-P3-A6SX TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 
        1954         1917         1968          400          553          357 
TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 
         245          218          228          225          387          567 
TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-UF-A718 
         149          135          135          157          168         1326 
TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH 
        1663         1319          484          735         1497          665 
TCGA-UF-A7JJ TCGA-UF-A7JS 
         214          413 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                55                  2 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              1974               5480 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             563.0              723.5 
[1] "55.0 - 1974.0 (563.0)" "2.0 - 5480.0 (723.5)" 
[1] "hr=" "2.5"
D66V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  14Q LOSS MUTATED         0       10         4        27         1         0
  14Q LOSS WILD-TYPE      26       65        70       208        11         1
D66V3, multiclass
           clus
vv          14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  STAGE I                  0                 26
  STAGE II                10                 65
  STAGE III                4                 70
  STAGE IVA               27                208
  STAGE IVB                1                 11
  STAGE IVC                0                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  14Q LOSS MUTATED       2  12   9  20
  14Q LOSS WILD-TYPE    45 115  85 142
D66V4, multiclass
       clus
vv      14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  T0+T1                2                 45
  T2                  12                115
  T3                   9                 85
  T4                  20                142
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  14Q LOSS MUTATED    18   8  13   1
  14Q LOSS WILD-TYPE 152  55 139   7
D66V5, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  N0               18                152
  N1                8                 55
  N2               13                139
  N3                1                  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"
                    vv
clus                  M0  M1  MX
  14Q LOSS MUTATED    20   0   4
  14Q LOSS WILD-TYPE 147   1  54
D66V6, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  M0               20                147
  M1                0                  1
  MX                4                 54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V7, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    10  43
  14Q LOSS WILD-TYPE 122 313
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     10   43
  14Q LOSS WILD-TYPE  122  313
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE               10                122
  MALE                 43                313
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  14Q LOSS MUTATED                                      50
  14Q LOSS WILD-TYPE                                   427
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  14Q LOSS MUTATED                                                             0
  14Q LOSS WILD-TYPE                                                           1
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  14Q LOSS MUTATED                                                     3
  14Q LOSS WILD-TYPE                                                   7
D66V8, multiclass
                                                             clus
vv                                                            14Q LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     50
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        3
                                                             clus
vv                                                            14Q LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      427
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                  1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                          7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V9, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    10  43
  14Q LOSS WILD-TYPE  69 366
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     10   43
  14Q LOSS WILD-TYPE   69  366
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  NO                10                 69
  YES               43                366
[1] 2 2
[1] FALSE
D66V10, continuous
D66V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  14Q LOSS MUTATED                                  0     0
  14Q LOSS WILD-TYPE                                2    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  14Q LOSS MUTATED                           8    45
  14Q LOSS WILD-TYPE                        36   370
D66V12, multiclass
                                  clus
vv                                 14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                 11
  BLACK OR AFRICAN AMERICAN                       8                 36
  WHITE                                          45                370
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V13, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED     2  43
  14Q LOSS WILD-TYPE  22 388
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      2   43
  14Q LOSS WILD-TYPE   22  388
                        clus
vv                       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                 22
  NOT HISPANIC OR LATINO               43                388
[1] 2 2
[1] FALSE

Clustering(67) Variable = 15Q LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                  0   1
  15Q LOSS MUTATED    53  26
  15Q LOSS WILD-TYPE 248  87
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                79                335 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                26                 87 
$`15Q LOSS MUTATED`
TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-7269 
        1288         1762          520         1747          190          236 
TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4II TCGA-BA-A6DE TCGA-BA-A8YP TCGA-BB-4225 
         895          855          918          182          142          140 
TCGA-BB-7870 TCGA-CN-4725 TCGA-CN-4728 TCGA-CN-4730 TCGA-CN-5359 TCGA-CN-5363 
        1153         1157         1151          817         1980         1977 
TCGA-CN-5370 TCGA-CN-6012 TCGA-CN-6021 TCGA-CN-6024 TCGA-CN-6996 TCGA-CN-6997 
        1975          629         1970          224          432          429 
TCGA-CN-6998 TCGA-CN-A499 TCGA-CN-A63W TCGA-CQ-5330 TCGA-CQ-5332 TCGA-CQ-6224 
          46          535          348         1393          317          985 
TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7067 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 
        1959         1179          509         1950         1353         1960 
TCGA-CQ-A4CE TCGA-CR-6478 TCGA-CR-7402 TCGA-CV-5435 TCGA-CV-5441 TCGA-CV-5966 
         785         1969          911         1438         2886          519 
TCGA-CV-5970 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-6441 TCGA-CV-6954 TCGA-CV-7095 
         406         1478         1840         1970         1957         1970 
TCGA-CV-7242 TCGA-CV-7424 TCGA-CV-7432 TCGA-CV-7435 TCGA-CV-A45R TCGA-CV-A460 
        1095         1947         1937         1959         5480         1946 
TCGA-CV-A6JZ TCGA-CX-7219 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6826 TCGA-D6-A6EO 
         714          828          292          701          154          435 
TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5631 TCGA-DQ-7592 TCGA-F7-A50I TCGA-F7-A61S 
         338         1778          548          299           92            3 
TCGA-F7-A623 TCGA-H7-A76A TCGA-IQ-A61E TCGA-IQ-A61O TCGA-KU-A66T TCGA-P3-A5QA 
           6          206          588          360          552         1726 
TCGA-P3-A6T4 TCGA-QK-A6IG TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-UF-A718 TCGA-UF-A7JA 
        1968          218          149          135         1326         1894 
TCGA-UF-A7JD 
         735 

$`15Q LOSS WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 
         102          462          283          415         1983          276 
TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6869 
         248          722          725          623         1636          644 
TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-A4IH TCGA-BA-A6D8 
         451           63          384          113          622          850 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BB-4217 
         351          216         1976          314          623          187 
TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 
        2878          278          133          558          310          536 
TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 
         423          687          638          428          436         1955 
TCGA-BB-8601 TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4726 
         624            5            4          799          721          142 
TCGA-CN-4727 TCGA-CN-4729 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 
        1230          392          993          642         1250          395 
TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 
         625         1960         1330          811         1268         1988 
TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5365 TCGA-CN-5366 
        1007         1045          173         1081         1980         1966 
TCGA-CN-5367 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6013 
        1966          683          290          630          933          628 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6022 
         594          629           45          432           98          202 
TCGA-CN-6023 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-A498 
        1110          318          611          394          735          443 
TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V 
         391          904          645          225          526          484 
TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-5324 
         175          367          223          298         1466         1207 
TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 
         654         1660         1422         1399          341          129 
TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6228 TCGA-CQ-7063 TCGA-CQ-7064 
        1253         1000         1057         1959         1750         1560 
TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C9 TCGA-CQ-A4CA 
        1007         1309         1274          877          707         1963 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 
         893          998          391          303          950         2562 
TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 
         358         1663         1152          799         1777         1521 
TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6480 
        1966         1050         1125         1971          514          362 
TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 
         311          345          354          234          379          350 
TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 
         479         1956         1435         1191         1440         1245 
TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 
        1960          105         1979          759          889           30 
TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 
         972         1968         1036          796         1954          997 
TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 
        1430         1951          392          907          913          946 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 
         908          898          930          216          156          181 
TCGA-CR-7401 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 
        1077         1472         1955          522         1950         3295 
TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 
         584          546         1978         2327         1958         2437 
TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 
         701         2641          215         1315         1665          641 
TCGA-CV-6436 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6942 
        1899         1948         1969         1952         1959         3835 
TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 
        1948         1969         1966         1969         1959         3837 
TCGA-CV-7091 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 
        1959         1970         1936         1959         1939         1945 
TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7243 TCGA-CV-7245 
        1987         1979         1952         1444          954          797 
TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 
        1967         1960         1976         1099         1974         1948 
TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7433 
        1955         1957         1937         1973         1972         1984 
TCGA-CV-7434 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A45Y TCGA-CV-A45Z 
        1958         1981          851         1945         1960         1940 
TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN 
        1954         1722         1977         1970         1075          906 
TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6K0 TCGA-CV-A6K1 
        1959          670          110          646          606          685 
TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-D6-6516 TCGA-D6-6824 
        1950          317          321          237          773           77 
TCGA-D6-6825 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB 
         491          568          106          128          539          376 
TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-DQ-5625 
         483          232          424          368          389         1081 
TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 
         516         1030         1965          575          775          622 
TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 
         369          368          324          340         1131          490 
TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50J TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 
         658           15          585          384           14           13 
TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-HD-7229 
         407           58          133          414          403            2 
TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 
           5           25           37           55           44           24 
TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 
          25           11           49           10          111           33 
TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61G TCGA-IQ-A61H 
        1057          485          122          441          360          412 
TCGA-IQ-A61J TCGA-IQ-A61L TCGA-KU-A66S TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W 
         440          351          224          378          168           14 
TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 
          34          392           56          111          112          254 
TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 
         240          910         1559         1120         1954          578 
TCGA-P3-A6T2 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IH 
        1917          400          553          357          245          228 
TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A8Z7 TCGA-QK-A8ZB TCGA-QK-AA3J 
         225          387          567          198          135          157 
TCGA-QK-AA3K TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 
         168         1663         1319         1252         1278         1043 
TCGA-UF-A7JC TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JS 
         484         1497          665          214          413 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 3                  2 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              5480               3837 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               855                658 
[1] "3.0 - 5480.0 (855.0)" "2.0 - 3837.0 (658.0)"
[1] "hr=" "1.2"
D67V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  15Q LOSS MUTATED         3       17        13        43         3         0
  15Q LOSS WILD-TYPE      23       58        61       192         9         1
D67V3, multiclass
           clus
vv          15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  STAGE I                  3                 23
  STAGE II                17                 58
  STAGE III               13                 61
  STAGE IVA               43                192
  STAGE IVB                3                  9
  STAGE IVC                0                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  15Q LOSS MUTATED       6  25  21  29
  15Q LOSS WILD-TYPE    41 102  73 133
D67V4, multiclass
       clus
vv      15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T0+T1                6                 41
  T2                  25                102
  T3                  21                 73
  T4                  29                133
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  15Q LOSS MUTATED    29  10  31   3
  15Q LOSS WILD-TYPE 141  53 121   5
D67V5, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  N0               29                141
  N1               10                 53
  N2               31                121
  N3                3                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  15Q LOSS MUTATED    28   0  13
  15Q LOSS WILD-TYPE 139   1  45
D67V6, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  M0               28                139
  M1                0                  1
  MX               13                 45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V7, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED    24  71
  15Q LOSS WILD-TYPE 108 285
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     24   71
  15Q LOSS WILD-TYPE  108  285
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE               24                108
  MALE                 71                285
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  15Q LOSS MUTATED                                      94
  15Q LOSS WILD-TYPE                                   383
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  15Q LOSS MUTATED                                                             1
  15Q LOSS WILD-TYPE                                                           0
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  15Q LOSS MUTATED                                                     0
  15Q LOSS WILD-TYPE                                                  10
D67V8, multiclass
                                                             clus
vv                                                            15Q LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     94
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        0
                                                             clus
vv                                                            15Q LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      383
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                  0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V9, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED    18  77
  15Q LOSS WILD-TYPE  61 332
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     18   77
  15Q LOSS WILD-TYPE   61  332
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  NO                18                 61
  YES               77                332
[1] 2 2
[1] FALSE
D67V10, continuous
D67V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  15Q LOSS MUTATED                                  1     2
  15Q LOSS WILD-TYPE                                1     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  15Q LOSS MUTATED                           9    79
  15Q LOSS WILD-TYPE                        35   336
D67V12, multiclass
                                  clus
vv                                 15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  1
  ASIAN                                           2                  9
  BLACK OR AFRICAN AMERICAN                       9                 35
  WHITE                                          79                336
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V13, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     8  80
  15Q LOSS WILD-TYPE  16 351
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      8   80
  15Q LOSS WILD-TYPE   16  351
                        clus
vv                       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    8                 16
  NOT HISPANIC OR LATINO               80                351
[1] 2 2
[1] FALSE

Clustering(68) Variable = 16P LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                  0   1
  16P LOSS MUTATED    35  12
  16P LOSS WILD-TYPE 266 101
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                47                367 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                12                101 
$`16P LOSS MUTATED`
TCGA-4P-AA8J TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-7269 TCGA-BA-A4IH TCGA-BA-A6DE 
         102          415          276          236          622          182 
TCGA-BB-7870 TCGA-BB-8596 TCGA-BB-8601 TCGA-CN-4729 TCGA-CN-5363 TCGA-CN-5374 
        1153         1955          624          392         1977          290 
TCGA-CN-A499 TCGA-CN-A63T TCGA-CQ-5330 TCGA-CQ-6224 TCGA-CQ-A4C7 TCGA-CR-6473 
         535          225         1393          985         1960         1125 
TCGA-CR-7368 TCGA-CR-7374 TCGA-CR-7383 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7402 
        1245           30         1954          156          181          911 
TCGA-CV-5436 TCGA-CV-7235 TCGA-CV-7418 TCGA-CV-7424 TCGA-CV-7432 TCGA-CX-7082 
         584         1952         1955         1947         1937          317 
TCGA-D6-A4Z9 TCGA-D6-A6EM TCGA-F7-A50G TCGA-F7-A50I TCGA-HD-7753 TCGA-HD-8224 
         539          232           15           92            5           55 
TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-KU-A6H7 TCGA-MZ-A6I9 TCGA-MZ-A7D7 
         588          360          412          378          254          240 
TCGA-P3-A6SW TCGA-QK-A6IG TCGA-QK-A8ZA TCGA-QK-AA3K TCGA-UF-A719 
        1120          218          135          168         1663 

