[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/10005940/HNSC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/HNSC-TP/10013760/transformed.cor.cli.txt"

nPatients in clinical file=423, in cluster file=511, common to both=417
[1]  80 417
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               53               364 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               53               364 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               95               322 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               95               322 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               73               344 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               73               344 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               58               359 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               58               359 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               68               349 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               68               349 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              207               210 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              207               210 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               34               383 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               34               383 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               29               388 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               29               388 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              160               257 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              160               257 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               53               364 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               53               364 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               63               354 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               63               354 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               48               369 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               48               369 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              152               265 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              152               265 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              103               314 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              103               314 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              116               301 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              116               301 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              245               172 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              245               172 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               83               334 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               83               334 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
              110               307 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
              110               307 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                30                387 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                30                387 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                28                389 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                28                389 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                56                361 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                56                361 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                58                359 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                58                359 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               118                299 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               118                299 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                70                347 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                70                347 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                49                368 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                49                368 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
               123                294 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
               123                294 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                64                353 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                64                353 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                84                333 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                84                333 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                87                330 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                87                330 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                53                364 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                53                364 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                69                348 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                69                348 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                95                322 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                95                322 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                37                380 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                37                380 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                40                377 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                40                377 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                58                359 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                58                359 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               154                263 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               154                263 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               162                255 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               162                255 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                27                390 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                27                390 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                90                327 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                90                327 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               70               347 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               70               347 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               45               372 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               45               372 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               31               386 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               31               386 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               27               390 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               27               390 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               34               383 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               34               383 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              240               177 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              240               177 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               56               361 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               56               361 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              156               261 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              156               261 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              121               296 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              121               296 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               40               377 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               40               377 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              133               284 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              133               284 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               56               361 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               56               361 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               57               360 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               57               360 
[1] "7P LOSS MUTATION ANALYSIS"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               21               396 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               21               396 
[1] "7Q LOSS MUTATION ANALYSIS"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               37               380 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               37               380 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              152               265 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              152               265 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               25               392 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               25               392 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              142               275 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              142               275 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               66               351 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               66               351 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               127                290 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               127                290 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                85                332 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                85                332 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               109                308 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               109                308 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               134                283 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               134                283 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                27                390 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                27                390 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                23                394 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                23                394 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               130                287 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               130                287 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                37                380 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                37                380 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                76                341 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                76                341 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                48                369 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                48                369 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                60                357 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                60                357 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                91                326 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                91                326 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                30                387 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                30                387 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                85                332 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                85                332 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               177                240 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               177                240 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                80                337 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                80                337 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                68                349 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                68                349 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                42                375 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                42                375 
[1] "20Q LOSS MUTATION ANALYSIS"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                25                392 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                25                392 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               159                258 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               159                258 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                64                353 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                64                353 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               65               352 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               65               352 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDESEASE"                  
 [6] "NEOPLASM.DISEASESTAGE"                 
 [7] "PATHOLOGY.T.STAGE"                     
 [8] "PATHOLOGY.N.STAGE"                     
 [9] "PATHOLOGY.M.STAGE"                     
[10] "DCCUPLOADDATE"                         
[11] "GENDER"                                
[12] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[13] "DAYSTOLASTKNOWNALIVE"                  
[14] "RADIATIONTHERAPY"                      
[15] "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 417 columns.

[1] "Batch" "22"   
[1] "Last Follow UP"
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 
         462          283          415           NA          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-A6D8 TCGA-BA-A6DA 
         384          113          236          895          513          351 
TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BB-4217 TCGA-BB-4223 
         216           NA          182           NA          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 
        2161          624            5            4          799          721 
TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 
         485          142          452          613          392          462 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 
         993          642          369          395          240           NA 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 
        1330          811         1268           NA          488          512 
TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 
         173           NA         1081           NA           NA           NA 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 
          NA           NA           NA           NA          413          290 
TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 
         630          424          629          433          594          629 
TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 
          45          432           98           NA          202          424 
TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6995 
         224          318          611          394          119           NA 
TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63T 
         432          429           46          443          447          225 
TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 TCGA-CN-A642 
         526          484          348          175          367           NA 
TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5329 
        1466         1207          654           NA         1660         1422 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 
         896         1399          317          341          129          870 
TCGA-CQ-6220 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 
          NA         1000         1057          985           NA           NA 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 
          NA          815         1461         1378         1007          509 
TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
        1309          901          877          968           NA          613 
TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH 
          NA          545          548          393          391          303 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 
         608         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           NA         1050         1125           NA 
TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 
         514           NA          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           NA         1435 
TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 
        1191         1440         1245           NA          105           NA 
TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 
         759          889           30          972           NA         1036 
TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 
          NA          796           NA          997         1430           NA 
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-5435 
        1472         4241          522         3930         3295         1438 
TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 
         584          546         3270         2886         2327         2784 
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-6933 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 
          NA           NA           NA           NA           NA           NA 
TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 
          NA           NA           NA           NA         3835           NA 
TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6953 
          NA           NA           NA           NA           NA           NA 
TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 
          NA           NA           NA           NA           NA           NA 
TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 
          NA           NA         3837         3381           NA           NA 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 
          NA           NA           NA           NA           NA           NA 
TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 
          NA           NA           NA         3497         1724           NA 
TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 
        1444         1095          954          797           NA           NA 
TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7255 TCGA-CV-7261 