$`16P LOSS WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 
         462          283         1983          248          722         1288 
TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 
        1762          520          725          623         1636         1747 
TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 
         190          644          451           63          384          113 
TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB 
         895          855          918          850          351          216 
TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 
        1976          314          623          142          187         2878 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 
         278          140          133          558          310          536 
TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7871 TCGA-BB-7872 TCGA-C9-A47Z 
         423          687          638          428          436            5 
TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 
           4          799          721         1157          142         1230 
TCGA-CN-4728 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 
        1151          817          993          642         1250          395 
TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 
         625         1960         1330          811         1268         1988 
TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5365 
        1007         1045          173         1980         1081         1980 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6010 TCGA-CN-6011 
        1966         1966         1975          683          630          933 
TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 
         629          628          594          629           45          432 
TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 
          98         1970          202         1110          224          318 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 
         611          394          735          432          429           46 
TCGA-CN-A498 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63U TCGA-CN-A63V 
         443          391          904          645          526          484 
TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 
         348          175          367          223          298         1466 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5331 TCGA-CQ-5332 
        1207          654         1660         1422         1399          317 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6227 
         341          129         1253         1000         1057         1959 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 
        1959         1179         1750         1560         1007          509 
TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 
        1309         1274          877         1950         1353          707 
TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH 
        1963          893          998          785          391          303 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 
         950         2562          358         1663         1152          799 
TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6474 TCGA-CR-6477 
        1777         1521         1966         1050         1971          514 
TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 
        1969          362          311          345          354          234 
TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 
         379          350          479         1956         1435         1191 
TCGA-CR-7367 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 
        1440         1960          105         1979          759          889 
TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7386 
         972         1968         1036          796          997         1430 
TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
        1951          392          907          913          946          908 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7401 TCGA-CR-7404 TCGA-CV-5430 
         898          930          216         1077         1472         1955 
TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5439 TCGA-CV-5440 
         522         1950         3295         1438          546         1978 
TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 
        2886         2327         1958         2437          519          406 
TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 
         701         2641         1478         1840          215         1315 
TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 
        1665          641         1899         1970         1948         1969 
TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6952 
        1952         1959         3835         1948         1969         1966 
TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 
        1957         1969         1959         3837         1959         1970 
TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7180 
        1970         1936         1959         1939         1945         1987 
TCGA-CV-7183 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 
        1979         1444         1095          954          797         1967 
TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7422 
        1960         1976         1099         1974         1948         1957 
TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 
        1937         1973         1972         1984         1958         1959 
TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45Y TCGA-CV-A45Z 
        1981          851         1945         5480         1960         1940 
TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE 
        1946         1954         1722         1977         1970         1075 
TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ 
         906         1959          670          110          646          714 
TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 
         606          685         1950          321          237          828 
TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 
         773          292          701           77          491          154 
TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EO 
         568          106          128          376          483          435 
TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 
         424          368          389          338         1778         1081 
TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 
         516         1030          548         1965          575          775 
TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
         622          299          369          368          324          340 
TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V 
        1131          490          658          585            3          384 
TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 
          14           13            6          407           58          133 
TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7917 
         414          403          206            2           25           37 
TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 
          44           24           25           11           49           10 
TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 
         111           33         1057          485          122          441 
TCGA-IQ-A61J TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H8 
         440          351          360          224          552          168 
TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G 
          14           34          392           56          111          112 
TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 
         910         1726         1559         1954          578         1917 
TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IH 
        1968          400          553          357          245          228 
TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-QK-A8ZB 
         225          387          567          198          149          135 
TCGA-QK-AA3J TCGA-UF-A718 TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 
         157         1326         1319         1252         1278         1043 
TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ 
        1894          484          735         1497          665          214 
TCGA-UF-A7JS 
         413 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 5                  2 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              1977               5480 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
               412                735 
[1] "5.0 - 1977.0 (412.0)" "2.0 - 5480.0 (735.0)"
[1] "hr=" "1.9"
D68V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  16P LOSS MUTATED         3        9         8        29         2         0
  16P LOSS WILD-TYPE      23       66        66       206        10         1
D68V3, multiclass
           clus
vv          16P LOSS MUTATED 16P LOSS WILD-TYPE
  STAGE I                  3                 23
  STAGE II                 9                 66
  STAGE III                8                 66
  STAGE IVA               29                206
  STAGE IVB                2                 10
  STAGE IVC                0                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  16P LOSS MUTATED       3  21  16  11
  16P LOSS WILD-TYPE    44 106  78 151
D68V4, multiclass
       clus
vv      16P LOSS MUTATED 16P LOSS WILD-TYPE
  T0+T1                3                 44
  T2                  21                106
  T3                  16                 78
  T4                  11                151
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  16P LOSS MUTATED    12  10  22   2
  16P LOSS WILD-TYPE 158  53 130   6
D68V5, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  N0               12                158
  N1               10                 53
  N2               22                130
  N3                2                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  16P LOSS MUTATED    17   0  13
  16P LOSS WILD-TYPE 150   1  45
D68V6, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  M0               17                150
  M1                0                  1
  MX               13                 45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V7, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    18  39
  16P LOSS WILD-TYPE 114 317
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     18   39
  16P LOSS WILD-TYPE  114  317
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE               18                114
  MALE                 39                317
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  16P LOSS MUTATED                                      55
  16P LOSS WILD-TYPE                                   422
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  16P LOSS MUTATED                                                             0
  16P LOSS WILD-TYPE                                                           1
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  16P LOSS MUTATED                                                     2
  16P LOSS WILD-TYPE                                                   8
D68V8, multiclass
                                                             clus
vv                                                            16P LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     55
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        2
                                                             clus
vv                                                            16P LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      422
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                  1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                          8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V9, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     5  52
  16P LOSS WILD-TYPE  74 357
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      5   52
  16P LOSS WILD-TYPE   74  357
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  NO                 5                 74
  YES               52                357
[1] 2 2
[1] FALSE
D68V10, continuous
D68V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16P LOSS MUTATED                                  0     1
  16P LOSS WILD-TYPE                                2    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16P LOSS MUTATED                           7    47
  16P LOSS WILD-TYPE                        37   368
D68V12, multiclass
                                  clus
vv                                 16P LOSS MUTATED 16P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           1                 10
  BLACK OR AFRICAN AMERICAN                       7                 37
  WHITE                                          47                368
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V13, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     4  51
  16P LOSS WILD-TYPE  20 380
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      4   51
  16P LOSS WILD-TYPE   20  380
                        clus
vv                       16P LOSS MUTATED 16P LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                 20
  NOT HISPANIC OR LATINO               51                380
[1] 2 2
[1] FALSE

Clustering(69) Variable = 16Q LOSS MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                  0   1
  16Q LOSS MUTATED    48  14
  16Q LOSS WILD-TYPE 253  99
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                62                352 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                14                 99 
$`16Q LOSS MUTATED`
TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5153 TCGA-BA-5559 TCGA-BA-A4IH TCGA-BB-4225 
         415          276         1762         1747          622          140 
TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-8596 TCGA-BB-8601 
         310          536          638         1153         1955          624 
TCGA-CN-4729 TCGA-CN-5356 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5374 TCGA-CN-6012 
         392         1045         1081         1977          290          629 
TCGA-CN-6021 TCGA-CN-A499 TCGA-CN-A63T TCGA-CN-A63U TCGA-CQ-6224 TCGA-CQ-A4C7 
        1970          535          225          526          985         1960 
TCGA-CR-5243 TCGA-CR-6467 TCGA-CR-6473 TCGA-CR-6481 TCGA-CR-6484 TCGA-CR-7368 
        2562         1777         1125          311          354         1245 
TCGA-CR-7370 TCGA-CR-7398 TCGA-CR-7402 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-7235 
         105          156          911         1958         2437         1952 
TCGA-CV-7418 TCGA-CV-7424 TCGA-CV-7428 TCGA-CV-7432 TCGA-CV-A460 TCGA-CX-7082 
        1955         1947         1973         1937         1946          317 
TCGA-D6-6827 TCGA-D6-A4Z9 TCGA-D6-A6EM TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 
         568          539          232          575          775          622 
TCGA-F7-A50I TCGA-HD-8224 TCGA-IQ-A61E TCGA-IQ-A61H TCGA-KU-A6H7 TCGA-MZ-A6I9 
          92           55          588          412          378          254 
TCGA-P3-A5QE TCGA-P3-A6SW TCGA-QK-A6IF TCGA-QK-A8ZA TCGA-QK-AA3K TCGA-UF-A719 
        1559         1120          245          135          168         1663 
TCGA-UF-A71E TCGA-UF-A7J9 
        1278         1043 

$`16Q LOSS WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-5151 
         102          462          283         1983          248          722 
TCGA-BA-5152 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6868 
        1288          520          725          623         1636          190 
TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 
         644          451           63          384          113          236 
TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB 
         895          855          918          850          351          216 
TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 
         182         1976          314          623          142          187 
TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7863 TCGA-BB-7864 
        2878          278          133          558          423          687 
TCGA-BB-7871 TCGA-BB-7872 TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 
         428          436            5            4          799          721 
TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4730 TCGA-CN-4731 
        1157          142         1230         1151          817          993 
TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 
         642         1250          395          625         1960         1330 
TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5359 
         811         1268         1988         1007          173         1980 
TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6010 
        1980         1966         1966         1975          683          630 
TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 
         933          628          594          629           45          432 
TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 
          98          202         1110          224          318          611 
TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 
         394          735          432          429           46          443 
TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y 
         391          904          645          484          348          175 
TCGA-CN-A641 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
         367          223          298         1466         1207          654 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 
        1660         1422         1393         1399          317          341 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6227 TCGA-CQ-6228 
         129         1253         1000         1057         1959         1959 
TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 
        1179         1750         1560         1007          509         1309 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CA 
        1274          877         1950         1353          707         1963 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI 
         893          998          785          391          303          950 
TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6470 TCGA-CR-6471 
         358         1663         1152          799         1521         1966 
TCGA-CR-6472 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6482 
        1050         1971          514         1969          362          345 
TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 
         234          379          350          479         1956         1435 
TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 
        1191         1440         1960         1979          759          889 
TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 
          30          972         1968         1036          796         1954 
TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 
         997         1430         1951          392          907          913 
TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7399 
         946          908          898          930          216          181 
TCGA-CR-7401 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 
        1077         1472         1955          522         1950         3295 
TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 
        1438          584          546         1978         2886         2327 
TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 
         519          406          701         2641         1478         1840 
TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 
         215         1315         1665          641         1899         1970 
TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 
        1948         1969         1952         1959         3835         1948 
TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 
        1969         1966         1957         1969         1959         3837 
TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 
        1959         1970         1970         1936         1959         1939 
TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 
        1945         1987         1979         1444         1095          954 
TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7406 
         797         1967         1960         1976         1099         1974 
TCGA-CV-7410 TCGA-CV-7422 TCGA-CV-7427 TCGA-CV-7430 TCGA-CV-7433 TCGA-CV-7434 
        1948         1957         1937         1972         1984         1958 
TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45Y 
        1959         1981          851         1945         5480         1960 
TCGA-CV-A45Z TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE 
        1940         1954         1722         1977         1970         1075 
TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ 
         906         1959          670          110          646          714 
TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 
         606          685         1950          321          237          828 
TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 
         773          292          701           77          491          154 
TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EO TCGA-D6-A6EP 
         106          128          376          483          435          424 
TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 
         368          389          338         1778         1081          516 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 
        1030          548         1965          299          369          368 
TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G 
         324          340         1131          490          658           15 
TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 
         585            3          384           14           13            6 
TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A 
         407           58          133          414          403          206 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8314 TCGA-HD-8634 
           2            5           25           37           44           24 
TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 
          25           11           49           10          111           33 
TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61G TCGA-IQ-A61J 
        1057          485          122          441          360          440 
TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H8 TCGA-MT-A51W 
         351          360          224          552          168           14 
TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A7D7 
          34          392           56          111          112          240 
TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T4 
         910         1726         1954          578         1917         1968 
TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II 
         400          553          357          218          228          225 
TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-QK-A8ZB TCGA-QK-AA3J 
         387          567          198          149          135          157 
TCGA-UF-A718 TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD 
        1326         1319         1252         1894          484          735 
TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JS 
        1497          665          214          413 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                55                  2 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              2562               5480 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             626.5              710.5 
[1] "55.0 - 2562.0 (626.5)" "2.0 - 5480.0 (710.5)" 
[1] "hr=" "1.1"
D69V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  16Q LOSS MUTATED         2       10        10        30         2         0
  16Q LOSS WILD-TYPE      24       65        64       205        10         1
D69V3, multiclass
           clus
vv          16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  STAGE I                  2                 24
  STAGE II                10                 65
  STAGE III               10                 64
  STAGE IVA               30                205
  STAGE IVB                2                 10
  STAGE IVC                0                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  16Q LOSS MUTATED       5  21  14  15
  16Q LOSS WILD-TYPE    42 106  80 147
D69V4, multiclass
       clus
vv      16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  T0+T1                5                 42
  T2                  21                106
  T3                  14                 80
  T4                  15                147
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  16Q LOSS MUTATED    16  11  21   2
  16Q LOSS WILD-TYPE 154  52 131   6
D69V5, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  N0               16                154
  N1               11                 52
  N2               21                131
  N3                2                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  16Q LOSS MUTATED    19   0  11
  16Q LOSS WILD-TYPE 148   1  47
D69V6, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  M0               19                148
  M1                0                  1
  MX               11                 47
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V7, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    15  57
  16Q LOSS WILD-TYPE 117 299
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     15   57
  16Q LOSS WILD-TYPE  117  299
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE               15                117
  MALE                 57                299
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  16Q LOSS MUTATED                                      68
  16Q LOSS WILD-TYPE                                   409
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  16Q LOSS MUTATED                                                             0
  16Q LOSS WILD-TYPE                                                           1
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  16Q LOSS MUTATED                                                     4
  16Q LOSS WILD-TYPE                                                   6
D69V8, multiclass
                                                             clus
vv                                                            16Q LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     68
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        4
                                                             clus
vv                                                            16Q LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      409
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                  1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                          6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V9, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED     9  63
  16Q LOSS WILD-TYPE  70 346
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      9   63
  16Q LOSS WILD-TYPE   70  346
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  NO                 9                 70
  YES               63                346
[1] 2 2
[1] FALSE
D69V10, continuous
D69V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16Q LOSS MUTATED                                  0     2
  16Q LOSS WILD-TYPE                                2     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16Q LOSS MUTATED                           8    61
  16Q LOSS WILD-TYPE                        36   354
D69V12, multiclass
                                  clus
vv                                 16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           2                  9
  BLACK OR AFRICAN AMERICAN                       8                 36
  WHITE                                          61                354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V13, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED     3  65
  16Q LOSS WILD-TYPE  21 366
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      3   65
  16Q LOSS WILD-TYPE   21  366
                        clus
vv                       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                 21
  NOT HISPANIC OR LATINO               65                366
[1] 2 2
[1] FALSE

Clustering(70) Variable = 17P LOSS MUTATION ANALYSIS
D70V1, survival
                    sevent
clus2                  0   1
  17P LOSS MUTATED    58  29
  17P LOSS WILD-TYPE 243  84
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                87                327 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                29                 84 
$`17P LOSS MUTATED`
TCGA-BA-5149 TCGA-BA-5152 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6870 
         248         1288          623         1747          190          451 
TCGA-BA-6871 TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DE TCGA-BA-A8YP 
          63          622          918          850          182          142 
TCGA-BB-4223 TCGA-BB-7862 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-CN-4725 
        2878          536          638         1153          428         1157 
TCGA-CN-4730 TCGA-CN-4735 TCGA-CN-4739 TCGA-CN-4742 TCGA-CN-5360 TCGA-CN-5374 
         817         1250         1330         1988         1081          290 
TCGA-CN-6988 TCGA-CN-A49A TCGA-CN-A63W TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 
         318          391          348         1000         1057          985 
TCGA-CQ-6228 TCGA-CQ-7067 TCGA-CQ-7069 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CR-6472 
        1959          509         1274         1960          707         1050 
TCGA-CR-6481 TCGA-CR-6484 TCGA-CR-7364 TCGA-CR-7371 TCGA-CR-7390 TCGA-CR-7398 
         311          354         1435         1979          907          156 
TCGA-CV-5431 TCGA-CV-5439 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5978 
         522          546         2437          519          406          215 
TCGA-CV-6441 TCGA-CV-6961 TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7245 TCGA-CV-7406 
        1970         1959         1945         1987          797         1974 
TCGA-CV-7424 TCGA-CV-7428 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A460 TCGA-CV-A6JU 
        1947         1973         1959         1981         1946          110 
TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6823 TCGA-D6-6826 TCGA-D6-8569 TCGA-D6-A6EM 
         237          828          701          154          128          232 
TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7591 TCGA-DQ-7595 TCGA-F7-A50G TCGA-F7-A50J 
         516         1965          622          324           15          585 
TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-A6C5 TCGA-HD-8635 TCGA-IQ-7630 TCGA-IQ-A61G 
          13            6          403           25          485          360 
TCGA-IQ-A61H TCGA-MT-A67D TCGA-MT-A67G TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SX 
         412           56          112         1726         1559         1954 
TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A8ZA 
         400          553          135 

$`17P LOSS WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 
         102          462          283          415         1983          276 
TCGA-BA-5151 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6869 
         722         1762          520          725         1636          644 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A6DA 
         384          113          236          895          855          351 
TCGA-BA-A6DB TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BB-4217 TCGA-BB-4224 
         216         1976          314          623          187          278 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7863 TCGA-BB-7864 
         140          133          558          310          423          687 
TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 
         436         1955          624            5            4          799 
TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4731 
         721          142         1230         1151          392          993 
TCGA-CN-4733 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4740 TCGA-CN-4741 
         642          395          625         1960          811         1268 
TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5363 TCGA-CN-5365 
        1007         1045          173         1980         1977         1980 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6010 TCGA-CN-6011 
        1966         1966         1975          683          630          933 
TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 
         629          628          594          629           45          432 
TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6989 
          98         1970          202         1110          224          611 
TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 
         394          735          432          429           46          443 
TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V 
         535          904          645          225          526          484 
TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-5324 
         175          367          223          298         1466         1207 
TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 
         654         1660         1422         1393         1399          317 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7063 
         341          129         1253         1959         1179         1750 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 
        1560         1007         1309          877         1950         1353 
TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH 
        1963          893          998          785          391          303 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 
         950         2562          358         1663         1152          799 
TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 
        1777         1521         1966         1125         1971          514 
TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 
        1969          362          345          234          379          350 
TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 
         479         1956         1191         1440         1245         1960 
TCGA-CR-7370 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 
         105          759          889           30          972         1968 
TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 
        1036          796         1954          997         1430         1951 
TCGA-CR-7389 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 
         392          913          946          908          898          930 
TCGA-CR-7397 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 
         216          181         1077          911         1472         1955 
TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5440 TCGA-CV-5441 
        1950         3295         1438          584         1978         2886 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 
        2327         1958          701         2641         1478         1840 
TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6934 TCGA-CV-6935 
        1315         1665          641         1899         1948         1969 
TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6952 
        1952         1959         3835         1948         1969         1966 
TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 
        1957         1969         3837         1959         1970         1970 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 
        1936         1959         1939         1979         1952         1444 
TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 
        1095          954         1967         1960         1976         1099 
TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7427 TCGA-CV-7430 TCGA-CV-7432 
        1948         1955         1957         1937         1972         1937 
TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45Y 
        1984         1958          851         1945         5480         1960 
TCGA-CV-A45Z TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE 
        1940         1954         1722         1977         1970         1075 
TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 
         906         1959          670          646          714          606 
TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-D6-6516 TCGA-D6-6517 
         685         1950          317          321          773          292 
TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-D6-A4ZB 
          77          491          568          106          539          376 
TCGA-D6-A6EK TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q 
         483          435          424          368          389          338 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7589 TCGA-DQ-7590 
        1778         1081         1030          548          575          775 
TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 
         299          369          368          340         1131          490 
TCGA-F7-8489 TCGA-F7-A50I TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-H7-7774 
         658           92            3          384           14          407 
TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 
          58          133          414          206            2            5 
TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-A4C1 
          25           37           55           44           24           11 
TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7631 
          49           10          111           33         1057          122 
TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61J TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S 
         441          588          440          351          360          224 
TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A 
         552          378          168           14           34          392 
TCGA-MT-A67F TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A6SW TCGA-P3-A6T0 
         111          254          240          910         1120          578 
TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH 
        1917         1968          357          245          218          228 
TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-QK-A8ZB 
         225          387          567          198          149          135 
TCGA-QK-AA3J TCGA-QK-AA3K TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71D 
         157          168         1326         1663         1319         1252 
TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF 
        1278         1043         1894          484          735         1497 
TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JS 
         665          214          413 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 6                  2 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              2878               5480 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               622                722 
[1] "6.0 - 2878.0 (622.0)" "2.0 - 5480.0 (722.0)"
[1] "hr=" "1.2"
D70V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  17P LOSS MUTATED         2       20        18        44         4         1
  17P LOSS WILD-TYPE      24       55        56       191         8         0
D70V3, multiclass
           clus
vv          17P LOSS MUTATED 17P LOSS WILD-TYPE
  STAGE I                  2                 24
  STAGE II                20                 55
  STAGE III               18                 56
  STAGE IVA               44                191
  STAGE IVB                4                  8
  STAGE IVC                1                  0
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  17P LOSS MUTATED       8  29  23  30
  17P LOSS WILD-TYPE    39  98  71 132
D70V4, multiclass
       clus
vv      17P LOSS MUTATED 17P LOSS WILD-TYPE
  T0+T1                8                 39
  T2                  29                 98
  T3                  23                 71
  T4                  30                132
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  17P LOSS MUTATED    33  16  32   2
  17P LOSS WILD-TYPE 137  47 120   6
D70V5, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  N0               33                137
  N1               16                 47
  N2               32                120
  N3                2                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  17P LOSS MUTATED    30   1  14
  17P LOSS WILD-TYPE 137   0  44
D70V6, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  M0               30                137
  M1                1                  0
  MX               14                 44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V7, binary
                    cls
clus                   0   1
  17P LOSS MUTATED    26  75
  17P LOSS WILD-TYPE 106 281
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     26   75
  17P LOSS WILD-TYPE  106  281
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE               26                106
  MALE                 75                281
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  17P LOSS MUTATED                                      99
  17P LOSS WILD-TYPE                                   378
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  17P LOSS MUTATED                                                             0
  17P LOSS WILD-TYPE                                                           1
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  17P LOSS MUTATED                                                     2
  17P LOSS WILD-TYPE                                                   8
D70V8, multiclass
                                                             clus
vv                                                            17P LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     99
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        2
                                                             clus
vv                                                            17P LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      378
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                  1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                          8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V9, binary
                    cls
clus                   0   1
  17P LOSS MUTATED    19  82
  17P LOSS WILD-TYPE  60 327
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     19   82
  17P LOSS WILD-TYPE   60  327
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  NO                19                 60
  YES               82                327
[1] 2 2
[1] FALSE
D70V10, continuous
D70V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17P LOSS MUTATED                                  0     2
  17P LOSS WILD-TYPE                                2     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17P LOSS MUTATED                          12    84
  17P LOSS WILD-TYPE                        32   331
D70V12, multiclass
                                  clus
vv                                 17P LOSS MUTATED 17P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           2                  9
  BLACK OR AFRICAN AMERICAN                      12                 32
  WHITE                                          84                331
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V13, binary
                    cls
clus                   0   1
  17P LOSS MUTATED     9  87
  17P LOSS WILD-TYPE  15 344
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      9   87
  17P LOSS WILD-TYPE   15  344
                        clus
vv                       17P LOSS MUTATED 17P LOSS WILD-TYPE
  HISPANIC OR LATINO                    9                 15
  NOT HISPANIC OR LATINO               87                344
[1] 2 2
[1] FALSE

Clustering(71) Variable = 17Q LOSS MUTATION ANALYSIS
D71V1, survival
                    sevent
clus2                  0   1
  17Q LOSS MUTATED    20   9
  17Q LOSS WILD-TYPE 281 104
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                29                385 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 9                104 
$`17Q LOSS MUTATED`
TCGA-BA-4075 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-A4II 
         283         1747          190          451           63          918 
TCGA-BB-4223 TCGA-CN-4739 TCGA-CN-5374 TCGA-CN-6011 TCGA-CQ-6221 TCGA-CQ-6224 
        2878         1330          290          933         1000          985 
TCGA-CQ-7067 TCGA-CQ-A4C7 TCGA-CR-6484 TCGA-CV-5966 TCGA-D6-6823 TCGA-D6-6826 
         509         1960          354          519          701          154 
TCGA-F7-A50G TCGA-F7-A620 TCGA-HD-8635 TCGA-IQ-7630 TCGA-IQ-A61G TCGA-IQ-A61H 
          15           13           25          485          360          412 
TCGA-MT-A67G TCGA-MZ-A7D7 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SX 
         112          240         1726         1559         1954 

$`17Q LOSS WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
         102          462          415         1983          276          248 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 
         722         1288         1762          520          725          623 
TCGA-BA-5558 TCGA-BA-6869 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF 
        1636          644          384          113          236          895 
TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE 
         855          622          850          351          216          182 
TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4224 
        1976          314          623          142          187          278 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 
         140          133          558          310          536          423 
TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 
         687          638         1153          428          436         1955 
TCGA-BB-8601 TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 
         624            5            4          799          721         1157 
TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 
         142         1230         1151          392          817          993 
TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4740 
         642         1250          395          625         1960          811 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 
        1268         1988         1007         1045          173         1980 
TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 
        1081         1977         1980         1966         1966         1975 
TCGA-CN-5373 TCGA-CN-6010 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 
         683          630          629          628          594          629 
TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 
          45          432           98         1970          202         1110 
TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 
         224          318          611          394          735          432 
TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B 
         429           46          443          535          391          904 
TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y 
         645          225          526          484          348          175 
TCGA-CN-A641 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
         367          223          298         1466         1207          654 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 
        1660         1422         1393         1399          317          341 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6223 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 
         129         1253         1057         1959         1959         1179 
TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 
        1750         1560         1007         1309         1274          877 
TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD 
        1950         1353          707         1963          893          998 
TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 
         785          391          303          950         2562          358 
TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 
        1663         1152          799         1777         1521         1966 
TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 
        1050         1125         1971          514         1969          362 
TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 
         311          345          234          379          350          479 
TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 
        1956         1435         1191         1440         1245         1960 
TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 
         105         1979          759          889           30          972 
TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 
        1968         1036          796         1954          997         1430 
TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
        1951          392          907          913          946          908 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 
         898          930          216          156          181         1077 
TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 
         911         1472         1955          522         1950         3295 
TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 
        1438          584          546         1978         2886         2327 
TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 
        1958         2437          406          701         2641         1478 
TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 
        1840          215         1315         1665          641         1899 
TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6942 
        1970         1948         1969         1952         1959         3835 
TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 
        1948         1969         1966         1957         1969         1959 
TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 
        3837         1959         1970         1970         1936         1959 
TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 
        1939         1945         1987         1979         1952         1444 
TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7254 
        1095          954          797         1967         1960         1976 
TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 
        1099         1974         1948         1955         1957         1947 
TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 
        1937         1973         1972         1937         1984         1958 
TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45Y 
        1959         1981          851         1945         5480         1960 
TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD 
        1940         1946         1954         1722         1977         1970 
TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY 
        1075          906         1959          670          110          646 
TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 
         714          606          685         1950          317          321 
TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 
         237          828          773          292           77          491 
TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK 
         568          106          128          539          376          483 
TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q 
         232          435          424          368          389          338 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 
        1778         1081          516         1030          548         1965 
TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 
         575          775          622          299          369          368 
TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50I 
         324          340         1131          490          658           92 
TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A623 TCGA-H7-7774 
         585            3          384           14            6          407 
TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 
          58          133          414          403          206            2 
TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 
           5           25           37           55           44           24 
TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 
          11           49           10          111           33         1057 
TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61J TCGA-IQ-A61L TCGA-IQ-A61O 
         122          441          588          440          351          360 
TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X 
         224          552          378          168           14           34 
TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A6SW 
         392           56          111          254          910         1120 
TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 
         578         1917         1968          400          553          357 
TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 
         245          218          228          225          387          567 
TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K 
         198          149          135          135          157          168 
TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 
        1326         1663         1319         1252         1278         1043 
TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ 
        1894          484          735         1497          665          214 
TCGA-UF-A7JS 
         413 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                13                  2 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              2878               5480 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
               485                721 
[1] "13.0 - 2878.0 (485.0)" "2.0 - 5480.0 (721.0)" 
[1] "hr=" "1.8"
D71V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  17Q LOSS MUTATED         2        4         8        13         0         0
  17Q LOSS WILD-TYPE      24       71        66       222        12         1
D71V3, multiclass
           clus
vv          17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  STAGE I                  2                 24
  STAGE II                 4                 71
  STAGE III                8                 66
  STAGE IVA               13                222
  STAGE IVB                0                 12
  STAGE IVC                0                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  17Q LOSS MUTATED       4  11   6   7
  17Q LOSS WILD-TYPE    43 116  88 155
D71V4, multiclass
       clus
vv      17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  T0+T1                4                 43
  T2                  11                116
  T3                   6                 88
  T4                   7                155
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  17Q LOSS MUTATED     9   7  10   0
  17Q LOSS WILD-TYPE 161  56 142   8
D71V5, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  N0                9                161
  N1                7                 56
  N2               10                142
  N3                0                  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"
                    vv
clus                  M0  M1  MX
  17Q LOSS MUTATED     9   0   9
  17Q LOSS WILD-TYPE 158   1  49
D71V6, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  M0                9                158
  M1                0                  1
  MX                9                 49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V7, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     8  24
  17Q LOSS WILD-TYPE 124 332
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      8   24
  17Q LOSS WILD-TYPE  124  332
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE                8                124
  MALE                 24                332
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  17Q LOSS MUTATED                                      31
  17Q LOSS WILD-TYPE                                   446
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  17Q LOSS MUTATED                                                             0
  17Q LOSS WILD-TYPE                                                           1
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  17Q LOSS MUTATED                                                     1
  17Q LOSS WILD-TYPE                                                   9
D71V8, multiclass
                                                             clus
vv                                                            17Q LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     31
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        1
                                                             clus
vv                                                            17Q LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      446
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                  1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                          9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V9, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     8  24
  17Q LOSS WILD-TYPE  71 385
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      8   24
  17Q LOSS WILD-TYPE   71  385
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  NO                 8                 71
  YES               24                385
[1] 2 2
[1] FALSE
D71V10, continuous
D71V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17Q LOSS MUTATED                                  0     1
  17Q LOSS WILD-TYPE                                2    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17Q LOSS MUTATED                           3    27
  17Q LOSS WILD-TYPE                        41   388
D71V12, multiclass
                                  clus
vv                                 17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           1                 10
  BLACK OR AFRICAN AMERICAN                       3                 41
  WHITE                                          27                388
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V13, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     3  27
  17Q LOSS WILD-TYPE  21 404
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      3   27
  17Q LOSS WILD-TYPE   21  404
                        clus
vv                       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                 21
  NOT HISPANIC OR LATINO               27                404
[1] 2 2
[1] FALSE

Clustering(72) Variable = 18P LOSS MUTATION ANALYSIS
D72V1, survival
                    sevent
clus2                  0   1
  18P LOSS MUTATED    50  23
  18P LOSS WILD-TYPE 251  90
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                73                341 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                23                 90 
$`18P LOSS MUTATED`
TCGA-BA-4075 TCGA-BA-5557 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-A4IF TCGA-BA-A6D8 
         283          623          190          451          895          850 
TCGA-BA-A6DB TCGA-BB-8601 TCGA-CN-4727 TCGA-CN-4735 TCGA-CN-4739 TCGA-CN-4740 
         216          624         1230         1250         1330          811 
TCGA-CN-5370 TCGA-CN-6010 TCGA-CN-6019 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6998 
        1975          630          432          735          432           46 
TCGA-CN-A499 TCGA-CQ-5325 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-7072 TCGA-CQ-A4C7 
         535          654         1057          985         1950         1960 
TCGA-CQ-A4CG TCGA-CR-6484 TCGA-CR-7367 TCGA-CR-7373 TCGA-CR-7374 TCGA-CV-5435 
         391          354         1440          889           30         1438 
TCGA-CV-5439 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-6003 TCGA-CV-6942 TCGA-CV-6960 
         546         2437          519         1665         3835         1969 
TCGA-CV-6961 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7235 TCGA-CV-7245 TCGA-CV-7261 
        1959         1959         1970         1952          797         1099 
TCGA-CV-7424 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-A460 TCGA-CX-7219 TCGA-DQ-5624 
        1947         1937         1984         1946          828         1778 
TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-7588 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50I 
         516         1030         1965         1131          658           92 
TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-A6C4 TCGA-HD-7229 TCGA-IQ-7630 TCGA-IQ-A61E 
          13            6          414            2          485          588 
TCGA-IQ-A61H TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-MT-A51W TCGA-MT-A67D 
         412          351          360          224           14           56 
TCGA-P3-A6T0 TCGA-P3-A6T8 TCGA-QK-A6IH TCGA-QK-A8Z9 TCGA-UF-A71D TCGA-UF-A7JF 
         578          400          228          149         1252         1497 
TCGA-UF-A7JS 
         413 

$`18P LOSS WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
         102          462          415         1983          276          248 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 
         722         1288         1762          520          725         1636 
TCGA-BA-5559 TCGA-BA-6869 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 
        1747          644           63          384          113          236 
TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6DA TCGA-BA-A6DE TCGA-BA-A6DG 
         855          622          918          351          182         1976 
TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 
         314          623          142          187         2878          278 
TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 
         140          133          558          310          536          423 
TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 
         687          638         1153          428          436         1955 
TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 
           5            4          799          721         1157          142 
TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4736 
        1151          392          817          993          642          395 
TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 
         625         1960         1268         1988         1007         1045 
TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 
         173         1980         1081         1977         1980         1966 
TCGA-CN-5367 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 
        1966          683          290          933          629          628 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 
         594          629           45           98         1970          202 
TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6997 
        1110          224          318          611          394          429 
TCGA-CN-A498 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U 
         443          391          904          645          225          526 
TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A6V1 TCGA-CN-A6V3 
         484          348          175          367          223          298 
TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 
        1466         1207         1660         1422         1393         1399 
TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6227 
         317          341          129         1253         1000         1959 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 
        1959         1179         1750         1560         1007          509 
TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CA 
        1309         1274          877         1353          707         1963 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 
         893          998          785          303          950         2562 
TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 
         358         1663         1152          799         1777         1521 
TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 
        1966         1050         1125         1971          514         1969 
TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 
         362          311          345          234          379          350 
TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7368 TCGA-CR-7369 
         479         1956         1435         1191         1245         1960 
TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 
         105         1979          759          972         1968         1036 
TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 
         796         1954          997         1430         1951          392 
TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 
         907          913          946          908          898          930 
TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 
         216          156          181         1077          911         1472 
TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5436 TCGA-CV-5440 
        1955          522         1950         3295          584         1978 
TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 
        2886         2327         1958          406          701         2641 
TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6436 
        1478         1840          215         1315          641         1899 
TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6943 
        1970         1948         1969         1952         1959         1948 
TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-7090 TCGA-CV-7097 TCGA-CV-7099 
        1969         1966         1957         3837         1970         1936 
TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7238 
        1959         1939         1945         1987         1979         1444 
TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7406 
        1095          954         1967         1960         1976         1974 
TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 
        1948         1955         1957         1937         1973         1972 
TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A45R 
        1958         1959         1981          851         1945         5480 
TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD 
        1960         1940         1954         1722         1977         1970 
TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JY 
        1075          906         1959          670          110          646 
TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 
         714          606          685         1950          317          321 
TCGA-CX-7086 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 
         237          773          292          701           77          491 
TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB 
         154          568          106          128          539          376 
TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES 
         483          232          435          424          368          389 
TCGA-D6-A74Q TCGA-DQ-5625 TCGA-DQ-5631 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 
         338         1081          548          575          775          622 
TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-8298 
         299          369          368          324          340          490 
TCGA-F7-A50G TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-H7-7774 
          15          585            3          384           14          407 
TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7753 TCGA-HD-7754 
          58          133          403          206            5           25 
TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 
          37           55           44           24           25           11 
TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7631 
          49           10          111           33         1057          122 
TCGA-IQ-7632 TCGA-IQ-A61G TCGA-IQ-A61J TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 
         441          360          440          552          378          168 
TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-MZ-A7D7 
          34          392          111          112          254          240 
TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T2 
         910         1726         1559         1120         1954         1917 
TCGA-P3-A6T4 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6II 
        1968          553          357          245          218          225 
TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A8Z7 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J 
         387          567          198          135          135          157 
TCGA-QK-AA3K TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 
         168         1326         1663         1319         1278         1043 
TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JH TCGA-UF-A7JJ 
        1894          484          735          665          214 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 2                  3 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              3835               5480 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               658                701 
[1] "2.0 - 3835.0 (658.0)" "3.0 - 5480.0 (701.0)"
[1] "hr=" "1.3"
D72V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  18P LOSS MUTATED         5       18        17        45         2         0
  18P LOSS WILD-TYPE      21       57        57       190        10         1
D72V3, multiclass
           clus
vv          18P LOSS MUTATED 18P LOSS WILD-TYPE
  STAGE I                  5                 21
  STAGE II                18                 57
  STAGE III               17                 57
  STAGE IVA               45                190
  STAGE IVB                2                 10
  STAGE IVC                0                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  18P LOSS MUTATED       9  25  19  34
  18P LOSS WILD-TYPE    38 102  75 128
D72V4, multiclass
       clus
vv      18P LOSS MUTATED 18P LOSS WILD-TYPE
  T0+T1                9                 38
  T2                  25                102
  T3                  19                 75
  T4                  34                128
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  18P LOSS MUTATED    37  14  28   1
  18P LOSS WILD-TYPE 133  49 124   7
D72V5, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  N0               37                133
  N1               14                 49
  N2               28                124
  N3                1                  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"
                    vv
clus                  M0  M1  MX
  18P LOSS MUTATED    32   0  11
  18P LOSS WILD-TYPE 135   1  47
D72V6, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  M0               32                135
  M1                0                  1
  MX               11                 47
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V7, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    32  64
  18P LOSS WILD-TYPE 100 292
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     32   64
  18P LOSS WILD-TYPE  100  292
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE               32                100
  MALE                 64                292
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  18P LOSS MUTATED                                      94
  18P LOSS WILD-TYPE                                   383
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  18P LOSS MUTATED                                                             1
  18P LOSS WILD-TYPE                                                           0
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  18P LOSS MUTATED                                                     1
  18P LOSS WILD-TYPE                                                   9
D72V8, multiclass
                                                             clus
vv                                                            18P LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     94
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        1
                                                             clus
vv                                                            18P LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      383
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                  0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                          9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V9, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    17  79
  18P LOSS WILD-TYPE  62 330
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     17   79
  18P LOSS WILD-TYPE   62  330
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  NO                17                 62
  YES               79                330
[1] 2 2
[1] FALSE
D72V10, continuous
D72V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18P LOSS MUTATED                                  0     2
  18P LOSS WILD-TYPE                                2     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18P LOSS MUTATED                          12    79
  18P LOSS WILD-TYPE                        32   336
D72V12, multiclass
                                  clus
vv                                 18P LOSS MUTATED 18P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           2                  9
  BLACK OR AFRICAN AMERICAN                      12                 32
  WHITE                                          79                336
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V13, binary
                    cls
clus                   0   1
  18P LOSS MUTATED     9  79
  18P LOSS WILD-TYPE  15 352
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      9   79
  18P LOSS WILD-TYPE   15  352
                        clus
vv                       18P LOSS MUTATED 18P LOSS WILD-TYPE
  HISPANIC OR LATINO                    9                 15
  NOT HISPANIC OR LATINO               79                352
[1] 2 2
[1] FALSE

Clustering(73) Variable = 18Q LOSS MUTATION ANALYSIS
D73V1, survival
                    sevent
clus2                  0   1
  18Q LOSS MUTATED   118  49
  18Q LOSS WILD-TYPE 183  64
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               167                247 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                49                 64 
$`18Q LOSS MUTATED`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6868 
         102          462          283          623         1636          190 
TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4II 
         451          384          113          236          895          918 
TCGA-BA-A6D8 TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DL TCGA-BB-4224 TCGA-BB-7862 
         850          216          182          623          278          536 
TCGA-BB-7872 TCGA-BB-8601 TCGA-C9-A47Z TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 
         436          624            5          721         1157          142 
TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4735 TCGA-CN-4737 TCGA-CN-4739 TCGA-CN-4740 
        1230         1151         1250          625         1330          811 
TCGA-CN-5355 TCGA-CN-5363 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 
        1007         1977         1966         1966         1975          683 
TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6019 TCGA-CN-6022 TCGA-CN-6994 TCGA-CN-6996 
         630          933          432          202          735          432 
TCGA-CN-6998 TCGA-CN-A499 TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A641 
          46          535          225          526          348          367 
TCGA-CQ-5325 TCGA-CQ-5332 TCGA-CQ-6218 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 
         654          317         1253         1057          985         1959 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7072 
        1959         1179         1560         1007          509         1950 
TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CB TCGA-CQ-A4CG TCGA-CR-5247 TCGA-CR-6474 
        1353         1960          893          391          358         1971 
TCGA-CR-6484 TCGA-CR-6493 TCGA-CR-7365 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7377 
         354         1956         1191          889           30         1968 
TCGA-CR-7386 TCGA-CR-7399 TCGA-CR-7402 TCGA-CV-5435 TCGA-CV-5439 TCGA-CV-5440 
        1430          181          911         1438          546         1978 
TCGA-CV-5441 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5973 TCGA-CV-5976 
        2886         2437          519          406         2641         1478 
TCGA-CV-5977 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6935 TCGA-CV-6942 TCGA-CV-6945 
        1840         1315         1665         1969         3835         1969 
TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 
        1957         1969         3837         1959         1970         1970 
TCGA-CV-7101 TCGA-CV-7180 TCGA-CV-7235 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 
        1939         1987         1952          954          797         1967 
TCGA-CV-7424 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7440 
        1947         1972         1937         1984         1958         1981 
TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JZ TCGA-CV-A6K1 TCGA-CX-7086 TCGA-CX-7219 
         670          110          714          685          237          828 
TCGA-D6-6516 TCGA-D6-6823 TCGA-D6-6825 TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-DQ-5624 
         773          701          491          106          539         1778 
TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-7588 TCGA-DQ-7595 TCGA-F7-7848 TCGA-F7-8489 
         516         1030         1965          324         1131          658 
TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-8501 
          15           92           14           13            6           58 
TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-7917 TCGA-HD-8224 
         133          414          403            2           37           55 
TCGA-HD-8635 TCGA-HD-A6HZ TCGA-IQ-7630 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H 
          25          111          485          588          360          412 
TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-MT-A51W TCGA-MT-A51X 
         351          360          224          552           14           34 
TCGA-MT-A67D TCGA-P3-A5QA TCGA-P3-A6T0 TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A64Z 
          56         1726          578         1968          400          553 
TCGA-QK-A652 TCGA-QK-A6IH TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-AA3K TCGA-UF-A71B 
         357          228          149          135          168         1319 
TCGA-UF-A71D TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JS 
        1252          484          735         1497          413 

$`18Q LOSS WILD-TYPE`
TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 
         415         1983          276          248          722         1288 
TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5559 TCGA-BA-6869 TCGA-BA-6871 
        1762          520          725         1747          644           63 
TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A6DA TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A8YP 
         855          622          351         1976          314          142 
TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 
         187         2878          140          133          558          310 
TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-8596 
         423          687          638         1153          428         1955 
TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
           4          799          392          817          993          642 
TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5358 
         395         1960         1268         1988         1045          173 
TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5365 TCGA-CN-5374 TCGA-CN-6012 TCGA-CN-6013 
        1980         1081         1980          290          629          628 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6023 
         594          629           45           98         1970         1110 
TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A498 
         224          318          611          394          429          443 
TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A6V1 
         391          904          645          484          175          223 
TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 
         298         1466         1207         1660         1422         1393 
TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7068 
        1399          341          129         1000         1750         1309 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CD TCGA-CQ-A4CE 
        1274          877          707         1963          998          785 
TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 
         303          950         2562         1663         1152          799 
TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6477 
        1777         1521         1966         1050         1125          514 
TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6488 
        1969          362          311          345          234          379 
TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-7364 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 
         350          479         1435         1440         1245         1960 
TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7376 TCGA-CR-7379 TCGA-CR-7382 
         105         1979          759          972         1036          796 
TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 
        1954          997         1951          392          907          913 
TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 
         946          908          898          930          216          156 
TCGA-CR-7401 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 
        1077         1472         1955          522         1950         3295 
TCGA-CV-5436 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5971 TCGA-CV-5978 TCGA-CV-6433 
         584         2327         1958          701          215          641 
TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6943 
        1899         1970         1948         1952         1959         1948 
TCGA-CV-6952 TCGA-CV-6961 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7183 
        1966         1959         1936         1959         1945         1979 
TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7406 
        1444         1095         1960         1976         1099         1974 
TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7435 
        1948         1955         1957         1937         1973         1959 
TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 
         851         1945         5480         1960         1940         1946 
TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN 
        1954         1722         1977         1970         1075          906 
TCGA-CV-A6JO TCGA-CV-A6JY TCGA-CV-A6K0 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 
        1959          646          606         1950          317          321 
TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8569 TCGA-D6-A4ZB 
         292           77          154          568          128          376 
TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES 
         483          232          435          424          368          389 
TCGA-D6-A74Q TCGA-DQ-5625 TCGA-DQ-5631 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 
         338         1081          548          575          775          622 
TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7596 TCGA-F7-8298 TCGA-F7-A50J 
         299          369          368          340          490          585 
TCGA-F7-A61S TCGA-F7-A61V TCGA-H7-7774 TCGA-H7-A76A TCGA-HD-7753 TCGA-HD-7754 
           3          384          407          206            5           25 
TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6I0 
          44           24           11           49           10           33 
TCGA-HL-7533 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61J TCGA-KU-A6H7 TCGA-KU-A6H8 
        1057          122          441          440          378          168 
TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 
         392          111          112          254          240          910 
TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T2 TCGA-QK-A6IF TCGA-QK-A6IG 
        1559         1120         1954         1917          245          218 
TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A8Z7 TCGA-QK-A8ZB TCGA-QK-AA3J 
         225          387          567          198          135          157 
TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JH 
        1326         1663         1278         1043         1894          665 
TCGA-UF-A7JJ 
         214 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 2                  3 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              3837               5480 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               670                725 
[1] "2.0 - 3837.0 (670.0)" "3.0 - 5480.0 (725.0)"
[1] "hr=" "1"  
D73V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  18Q LOSS MUTATED        11       33        30       104         5         0
  18Q LOSS WILD-TYPE      15       42        44       131         7         1
D73V3, multiclass
           clus
vv          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  STAGE I                 11                 15
  STAGE II                33                 42
  STAGE III               30                 44
  STAGE IVA              104                131
  STAGE IVB                5                  7
  STAGE IVC                0                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1 T2 T3 T4
  18Q LOSS MUTATED      20 55 39 70
  18Q LOSS WILD-TYPE    27 72 55 92
D73V4, multiclass
       clus
vv      18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T0+T1               20                 27
  T2                  55                 72
  T3                  39                 55
  T4                  70                 92
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  18Q LOSS MUTATED    66  28  72   3
  18Q LOSS WILD-TYPE 104  35  80   5
D73V5, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  N0               66                104
  N1               28                 35
  N2               72                 80
  N3                3                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  18Q LOSS MUTATED    63   0  28
  18Q LOSS WILD-TYPE 104   1  30
D73V6, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  M0               63                104
  M1                0                  1
  MX               28                 30
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V7, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED    50 148
  18Q LOSS WILD-TYPE  82 208
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     50  148
  18Q LOSS WILD-TYPE   82  208
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE               50                 82
  MALE                148                208
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  18Q LOSS MUTATED                                     196
  18Q LOSS WILD-TYPE                                   281
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  18Q LOSS MUTATED                                                             1
  18Q LOSS WILD-TYPE                                                           0
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  18Q LOSS MUTATED                                                     1
  18Q LOSS WILD-TYPE                                                   9
D73V8, multiclass
                                                             clus
vv                                                            18Q LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    196
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        1
                                                             clus
vv                                                            18Q LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      281
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                  0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                          9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V9, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED    36 162
  18Q LOSS WILD-TYPE  43 247
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     36  162
  18Q LOSS WILD-TYPE   43  247
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  NO                36                 43
  YES              162                247
[1] 2 2
[1] FALSE
D73V10, continuous
D73V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18Q LOSS MUTATED                                  0     7
  18Q LOSS WILD-TYPE                                2     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18Q LOSS MUTATED                          24   160
  18Q LOSS WILD-TYPE                        20   255
D73V12, multiclass
                                  clus
vv                                 18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           7                  4
  BLACK OR AFRICAN AMERICAN                      24                 20
  WHITE                                         160                255
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V13, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED    12 172
  18Q LOSS WILD-TYPE  12 259
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     12  172
  18Q LOSS WILD-TYPE   12  259
                        clus
vv                       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   12                 12
  NOT HISPANIC OR LATINO              172                259
[1] 2 2
[1] FALSE

Clustering(74) Variable = 19P LOSS MUTATION ANALYSIS
D74V1, survival
                    sevent
clus2                  0   1
  19P LOSS MUTATED    46  30
  19P LOSS WILD-TYPE 255  83
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                76                338 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                30                 83 
$`19P LOSS MUTATED`
TCGA-BA-4075 TCGA-BA-5149 TCGA-BA-5153 TCGA-BA-6868 TCGA-BA-A4IF TCGA-BA-A6DA 
         283          248         1762          190          895          351 
TCGA-BB-4227 TCGA-BB-8596 TCGA-C9-A47Z TCGA-CN-4725 TCGA-CN-4729 TCGA-CN-4737 
         133         1955            5         1157          392          625 
TCGA-CN-4738 TCGA-CN-5356 TCGA-CN-5363 TCGA-CN-5370 TCGA-CN-5374 TCGA-CN-6012 
        1960         1045         1977         1975          290          629 
TCGA-CN-6018 TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 
          45           98          202          394          735          432 
TCGA-CQ-5330 TCGA-CQ-6223 TCGA-CQ-7064 TCGA-CQ-7069 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
        1393         1057         1560         1274         1960          707 
TCGA-CR-6477 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7373 TCGA-CR-7377 TCGA-CR-7398 
         514         1435         1191          889         1968          156 
TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5439 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6441 
        3295         1438          546         1315         1665         1970 
TCGA-CV-6941 TCGA-CV-6945 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7180 TCGA-CV-7254 
        1959         1969         1970         1970         1987         1976 
TCGA-CV-7430 TCGA-CV-7440 TCGA-CV-A6JN TCGA-CV-A6K1 TCGA-D6-6825 TCGA-D6-6826 
        1972         1981          906          685          491          154 
TCGA-D6-8569 TCGA-D6-A6EM TCGA-D6-A6EQ TCGA-DQ-5624 TCGA-DQ-7588 TCGA-DQ-7592 
         128          232          368         1778         1965          299 
TCGA-F7-7848 TCGA-F7-A50I TCGA-F7-A61W TCGA-HD-7753 TCGA-HL-7533 TCGA-IQ-A61G 
        1131           92           14            5         1057          360 
TCGA-IQ-A61L TCGA-MT-A51X TCGA-P3-A6SX TCGA-QK-A652 TCGA-QK-A6IJ TCGA-QK-A8Z9 
         351           34         1954          357          387          149 
TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-UF-A719 TCGA-UF-A7JC 
         135          135         1663          484 

$`19P LOSS WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5151 
         102          462          415         1983          276          722 
TCGA-BA-5152 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 
        1288          520          725          623         1636         1747 
TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 
         644          451           63          384          113          236 
TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DB TCGA-BA-A6DE 
         855          622          918          850          216          182 
TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 
        1976          314          623          142          187         2878 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 
         278          140          558          310          536          423 
TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8601 
         687          638         1153          428          436          624 
TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 
           4          799          721          142         1230         1151 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4739 
         817          993          642         1250          395         1330 
TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5359 
         811         1268         1988         1007          173         1980 
TCGA-CN-5360 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5373 TCGA-CN-6010 
        1081         1980         1966         1966          683          630 
TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6021 
         933          628          594          629          432         1970 
TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6997 TCGA-CN-6998 
        1110          224          318          611          429           46 
TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T 
         443          535          391          904          645          225 
TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A6V1 
         526          484          348          175          367          223 
TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 
         298         1466         1207          654         1660         1422 
TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 
        1399          317          341          129         1253         1000 
TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7065 
         985         1959         1959         1179         1750         1007 
TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4CA 
         509         1309          877         1950         1353         1963 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI 
         893          998          785          391          303          950 
TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 
        2562          358         1663         1152          799         1777 
TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6478 
        1521         1966         1050         1125         1971         1969 
TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 
         362          311          345          354          234          379 
TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 
         350          479         1956         1440         1245         1960 
TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7379 
         105         1979          759           30          972         1036 
TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 
         796         1954          997         1430         1951          392 
TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 
         907          913          946          908          898          930 
TCGA-CR-7397 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 
         216          181         1077          911         1472         1955 
TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5436 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 
         522         1950          584         1978         2886         2327 
TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 
        1958         2437          519          406          701         2641 
TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6934 
        1478         1840          215          641         1899         1948 
TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6952 TCGA-CV-6954 
        1969         1952         3835         1948         1966         1957 
TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7099 TCGA-CV-7100 
        1969         1959         3837         1959         1936         1959 
TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7242 
        1939         1945         1979         1952         1444         1095 
TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7261 TCGA-CV-7406 
         954          797         1967         1960         1099         1974 
TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7428 
        1948         1955         1957         1947         1937         1973 
TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-A45O TCGA-CV-A45Q 
        1937         1984         1958         1959          851         1945 
TCGA-CV-A45R TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A464 
        5480         1960         1940         1946         1954         1722 
TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU 
        1977         1970         1075         1959          670          110 
TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 
         646          714          606         1950          317          321 
TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 
         237          828          773          292          701           77 
TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EO 
         568          106          539          376          483          435 
TCGA-D6-A6EP TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 
         424          389          338         1081          516         1030 
TCGA-DQ-5631 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7593 TCGA-DQ-7594 
         548          575          775          622          369          368 
TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50J 
         324          340          490          658           15          585 
TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8501 
           3          384           13            6          407           58 
TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7754 
         133          414          403          206            2           25 
TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 
          37           55           44           24           25           11 
TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-IQ-7630 TCGA-IQ-7631 
          49           10          111           33          485          122 
TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61O TCGA-KU-A66S 
         441          588          412          440          360          224 
TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A67A TCGA-MT-A67D 
         552          378          168           14          392           56 
TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QA 
         111          112          254          240          910         1726 
TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-P3-A6T8 
        1559         1120          578         1917         1968          400 
TCGA-QK-A64Z TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6V9 
         553          245          218          228          225          567 
TCGA-QK-A8Z7 TCGA-QK-AA3J TCGA-QK-AA3K TCGA-UF-A718 TCGA-UF-A71B TCGA-UF-A71D 
         198          157          168         1326         1319         1252 
TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH 
        1278         1043         1894          735         1497          665 
TCGA-UF-A7JJ TCGA-UF-A7JS 
         214          413 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 5                  2 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              3295               5480 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
               721                694 
[1] "5.0 - 3295.0 (721.0)" "2.0 - 5480.0 (694.0)"
[1] "hr=" "1.3"
D74V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  19P LOSS MUTATED         2       14        22        42         1         0
  19P LOSS WILD-TYPE      24       61        52       193        11         1
D74V3, multiclass
           clus
vv          19P LOSS MUTATED 19P LOSS WILD-TYPE
  STAGE I                  2                 24
  STAGE II                14                 61
  STAGE III               22                 52
  STAGE IVA               42                193
  STAGE IVB                1                 11
  STAGE IVC                0                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  19P LOSS MUTATED       5  28  21  28
  19P LOSS WILD-TYPE    42  99  73 134
D74V4, multiclass
       clus
vv      19P LOSS MUTATED 19P LOSS WILD-TYPE
  T0+T1                5                 42
  T2                  28                 99
  T3                  21                 73
  T4                  28                134
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  19P LOSS MUTATED    26  19  28   1
  19P LOSS WILD-TYPE 144  44 124   7
D74V5, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  N0               26                144
  N1               19                 44
  N2               28                124
  N3                1                  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"
                    vv
clus                  M0  M1  MX
  19P LOSS MUTATED    33   0   6
  19P LOSS WILD-TYPE 134   1  52
D74V6, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  M0               33                134
  M1                0                  1
  MX                6                 52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V7, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    19  71
  19P LOSS WILD-TYPE 113 285
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     19   71
  19P LOSS WILD-TYPE  113  285
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE               19                113
  MALE                 71                285
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  19P LOSS MUTATED                                      90
  19P LOSS WILD-TYPE                                   387
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  19P LOSS MUTATED                                                             0
  19P LOSS WILD-TYPE                                                           1
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  19P LOSS MUTATED                                                     0
  19P LOSS WILD-TYPE                                                  10
D74V8, multiclass
                                                             clus
vv                                                            19P LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     90
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        0
                                                             clus
vv                                                            19P LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      387
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                  1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V9, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    19  71
  19P LOSS WILD-TYPE  60 338
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     19   71
  19P LOSS WILD-TYPE   60  338
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  NO                19                 60
  YES               71                338
[1] 2 2
[1] FALSE
D74V10, continuous
D74V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19P LOSS MUTATED                                  1     2
  19P LOSS WILD-TYPE                                1     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19P LOSS MUTATED                          10    73
  19P LOSS WILD-TYPE                        34   342
D74V12, multiclass
                                  clus
vv                                 19P LOSS MUTATED 19P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  1
  ASIAN                                           2                  9
  BLACK OR AFRICAN AMERICAN                      10                 34
  WHITE                                          73                342
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V13, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     6  80
  19P LOSS WILD-TYPE  18 351
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      6   80
  19P LOSS WILD-TYPE   18  351
                        clus
vv                       19P LOSS MUTATED 19P LOSS WILD-TYPE
  HISPANIC OR LATINO                    6                 18
  NOT HISPANIC OR LATINO               80                351
[1] 2 2
[1] FALSE

Clustering(75) Variable = 19Q LOSS MUTATION ANALYSIS
D75V1, survival
                    sevent
clus2                  0   1
  19Q LOSS MUTATED    45  24
  19Q LOSS WILD-TYPE 256  89
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                69                345 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                24                 89 
$`19Q LOSS MUTATED`
TCGA-BA-4075 TCGA-BA-5149 TCGA-BA-5555 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6871 
         283          248          520          190          451           63 
TCGA-BA-6873 TCGA-BA-A4IF TCGA-BA-A6DA TCGA-BB-4227 TCGA-BB-8596 TCGA-BB-8601 
         113          895          351          133         1955          624 
TCGA-C9-A47Z TCGA-CN-4725 TCGA-CN-4737 TCGA-CN-5356 TCGA-CN-5363 TCGA-CN-5374 
           5         1157          625         1045         1977          290 
TCGA-CN-6018 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 
          45          611          394          735          432          429 
TCGA-CN-A49A TCGA-CQ-7064 TCGA-CQ-7069 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CI 
         391         1560         1274         1960          707          950 
TCGA-CR-6477 TCGA-CR-7365 TCGA-CR-7373 TCGA-CR-7377 TCGA-CR-7398 TCGA-CV-5432 
         514         1191          889         1968          156         1950 
TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5439 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6441 
        3295         1438          546         1315         1665         1970 
TCGA-CV-6941 TCGA-CV-6960 TCGA-CV-7097 TCGA-CV-7180 TCGA-CV-7254 TCGA-CV-7261 
        1959         1969         1970         1987         1976         1099 
TCGA-CV-7430 TCGA-CV-A6JN TCGA-CV-A6K1 TCGA-D6-6517 TCGA-D6-6826 TCGA-D6-8569 
        1972          906          685          292          154          128 
TCGA-D6-A6EM TCGA-D6-A6EP TCGA-DQ-7588 TCGA-F7-A61W TCGA-HD-7753 TCGA-IQ-A61L 
         232          424         1965           14            5          351 
TCGA-MT-A51X TCGA-P3-A6T2 TCGA-QK-A652 TCGA-QK-A6IJ TCGA-QK-A8ZA TCGA-QK-A8ZB 
          34         1917          357          387          135          135 
TCGA-UF-A719 TCGA-UF-A71D TCGA-UF-A7JC 
        1663         1252          484 

$`19Q LOSS WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5151 
         102          462          415         1983          276          722 
TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 
        1288         1762          725          623         1636         1747 
TCGA-BA-6869 TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II 
         644          384          236          855          622          918 
TCGA-BA-A6D8 TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A6DL 
         850          216          182         1976          314          623 
TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4228 
         142          187         2878          278          140          558 
TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 
         310          536          423          687          638         1153 
TCGA-BB-7871 TCGA-BB-7872 TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4726 
         428          436            4          799          721          142 
TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
        1230         1151          392          817          993          642 
TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 
        1250          395         1960         1330          811         1268 
TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5365 
        1988         1007          173         1980         1081         1980 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6010 TCGA-CN-6011 
        1966         1966         1975          683          630          933 
TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6020 
         629          628          594          629          432           98 
TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6998 
        1970          202         1110          224          318           46 
TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U 
         443          535          904          645          225          526 
TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A6V1 TCGA-CN-A6V3 
         484          348          175          367          223          298 
TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 
        1466         1207          654         1660         1422         1393 
TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 
        1399          317          341          129         1253         1000 
TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 
        1057          985         1959         1959         1179         1750 
TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 
        1007          509         1309          877         1950         1353 
TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH 
        1963          893          998          785          391          303 
TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 
        2562          358         1663         1152          799         1777 
TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6478 
        1521         1966         1050         1125         1971         1969 
TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 
         362          311          345          354          234          379 
TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7367 TCGA-CR-7368 
         350          479         1956         1435         1440         1245 
TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7374 TCGA-CR-7376 
        1960          105         1979          759           30          972 
TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 
        1036          796         1954          997         1430         1951 
TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 
         392          907          913          946          908          898 
TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 
         930          216          181         1077          911         1472 
TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5436 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 
        1955          522          584         1978         2886         2327 
TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 
        1958         2437          519          406          701         2641 
TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6934 
        1478         1840          215          641         1899         1948 
TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6952 
        1969         1952         3835         1948         1969         1966 
TCGA-CV-6954 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7099 
        1957         1959         3837         1959         1970         1936 
TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 
        1959         1939         1945         1979         1952         1444 
TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7406 
        1095          954          797         1967         1960         1974 
TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7428 
        1948         1955         1957         1947         1937         1973 
TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45O 
        1937         1984         1958         1959         1981          851 
TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 
        1945         5480         1960         1940         1946         1954 
TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JO TCGA-CV-A6JT 
        1722         1977         1970         1075         1959          670 
TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K2 TCGA-CX-7082 
         110          646          714          606         1950          317 
TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6823 TCGA-D6-6824 
         321          237          828          773          701           77 
TCGA-D6-6825 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK 
         491          568          106          539          376          483 
TCGA-D6-A6EO TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 
         435          368          389          338         1778         1081 
TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 
         516         1030          548          575          775          622 
TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 
         299          369          368          324          340         1131 
TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S 
         490          658           15           92          585            3 
TCGA-F7-A61V TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 
         384           13            6          407           58          133 
TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7917 
         414          403          206            2           25           37 
TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 
          55           44           24           25           11           49 
TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 
          10          111           33         1057          485          122 
TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61O 
         441          588          360          412          440          360 
TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A67A 
         224          552          378          168           14          392 
TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 
          56          111          112          254          240          910 
TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T4 
        1726         1559         1120         1954          578         1968 
TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II 
         400          553          245          218          228          225 
TCGA-QK-A6V9 TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-QK-AA3J TCGA-QK-AA3K TCGA-UF-A718 
         567          198          149          157          168         1326 
TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JD TCGA-UF-A7JF 
        1319         1278         1043         1894          735         1497 
TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JS 
         665          214          413 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 5                  2 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              3295               5480 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
               624                721 
[1] "5.0 - 3295.0 (624.0)" "2.0 - 5480.0 (721.0)"
[1] "hr=" "1.3"
D75V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  19Q LOSS MUTATED         1       10        22        37         2         0
  19Q LOSS WILD-TYPE      25       65        52       198        10         1
D75V3, multiclass
           clus
vv          19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  STAGE I                  1                 25
  STAGE II                10                 65
  STAGE III               22                 52
  STAGE IVA               37                198
  STAGE IVB                2                 10
  STAGE IVC                0                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  19Q LOSS MUTATED       4  21  24  23
  19Q LOSS WILD-TYPE    43 106  70 139
D75V4, multiclass
       clus
vv      19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  T0+T1                4                 43
  T2                  21                106
  T3                  24                 70
  T4                  23                139
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  19Q LOSS MUTATED    25  14  27   1
  19Q LOSS WILD-TYPE 145  49 125   7
D75V5, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  N0               25                145
  N1               14                 49
  N2               27                125
  N3                1                  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"
                    vv
clus                  M0  M1  MX
  19Q LOSS MUTATED    28   0   7
  19Q LOSS WILD-TYPE 139   1  51
D75V6, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  M0               28                139
  M1                0                  1
  MX                7                 51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V7, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    18  61
  19Q LOSS WILD-TYPE 114 295
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     18   61
  19Q LOSS WILD-TYPE  114  295
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE               18                114
  MALE                 61                295
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  19Q LOSS MUTATED                                      78
  19Q LOSS WILD-TYPE                                   399
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  19Q LOSS MUTATED                                                             0
  19Q LOSS WILD-TYPE                                                           1
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  19Q LOSS MUTATED                                                     1
  19Q LOSS WILD-TYPE                                                   9
D75V8, multiclass
                                                             clus
vv                                                            19Q LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     78
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        1
                                                             clus
vv                                                            19Q LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      399
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                  1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                          9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V9, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    15  64
  19Q LOSS WILD-TYPE  64 345
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     15   64
  19Q LOSS WILD-TYPE   64  345
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  NO                15                 64
  YES               64                345
[1] 2 2
[1] FALSE
D75V10, continuous
D75V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19Q LOSS MUTATED                                  0     2
  19Q LOSS WILD-TYPE                                2     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19Q LOSS MUTATED                          12    61
  19Q LOSS WILD-TYPE                        32   354
D75V12, multiclass
                                  clus
vv                                 19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           2                  9
  BLACK OR AFRICAN AMERICAN                      12                 32
  WHITE                                          61                354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V13, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     5  68
  19Q LOSS WILD-TYPE  19 363
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      5   68
  19Q LOSS WILD-TYPE   19  363
                        clus
vv                       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    5                 19
  NOT HISPANIC OR LATINO               68                363
[1] 2 2
[1] FALSE

Clustering(76) Variable = 20P LOSS MUTATION ANALYSIS
D76V1, survival
                    sevent
clus2                  0   1
  20P LOSS MUTATED    27  15
  20P LOSS WILD-TYPE 274  98
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                42                372 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                15                 98 
$`20P LOSS MUTATED`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-5152 TCGA-BA-5555 
         462          283          415         1983         1288          520 
TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6873 TCGA-BB-4227 TCGA-BB-7866 TCGA-BB-8601 
         451           63          113          133          638          624 
TCGA-CN-6011 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-A63W TCGA-CQ-A4CD TCGA-CQ-A4CG 
         933          394          735          348          998          391 
TCGA-CR-6474 TCGA-CR-6478 TCGA-CR-7364 TCGA-CR-7374 TCGA-CR-7379 TCGA-CR-7383 
        1971         1969         1435           30         1036         1954 
TCGA-CV-5440 TCGA-CV-7091 TCGA-CV-7101 TCGA-CV-7235 TCGA-CV-7254 TCGA-CV-7418 
        1978         1959         1939         1952         1976         1955 
TCGA-CV-7435 TCGA-CV-A460 TCGA-D6-6823 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-F7-7848 
        1959         1946          701          575          775         1131 
TCGA-F7-8298 TCGA-F7-A623 TCGA-HD-7917 TCGA-IQ-7630 TCGA-QK-A6V9 TCGA-UF-A719 
         490            6           37          485          567         1663 

$`20P LOSS WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5153 TCGA-BA-5556 
         102          276          248          722         1762          725 
TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6872 
         623         1636         1747          190          644          384 
TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 
         236          895          855          622          918          850 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A6DL 
         351          216          182         1976          314          623 
TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4228 
         142          187         2878          278          140          558 
TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-7871 
         310          536          423          687         1153          428 
TCGA-BB-7872 TCGA-BB-8596 TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 
         436         1955            5            4          799          721 
TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 
        1157          142         1230         1151          392          817 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 
         993          642         1250          395          625         1960 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 
        1330          811         1268         1988         1007         1045 
TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 
         173         1980         1081         1977         1980         1966 
TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6012 
        1966         1975          683          290          630          629 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 
         628          594          629           45          432           98 
TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 
        1970          202         1110          224          318          611 
TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A 
         432          429           46          443          535          391 
TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63Y 
         904          645          225          526          484          175 
TCGA-CN-A641 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
         367          223          298         1466         1207          654 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 
        1660         1422         1393         1399          317          341 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 
         129         1253         1000         1057          985         1959 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 
        1959         1179         1750         1560         1007          509 
TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 
        1309         1274          877         1950         1353         1960 
TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CE TCGA-CQ-A4CH TCGA-CQ-A4CI 
         707         1963          893          785          303          950 
TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 
        2562          358         1663         1152          799         1777 
TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6477 TCGA-CR-6480 
        1521         1966         1050         1125          514          362 
TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 
         311          345          354          234          379          350 
TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 
         479         1956         1191         1440         1245         1960 
TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7376 TCGA-CR-7377 
         105         1979          759          889          972         1968 
TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 
         796          997         1430         1951          392          907 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 
         913          946          908          898          930          216 
TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 
         156          181         1077          911         1472         1955 
TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 
         522         1950         3295         1438          584          546 
TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 
        2886         2327         1958         2437          519          406 
TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 
         701         2641         1478         1840          215         1315 
TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 
        1665          641         1899         1970         1948         1969 
TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6952 
        1952         1959         3835         1948         1969         1966 
TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7095 TCGA-CV-7097 
        1957         1969         1959         3837         1970         1970 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7238 
        1936         1959         1945         1987         1979         1444 
TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7261 
        1095          954          797         1967         1960         1099 
TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7428 
        1974         1948         1957         1947         1937         1973 
TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7440 TCGA-CV-A45O 
        1972         1937         1984         1958         1981          851 
TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A461 TCGA-CV-A464 
        1945         5480         1960         1940         1954         1722 
TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT 
        1977         1970         1075          906         1959          670 
TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 
         110          646          714          606          685         1950 
TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6517 
         317          321          237          828          773          292 
TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 
          77          491          154          568          106          128 
TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP 
         539          376          483          232          435          424 
TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 
         368          389          338         1778         1081          516 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 
        1030          548         1965          622          299          369 
TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I 
         368          324          340          658           15           92 
TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-H7-7774 
         585            3          384           14           13          407 
TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 
          58          133          414          403          206            2 
TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 
           5           25           55           44           24           25 
TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 
          11           49           10          111           33         1057 
TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J 
         122          441          588          360          412          440 
TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 
         351          360          224          552          378          168 
TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G 
          14           34          392           56          111          112 
TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW 
         254          240          910         1726         1559         1120 
TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A64Z 
        1954          578         1917         1968          400          553 
TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ 
         357          245          218          228          225          387 
TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K 
         198          149          135          135          157          168 
TCGA-UF-A718 TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA 
        1326         1319         1252         1278         1043         1894 
TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JS 
         484          735         1497          665          214          413 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 6                  2 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
              1983               5480 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
               718                694 
[1] "6.0 - 1983.0 (718.0)" "2.0 - 5480.0 (694.0)"
[1] "hr=" "1.3"
D76V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  20P LOSS MUTATED         3       10         5        20         0         0
  20P LOSS WILD-TYPE      23       65        69       215        12         1
D76V3, multiclass
           clus
vv          20P LOSS MUTATED 20P LOSS WILD-TYPE
  STAGE I                  3                 23
  STAGE II                10                 65
  STAGE III                5                 69
  STAGE IVA               20                215
  STAGE IVB                0                 12
  STAGE IVC                0                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  20P LOSS MUTATED       5  12   8  13
  20P LOSS WILD-TYPE    42 115  86 149
D76V4, multiclass
       clus
vv      20P LOSS MUTATED 20P LOSS WILD-TYPE
  T0+T1                5                 42
  T2                  12                115
  T3                   8                 86
  T4                  13                149
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  20P LOSS MUTATED    18   2  14   0
  20P LOSS WILD-TYPE 152  61 138   8
D76V5, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  N0               18                152
  N1                2                 61
  N2               14                138
  N3                0                  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"
                    vv
clus                  M0  M1  MX
  20P LOSS MUTATED    17   0   2
  20P LOSS WILD-TYPE 150   1  56
D76V6, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  M0               17                150
  M1                0                  1
  MX                2                 56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V7, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    11  35
  20P LOSS WILD-TYPE 121 321
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     11   35
  20P LOSS WILD-TYPE  121  321
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE               11                121
  MALE                 35                321
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  20P LOSS MUTATED                                      46
  20P LOSS WILD-TYPE                                   431
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  20P LOSS MUTATED                                                             0
  20P LOSS WILD-TYPE                                                           1
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  20P LOSS MUTATED                                                     0
  20P LOSS WILD-TYPE                                                  10
D76V8, multiclass
                                                             clus
vv                                                            20P LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     46
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        0
                                                             clus
vv                                                            20P LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      431
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                  1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V9, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     9  37
  20P LOSS WILD-TYPE  70 372
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      9   37
  20P LOSS WILD-TYPE   70  372
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  NO                 9                 70
  YES               37                372
[1] 2 2
[1] FALSE
D76V10, continuous
D76V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20P LOSS MUTATED                                  0     0
  20P LOSS WILD-TYPE                                2    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20P LOSS MUTATED                           5    39
  20P LOSS WILD-TYPE                        39   376
D76V12, multiclass
                                  clus
vv                                 20P LOSS MUTATED 20P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                 11
  BLACK OR AFRICAN AMERICAN                       5                 39
  WHITE                                          39                376
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V13, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     2  42
  20P LOSS WILD-TYPE  22 389
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      2   42
  20P LOSS WILD-TYPE   22  389
                        clus
vv                       20P LOSS MUTATED 20P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                 22
  NOT HISPANIC OR LATINO               42                389
[1] 2 2
[1] FALSE

Clustering(77) Variable = 20Q LOSS MUTATION ANALYSIS
D77V1, survival
                    sevent
clus2                  0   1
  20Q LOSS MUTATED    18   8
  20Q LOSS WILD-TYPE 283 105
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                26                388 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 8                105 
$`20Q LOSS MUTATED`
TCGA-BA-5152 TCGA-BA-6870 TCGA-BA-6871 TCGA-BB-7866 TCGA-BB-8601 TCGA-CN-4729 
        1288          451           63          638          624          392 
TCGA-CN-5360 TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-6473 TCGA-CR-7370 TCGA-CR-7402 
        1081          950         2562         1125          105          911 
TCGA-CV-5440 TCGA-CV-7091 TCGA-CV-7101 TCGA-CV-7235 TCGA-CV-7254 TCGA-CV-7418 
        1978         1959         1939         1952         1976         1955 
TCGA-CV-7435 TCGA-CV-A460 TCGA-D6-6826 TCGA-DQ-7590 TCGA-HD-7917 TCGA-IQ-7630 
        1959         1946          154          775           37          485 
TCGA-KU-A6H7 TCGA-UF-A719 
         378         1663 

$`20Q LOSS WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 
         102          462          283          415         1983          276 
TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 
         248          722         1762          520          725          623 
TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6872 TCGA-BA-6873 
        1636         1747          190          644          384          113 
TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 
         236          895          855          622          918          850 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A6DL 
         351          216          182         1976          314          623 
TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 
         142          187         2878          278          140          133 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7870 
         558          310          536          423          687         1153 
TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 
         428          436         1955            5            4          799 
TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4730 
         721         1157          142         1230         1151          817 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 
         993          642         1250          395          625         1960 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 
        1330          811         1268         1988         1007         1045 
TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 
         173         1980         1977         1980         1966         1966 
TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 
        1975          683          290          630          933          629 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 
         628          594          629           45          432           98 
TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 
        1970          202         1110          224          318          611 
TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 
         394          735          432          429           46          443 
TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U 
         535          391          904          645          225          526 
TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A6V1 TCGA-CN-A6V3 
         484          348          175          367          223          298 
TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 
        1466         1207          654         1660         1422         1393 
TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 
        1399          317          341          129         1253         1000 
TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 
        1057          985         1959         1959         1179         1750 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 
        1560         1007          509         1309         1274          877 
TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB 
        1950         1353         1960          707         1963          893 
TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5247 TCGA-CR-5248 
         998          785          391          303          358         1663 
TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 
        1152          799         1777         1521         1966         1050 
TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 
        1971          514         1969          362          311          345 
TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 
         354          234          379          350          479         1956 
TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7371 
        1435         1191         1440         1245         1960         1979 
TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 
         759          889           30          972         1968         1036 
TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 
         796         1954          997         1430         1951          392 
TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 
         907          913          946          908          898          930 
TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7404 TCGA-CV-5430 
         216          156          181         1077         1472         1955 
TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 
         522         1950         3295         1438          584          546 
TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 
        2886         2327         1958         2437          519          406 
TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 
         701         2641         1478         1840          215         1315 
TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 
        1665          641         1899         1970         1948         1969 
TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6952 
        1952         1959         3835         1948         1969         1966 
TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7095 TCGA-CV-7097 
        1957         1969         1959         3837         1970         1970 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7238 
        1936         1959         1945         1987         1979         1444 
TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7261 
        1095          954          797         1967         1960         1099 
TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7428 
        1974         1948         1957         1947         1937         1973 
TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7440 TCGA-CV-A45O 
        1972         1937         1984         1958         1981          851 
TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A461 TCGA-CV-A464 
        1945         5480         1960         1940         1954         1722 
TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT 
        1977         1970         1075          906         1959          670 
TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 
         110          646          714          606          685         1950 
TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6517 
         317          321          237          828          773          292 
TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 
         701           77          491          568          106          128 
TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP 
         539          376          483          232          435          424 
TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 
         368          389          338         1778         1081          516 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7591 TCGA-DQ-7592 
        1030          548         1965          575          622          299 
TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 
         369          368          324          340         1131          490 
TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V 
         658           15           92          585            3          384 
TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 
          14           13            6          407           58          133 
TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 
         414          403          206            2            5           25 
TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 
          55           44           24           25           11           49 
TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7631 TCGA-IQ-7632 
          10          111           33         1057          122          441 
TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61L TCGA-IQ-A61O 
         588          360          412          440          351          360 
TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A 
         224          552          168           14           34          392 
TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 
          56          111          112          254          240          910 
TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 
        1726         1559         1120         1954          578         1917 
TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG 
        1968          400          553          357          245          218 
TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A8Z7 TCGA-QK-A8Z9 
         228          225          387          567          198          149 
TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-UF-A718 TCGA-UF-A71B 
         135          135          157          168         1326         1319 
TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD 
        1252         1278         1043         1894          484          735 
TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JS 
        1497          665          214          413 

  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                37                  2 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
              2562               5480 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
            1015.5              684.0 
[1] "37.0 - 2562.0 (1015.5)" "2.0 - 5480.0 (684.0)"  
[1] "hr=" "1.1"
D77V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  20Q LOSS MUTATED         1        8         4         7         0         0
  20Q LOSS WILD-TYPE      25       67        70       228        12         1
D77V3, multiclass
           clus
vv          20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  STAGE I                  1                 25
  STAGE II                 8                 67
  STAGE III                4                 70
  STAGE IVA                7                228
  STAGE IVB                0                 12
  STAGE IVC                0                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  20Q LOSS MUTATED       2  10   3   5
  20Q LOSS WILD-TYPE    45 117  91 157
D77V4, multiclass
       clus
vv      20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  T0+T1                2                 45
  T2                  10                117
  T3                   3                 91
  T4                   5                157
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  20Q LOSS MUTATED     8   3   6   0
  20Q LOSS WILD-TYPE 162  60 146   8
D77V5, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  N0                8                162
  N1                3                 60
  N2                6                146
  N3                0                  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"
                    vv
clus                  M0  M1  MX
  20Q LOSS MUTATED     7   0   1
  20Q LOSS WILD-TYPE 160   1  57
D77V6, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  M0                7                160
  M1                0                  1
  MX                1                 57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V7, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     6  22
  20Q LOSS WILD-TYPE 126 334
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      6   22
  20Q LOSS WILD-TYPE  126  334
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  FEMALE                6                126
  MALE                 22                334
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  20Q LOSS MUTATED                                      27
  20Q LOSS WILD-TYPE                                   450
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  20Q LOSS MUTATED                                                             0
  20Q LOSS WILD-TYPE                                                           1
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  20Q LOSS MUTATED                                                     1
  20Q LOSS WILD-TYPE                                                   9
D77V8, multiclass
                                                             clus
vv                                                            20Q LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     27
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        1
                                                             clus
vv                                                            20Q LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      450
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                  1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                          9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V9, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     4  24
  20Q LOSS WILD-TYPE  75 385
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      4   24
  20Q LOSS WILD-TYPE   75  385
     clus
vv    20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  NO                 4                 75
  YES               24                385
[1] 2 2
[1] FALSE
D77V10, continuous
D77V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20Q LOSS MUTATED                                  0     0
  20Q LOSS WILD-TYPE                                2    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20Q LOSS MUTATED                           3    24
  20Q LOSS WILD-TYPE                        41   391
D77V12, multiclass
                                  clus
vv                                 20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                 11
  BLACK OR AFRICAN AMERICAN                       3                 41
  WHITE                                          24                391
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V13, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     1  25
  20Q LOSS WILD-TYPE  23 406
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      1   25
  20Q LOSS WILD-TYPE   23  406
                        clus
vv                       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 23
  NOT HISPANIC OR LATINO               25                406
[1] 2 2
[1] FALSE

Clustering(78) Variable = 21Q LOSS MUTATION ANALYSIS
D78V1, survival
                    sevent
clus2                  0   1
  21Q LOSS MUTATED   109  44
  21Q LOSS WILD-TYPE 192  69
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               153                261 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                44                 69 
$`21Q LOSS MUTATED`
TCGA-4P-AA8J TCGA-BA-4075 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6870 
         102          283         1636         1747          190          451 
TCGA-BA-6871 TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BB-7862 TCGA-BB-7864 TCGA-BB-8596 
          63          850          351          536          687         1955 
TCGA-BB-8601 TCGA-C9-A47Z TCGA-CN-4725 TCGA-CN-4728 TCGA-CN-4736 TCGA-CN-4738 
         624            5         1157         1151          395         1960 
TCGA-CN-4739 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5370 
        1330         1268         1988         1977         1980         1975 
TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6012 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6021 
         290          630          629           45          432         1970 
TCGA-CN-6022 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A499 
         202          735          432          429           46          535 
TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63W TCGA-CQ-5323 TCGA-CQ-5330 TCGA-CQ-5332 
         904          225          348         1466         1393          317 
TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 
        1057          985         1179         1560         1007          509 
TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CA 
        1274         1950         1353         1960          707         1963 
TCGA-CQ-A4CE TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5247 TCGA-CR-6477 TCGA-CR-6484 
         785          303          950          358          514          354 
TCGA-CR-6491 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 
         350         1191         1440         1960          105         1979 
TCGA-CR-7373 TCGA-CR-7388 TCGA-CR-7399 TCGA-CV-5431 TCGA-CV-5439 TCGA-CV-5440 
         889         1951          181          522          546         1978 
TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 
        2437          519         1478         1840          215         1315 
TCGA-CV-6003 TCGA-CV-6934 TCGA-CV-6941 TCGA-CV-6954 TCGA-CV-6961 TCGA-CV-7090 
        1665         1948         1959         1957         1959         3837 
TCGA-CV-7091 TCGA-CV-7097 TCGA-CV-7101 TCGA-CV-7180 TCGA-CV-7235 TCGA-CV-7242 
        1959         1970         1939         1987         1952         1095 
TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7422 TCGA-CV-7424 
         797         1967         1976         1099         1957         1947 
TCGA-CV-7432 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A6JN TCGA-CV-A6JU TCGA-CX-7082 
        1937         1959         1981          906          110          317 
TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6823 TCGA-D6-6826 TCGA-D6-A4Z9 
         237          828          773          701          154          539 
TCGA-D6-A4ZB TCGA-D6-A6EM TCGA-D6-A6EQ TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5629 
         376          232          368          338         1778          516 
TCGA-DQ-7588 TCGA-DQ-7592 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61W 
        1965          299           15           92          585           14 
TCGA-F7-A620 TCGA-H7-8501 TCGA-H7-8502 TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-8634 
          13           58          133            2            5           24 
TCGA-HD-A633 TCGA-HD-A6HZ TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J 
          49          111          588          360          412          440 
TCGA-IQ-A61L TCGA-KU-A66T TCGA-MT-A51X TCGA-MZ-A7D7 TCGA-P3-A5QA TCGA-P3-A6SX 
         351          552           34          240         1726         1954 
TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A6IG TCGA-QK-A6IH 
         578         1917         1968          400          218          228 
TCGA-QK-A6IJ TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-QK-AA3J TCGA-QK-AA3K TCGA-UF-A71E 
         387          198          149          157          168         1278 
TCGA-UF-A7J9 TCGA-UF-A7JD TCGA-UF-A7JH 
        1043          735          665 

$`21Q LOSS WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 
         462          415         1983          276          248          722 
TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-6869 
        1288         1762          520          725          623          644 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH 
         384          113          236          895          855          622 
TCGA-BA-A4II TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BA-A6DL 
         918          216          182         1976          314          623 
TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 
         142          187         2878          278          140          133 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7863 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 
         558          310          423          638         1153          428 
TCGA-BB-7872 TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4727 
         436            4          799          721          142         1230 
TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4737 
         392          817          993          642         1250          625 
TCGA-CN-4740 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 
         811         1007         1045          173         1980         1081 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5373 TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6016 
        1966         1966          683          933          628          594 
TCGA-CN-6017 TCGA-CN-6020 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 
         629           98         1110          224          318          611 
TCGA-CN-6992 TCGA-CN-A498 TCGA-CN-A49A TCGA-CN-A49C TCGA-CN-A63U TCGA-CN-A63V 
         394          443          391          645          526          484 
TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5324 TCGA-CQ-5325 
         175          367          223          298         1207          654 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 
        1660         1422         1399          341          129         1253 
TCGA-CQ-6221 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-7071 
        1000         1959         1959         1750         1309          877 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CG TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 
         893          998          391         2562         1663         1152 
TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 
         799         1777         1521         1966         1050         1125 
TCGA-CR-6474 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 
        1971         1969          362          311          345          234 
TCGA-CR-6488 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7368 TCGA-CR-7372 
         379          479         1956         1435         1245          759 
TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 
          30          972         1968         1036          796         1954 
TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 
         997         1430          392          907          913          946 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7401 
         908          898          930          216          156         1077 
TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 
         911         1472         1955         1950         3295         1438 
TCGA-CV-5436 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5970 TCGA-CV-5971 
         584         2886         2327         1958          406          701 
TCGA-CV-5973 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6935 TCGA-CV-6936 
        2641          641         1899         1970         1969         1952 
TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-6960 TCGA-CV-7095 
        3835         1948         1969         1966         1969         1970 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7183 TCGA-CV-7238 TCGA-CV-7243 
        1936         1959         1945         1979         1444          954 
TCGA-CV-7250 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7427 TCGA-CV-7428 
        1960         1974         1948         1955         1937         1973 
TCGA-CV-7430 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A45R 
        1972         1984         1958          851         1945         5480 
TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A468 
        1960         1940         1946         1954         1722         1977 
TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JY TCGA-CV-A6JZ 
        1970         1075         1959          670          646          714 
TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-D6-6517 TCGA-D6-6824 
         606          685         1950          321          292           77 
TCGA-D6-6825 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A6EK TCGA-D6-A6EO 
         491          568          106          128          483          435 
TCGA-D6-A6EP TCGA-D6-A6ES TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7589 
         424          389         1081         1030          548          575 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
         775          622          369          368          324          340 
TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A623 
        1131          490          658            3          384            6 
TCGA-H7-7774 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7754 TCGA-HD-7917 
         407          414          403          206           25           37 
TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A634 TCGA-HD-A6I0 
          55           44           25           11           10           33 
TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61O TCGA-KU-A66S 
        1057          485          122          441          360          224 
TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F 
         378          168           14          392           56          111 
TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A6SW TCGA-QK-A64Z 
         112          254          910         1559         1120          553 
TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6II TCGA-QK-A6V9 TCGA-QK-A8ZA TCGA-QK-A8ZB 
         357          245          225          567          135          135 
TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A7JA TCGA-UF-A7JC 
        1326         1663         1319         1252         1894          484 
TCGA-UF-A7JF TCGA-UF-A7JJ TCGA-UF-A7JS 
        1497          214          413 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 2                  3 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              3837               5480 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               687                714 
[1] "2.0 - 3837.0 (687.0)" "3.0 - 5480.0 (714.0)"
[1] "hr=" "1.1"
D78V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  21Q LOSS MUTATED         8       30        29        88         6         0
  21Q LOSS WILD-TYPE      18       45        45       147         6         1
D78V3, multiclass
           clus
vv          21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  STAGE I                  8                 18
  STAGE II                30                 45
  STAGE III               29                 45
  STAGE IVA               88                147
  STAGE IVB                6                  6
  STAGE IVC                0                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  21Q LOSS MUTATED      10  51  40  61
  21Q LOSS WILD-TYPE    37  76  54 101
D78V4, multiclass
       clus
vv      21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  T0+T1               10                 37
  T2                  51                 76
  T3                  40                 54
  T4                  61                101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  21Q LOSS MUTATED    57  28  58   4
  21Q LOSS WILD-TYPE 113  35  94   4
D78V5, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  N0               57                113
  N1               28                 35
  N2               58                 94
  N3                4                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1  MX
  21Q LOSS MUTATED    56   0  28
  21Q LOSS WILD-TYPE 111   1  30
D78V6, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  M0               56                111
  M1                0                  1
  MX               28                 30
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V7, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    47 130
  21Q LOSS WILD-TYPE  85 226
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     47  130
  21Q LOSS WILD-TYPE   85  226
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE               47                 85
  MALE                130                226
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  21Q LOSS MUTATED                                     173
  21Q LOSS WILD-TYPE                                   304
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  21Q LOSS MUTATED                                                             0
  21Q LOSS WILD-TYPE                                                           1
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  21Q LOSS MUTATED                                                     4
  21Q LOSS WILD-TYPE                                                   6
D78V8, multiclass
                                                             clus
vv                                                            21Q LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    173
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        4
                                                             clus
vv                                                            21Q LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      304
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                  1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                          6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V9, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    27 150
  21Q LOSS WILD-TYPE  52 259
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     27  150
  21Q LOSS WILD-TYPE   52  259
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  NO                27                 52
  YES              150                259
[1] 2 2
[1] FALSE
D78V10, continuous
D78V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  21Q LOSS MUTATED                                  1     7
  21Q LOSS WILD-TYPE                                1     4
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  21Q LOSS MUTATED                          23   140
  21Q LOSS WILD-TYPE                        21   275
D78V12, multiclass
                                  clus
vv                                 21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  1
  ASIAN                                           7                  4
  BLACK OR AFRICAN AMERICAN                      23                 21
  WHITE                                         140                275
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V13, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     8 155
  21Q LOSS WILD-TYPE  16 276
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      8  155
  21Q LOSS WILD-TYPE   16  276
                        clus
vv                       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    8                 16
  NOT HISPANIC OR LATINO              155                276
[1] 2 2
[1] FALSE

Clustering(79) Variable = 22Q LOSS MUTATION ANALYSIS
D79V1, survival
                    sevent
clus2                  0   1
  22Q LOSS MUTATED    48  15
  22Q LOSS WILD-TYPE 253  98
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                63                351 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                15                 98 
$`22Q LOSS MUTATED`
TCGA-4P-AA8J TCGA-BA-4075 TCGA-BA-5149 TCGA-BA-5558 TCGA-BA-6870 TCGA-BA-6871 
         102          283          248         1636          451           63 
TCGA-BA-A6DE TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-7861 TCGA-C9-A47Z 
         182         2878          278          140          310            5 
TCGA-CN-4725 TCGA-CN-4730 TCGA-CN-5355 TCGA-CN-5370 TCGA-CN-6018 TCGA-CN-6021 
        1157          817         1007         1975           45         1970 
TCGA-CN-6998 TCGA-CN-A63W TCGA-CQ-5327 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-A4C7 
          46          348         1660         1560         1007         1960 
TCGA-CQ-A4CA TCGA-CQ-A4CE TCGA-CR-5248 TCGA-CR-6488 TCGA-CR-6493 TCGA-CR-7373 
        1963          785         1663          379         1956          889 
TCGA-CR-7379 TCGA-CR-7398 TCGA-CR-7399 TCGA-CV-5973 TCGA-CV-5977 TCGA-CV-6003 
        1036          156          181         2641         1840         1665 
TCGA-CV-6441 TCGA-CV-6945 TCGA-CV-7091 TCGA-CV-7180 TCGA-CV-7432 TCGA-CV-A6JY 
        1970         1969         1959         1987         1937          646 
TCGA-CV-A6K1 TCGA-CX-7086 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A6EM TCGA-DQ-5631 
         685          237          128          539          232          548 
TCGA-DQ-7592 TCGA-DQ-7593 TCGA-F7-A50G TCGA-F7-A50J TCGA-F7-A623 TCGA-HD-A633 
         299          369           15          585            6           49 
TCGA-IQ-7630 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-MT-A51W TCGA-MT-A67G TCGA-P3-A5QA 
         485          588          360           14          112         1726 
TCGA-P3-A6T0 TCGA-QK-A6IH TCGA-QK-A6IJ 
         578          228          387 

$`22Q LOSS WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5151 TCGA-BA-5152 
         462          415         1983          276          722         1288 
TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6868 
        1762          520          725          623         1747          190 
TCGA-BA-6869 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG 
         644          384          113          236          895          855 
TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DG 
         622          918          850          351          216         1976 
TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-4217 TCGA-BB-4227 TCGA-BB-4228 
         314          623          142          187          133          558 
TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 
         536          423          687          638         1153          428 
TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 
         436         1955          624            4          799          721 
TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4731 TCGA-CN-4733 
         142         1230         1151          392          993          642 
TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 
        1250          395          625         1960         1330          811 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 
        1268         1988         1045          173         1980         1081 
TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5373 TCGA-CN-5374 
        1977         1980         1966         1966          683          290 
TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 
         630          933          629          628          594          629 
TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 
         432           98          202         1110          224          318 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-A498 
         611          394          735          432          429          443 
TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U 
         535          391          904          645          225          526 
TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 
         484          175          367          223          298         1466 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 
        1207          654         1422         1393         1399          317 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 
         341          129         1253         1000         1057          985 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7067 TCGA-CQ-7068 
        1959         1959         1179         1750          509         1309 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB 
        1274          877         1950         1353          707          893 
TCGA-CQ-A4CD TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 
         998          391          303          950         2562          358 
TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 
        1152          799         1777         1521         1966         1050 
TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 
        1125         1971          514         1969          362          311 
TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-7364 
         345          354          234          350          479         1435 
TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 
        1191         1440         1245         1960          105         1979 
TCGA-CR-7372 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7382 TCGA-CR-7383 
         759           30          972         1968          796         1954 
TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 
         997         1430         1951          392          907          913 
TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7401 
         946          908          898          930          216         1077 
TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 
         911         1472         1955          522         1950         3295 
TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 
        1438          584          546         1978         2886         2327 
TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5976 
        1958         2437          519          406          701         1478 
TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6934 TCGA-CV-6935 
         215         1315          641         1899         1948         1969 
TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6952 TCGA-CV-6954 
        1952         1959         3835         1948         1966         1957 
TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 
        1969         1959         3837         1970         1970         1936 
TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 
        1959         1939         1945         1979         1952         1444 
TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7254 
        1095          954          797         1967         1960         1976 
TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 
        1099         1974         1948         1955         1957         1947 
TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 
        1937         1973         1972         1984         1958         1959 
TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45Y TCGA-CV-A45Z 
        1981          851         1945         5480         1960         1940 
TCGA-CV-A460 TCGA-CV-A461 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE 
        1946         1954         1722         1977         1970         1075 
TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JZ TCGA-CV-A6K0 
         906         1959          670          110          714          606 
TCGA-CV-A6K2 TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6517 
        1950          317          321          828          773          292 
TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 
         701           77          491          154          568          106 
TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES 
         376          483          435          424          368          389 
TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-7588 
         338         1778         1081          516         1030         1965 
TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 
         575          775          622          368          324          340 
TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50I TCGA-F7-A61S TCGA-F7-A61V 
        1131          490          658           92            3          384 
TCGA-F7-A61W TCGA-F7-A620 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 
          14           13          407           58          133          414 
TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 
         403          206            2            5           25           37 
TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A634 
          55           44           24           25           11           10 
TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61H 
         111           33         1057          122          441          412 
TCGA-IQ-A61J TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 
         440          351          360          224          552          378 
TCGA-KU-A6H8 TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MZ-A6I9 
         168           34          392           56          111          254 
TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T2 
         240          910         1559         1120         1954         1917 
TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG 
        1968          400          553          357          245          218 
TCGA-QK-A6II TCGA-QK-A6V9 TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB 
         225          567          198          149          135          135 
TCGA-QK-AA3J TCGA-QK-AA3K TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71D 
         157          168         1326         1663         1319         1252 
TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JF 
        1278         1043         1894          484          735         1497 
TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JS 
         665          214          413 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 5                  2 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              2878               5480 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               548                725 
[1] "5.0 - 2878.0 (548.0)" "2.0 - 5480.0 (725.0)"
[1] "hr=" "1.1"
D79V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  22Q LOSS MUTATED         3       13        15        28         1         0
  22Q LOSS WILD-TYPE      23       62        59       207        11         1
D79V3, multiclass
           clus
vv          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  STAGE I                  3                 23
  STAGE II                13                 62
  STAGE III               15                 59
  STAGE IVA               28                207
  STAGE IVB                1                 11
  STAGE IVC                0                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T0+T1  T2  T3  T4
  22Q LOSS MUTATED       6  20  17  17
  22Q LOSS WILD-TYPE    41 107  77 145
D79V4, multiclass
       clus
vv      22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T0+T1                6                 41
  T2                  20                107
  T3                  17                 77
  T4                  17                145
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  22Q LOSS MUTATED    25  13  18   0
  22Q LOSS WILD-TYPE 145  50 134   8
D79V5, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  N0               25                145
  N1               13                 50
  N2               18                134
  N3                0                  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"
                    vv
clus                  M0  M1  MX
  22Q LOSS MUTATED    24   0   8
  22Q LOSS WILD-TYPE 143   1  50
D79V6, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  M0               24                143
  M1                0                  1
  MX                8                 50
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V7, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    24  45
  22Q LOSS WILD-TYPE 108 311
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     24   45
  22Q LOSS WILD-TYPE  108  311
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE               24                108
  MALE                 45                311
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  22Q LOSS MUTATED                                      69
  22Q LOSS WILD-TYPE                                   408
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  22Q LOSS MUTATED                                                             0
  22Q LOSS WILD-TYPE                                                           1
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  22Q LOSS MUTATED                                                     0
  22Q LOSS WILD-TYPE                                                  10
D79V8, multiclass
                                                             clus
vv                                                            22Q LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     69
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        0
                                                             clus
vv                                                            22Q LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      408
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                  1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V9, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED     7  62
  22Q LOSS WILD-TYPE  72 347
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      7   62
  22Q LOSS WILD-TYPE   72  347
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  NO                 7                 72
  YES               62                347
[1] 2 2
[1] FALSE
D79V10, continuous
D79V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  22Q LOSS MUTATED                                  1     3
  22Q LOSS WILD-TYPE                                1     8
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  22Q LOSS MUTATED                           6    56
  22Q LOSS WILD-TYPE                        38   359
D79V12, multiclass
                                  clus
vv                                 22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  1
  ASIAN                                           3                  8
  BLACK OR AFRICAN AMERICAN                       6                 38
  WHITE                                          56                359
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V13, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED     5  59
  22Q LOSS WILD-TYPE  19 372
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      5   59
  22Q LOSS WILD-TYPE   19  372
                        clus
vv                       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    5                 19
  NOT HISPANIC OR LATINO               59                372
[1] 2 2
[1] FALSE

Clustering(80) Variable = XQ LOSS MUTATION ANALYSIS
D80V1, survival
                   sevent
clus2                 0   1
  XQ LOSS MUTATED    45  23
  XQ LOSS WILD-TYPE 256  90
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               68               346 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               23                90 
$`XQ LOSS MUTATED`
TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-6868 TCGA-BA-A4IH TCGA-BA-A6D8 
         462          415          276          190          622          850 
TCGA-BA-A6DE TCGA-BA-A6DL TCGA-BA-A8YP TCGA-BB-7862 TCGA-BB-7871 TCGA-BB-8596 
         182          623          142          536          428         1955 
TCGA-CN-4725 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-5360 TCGA-CN-6010 TCGA-CN-6992 
        1157         1250          395         1081          630          394 
TCGA-CN-6997 TCGA-CN-A49A TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6227 TCGA-CQ-7064 
         429          391         1253         1000         1959         1560 
TCGA-CQ-7067 TCGA-CQ-A4CI TCGA-CR-5248 TCGA-CR-6472 TCGA-CR-6487 TCGA-CR-7371 
         509          950         1663         1050          234         1979 
TCGA-CR-7374 TCGA-CR-7383 TCGA-CR-7388 TCGA-CR-7390 TCGA-CR-7397 TCGA-CR-7398 
          30         1954         1951          907          216          156 
TCGA-CR-7399 TCGA-CV-5439 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-6441 TCGA-CV-6935 
         181          546         2641         1478         1970         1969 
TCGA-CV-6960 TCGA-CV-7095 TCGA-CV-7101 TCGA-CV-7235 TCGA-CV-7418 TCGA-CV-7430 
        1969         1970         1939         1952         1955         1972 
TCGA-CV-7435 TCGA-CV-A460 TCGA-CV-A6K1 TCGA-CX-7082 TCGA-D6-6827 TCGA-DQ-7588 
        1959         1946          685          317          568         1965 
TCGA-F7-7848 TCGA-F7-A50G TCGA-F7-A61W TCGA-H7-A6C5 TCGA-MZ-A6I9 TCGA-P3-A5QA 
        1131           15           14          403          254         1726 
TCGA-P3-A5QE TCGA-P3-A6T4 TCGA-QK-A6IH TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-UF-A7JC 
        1559         1968          228          135          157          484 
TCGA-UF-A7JD TCGA-UF-A7JS 
         735          413 

$`XQ LOSS WILD-TYPE`
TCGA-4P-AA8J TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 
         102          283         1983          248          722         1288 
TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 
        1762          520          725          623         1636         1747 
TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 
         644          451           63          384          113          236 
TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4II TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DG 
         895          855          918          351          216         1976 
TCGA-BA-A6DJ TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 
         314          187         2878          278          140          133 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 
         558          310          423          687          638         1153 
TCGA-BB-7872 TCGA-BB-8601 TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 
         436          624            5            4          799          721 
TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 
         142         1230         1151          392          817          993 
TCGA-CN-4733 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 
         642          625         1960         1330          811         1268 
TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5363 
        1988         1007         1045          173         1980         1977 
TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 
        1980         1966         1966         1975          683          290 
TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 
         933          629          628          594          629           45 
TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
         432           98         1970          202         1110          224 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A498 
         318          611          735          432           46          443 
TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V 
         535          904          645          225          526          484 
TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 
         348          175          367          223          298         1466 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 
        1207          654         1660         1422         1393         1399 
TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6228 
         317          341          129         1057          985         1959 
TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 
        1179         1750         1007         1309         1274          877 
TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB 
        1950         1353         1960          707         1963          893 
TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5243 TCGA-CR-5247 
         998          785          391          303         2562          358 
TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 
        1152          799         1777         1521         1966         1125 
TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 
        1971          514         1969          362          311          345 
TCGA-CR-6484 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 
         354          379          350          479         1956         1435 
TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7372 
        1191         1440         1245         1960          105          759 
TCGA-CR-7373 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7385 
         889          972         1968         1036          796          997 
TCGA-CR-7386 TCGA-CR-7389 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 
        1430          392          913          946          908          898 
TCGA-CR-7395 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 
         930         1077          911         1472         1955          522 
TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5440 TCGA-CV-5441 
        1950         3295         1438          584         1978         2886 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 
        2327         1958         2437          519          406          701 
TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 
        1840          215         1315         1665          641         1899 
TCGA-CV-6934 TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 
        1948         1952         1959         3835         1948         1969 
TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7097 
        1966         1957         1959         3837         1959         1970 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7238 
        1936         1959         1945         1987         1979         1444 
TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7254 
        1095          954          797         1967         1960         1976 
TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7427 
        1099         1974         1948         1957         1947         1937 
TCGA-CV-7428 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7440 TCGA-CV-A45O 
        1973         1937         1984         1958         1981          851 
TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A461 TCGA-CV-A464 
        1945         5480         1960         1940         1954         1722 
TCGA-CV-A468 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT 
        1977         1970         1075          906         1959          670 
TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K2 TCGA-CX-7085 
         110          646          714          606         1950          321 
TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 
         237          828          773          292          701           77 
TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB 
         491          154          106          128          539          376 
TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES 
         483          232          435          424          368          389 
TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 
         338         1778         1081          516         1030          548 
TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 
         575          775          622          299          369          368 
TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50I TCGA-F7-A50J 
         324          340          490          658           92          585 
TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8501 
           3          384           13            6          407           58 
TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 
         133          414          206            2            5           25 
TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 
          37           55           44           24           25           11 
TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 
          49           10          111           33         1057          485 
TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J 
         122          441          588          360          412          440 
TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-KU-A6H8 
         351          360          224          552          378          168 
TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G 
          14           34          392           56          111          112 
TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 
         240          910         1120         1954          578         1917 
TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6II 
         400          553          357          245          218          225 
TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-AA3K 
         387          567          198          149          135          168 
TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 
        1326         1663         1319         1252         1278         1043 
TCGA-UF-A7JA TCGA-UF-A7JF TCGA-UF-A7JH TCGA-UF-A7JJ 
        1894         1497          665          214 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               14                 2 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             2641              5480 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
              710               701 
[1] "14.0 - 2641.0 (710.0)" "2.0 - 5480.0 (701.0)" 
[1] "hr=" "1.3"
D80V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  XQ LOSS MUTATED         7        8        10        35         4         1
  XQ LOSS WILD-TYPE      19       67        64       200         8         0
D80V3, multiclass
           clus
vv          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  STAGE I                 7                19
  STAGE II                8                67
  STAGE III              10                64
  STAGE IVA              35               200
  STAGE IVB               4                 8
  STAGE IVC               1                 0
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T0+T1  T2  T3  T4
  XQ LOSS MUTATED      10  15  22  21
  XQ LOSS WILD-TYPE    37 112  72 141
D80V4, multiclass
       clus
vv      XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T0+T1              10                37
  T2                 15               112
  T3                 22                72
  T4                 21               141
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  XQ LOSS MUTATED    21  11  26   2
  XQ LOSS WILD-TYPE 149  52 126   6
D80V5, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  N0              21               149
  N1              11                52
  N2              26               126
  N3               2                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1  MX
  XQ LOSS MUTATED    27   1   6
  XQ LOSS WILD-TYPE 140   0  52
D80V6, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  M0              27               140
  M1               1                 0
  MX               6                52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V7, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    25  52
  XQ LOSS WILD-TYPE 107 304
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     25   52
  XQ LOSS WILD-TYPE  107  304
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE              25               107
  MALE                52               304
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  XQ LOSS MUTATED                                      73
  XQ LOSS WILD-TYPE                                   404
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  XQ LOSS MUTATED                                                             0
  XQ LOSS WILD-TYPE                                                           1
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  XQ LOSS MUTATED                                                     4
  XQ LOSS WILD-TYPE                                                   6
D80V8, multiclass
                                                             clus
vv                                                            XQ LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    73
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       4
                                                             clus
vv                                                            XQ LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     404
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                 1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V9, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    11  66
  XQ LOSS WILD-TYPE  68 343
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     11   66
  XQ LOSS WILD-TYPE   68  343
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  NO               11                68
  YES              66               343
[1] 2 2
[1] FALSE
D80V10, continuous
D80V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XQ LOSS MUTATED                                  0     1
  XQ LOSS WILD-TYPE                                2    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XQ LOSS MUTATED                           8    65
  XQ LOSS WILD-TYPE                        36   350
D80V12, multiclass
                                  clus
vv                                 XQ LOSS MUTATED XQ LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          1                10
  BLACK OR AFRICAN AMERICAN                      8                36
  WHITE                                         65               350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V13, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     2  69
  XQ LOSS WILD-TYPE  22 362
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      2   69
  XQ LOSS WILD-TYPE   22  362
                        clus
vv                       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                22
  NOT HISPANIC OR LATINO              69               362
[1] 2 2
[1] FALSE
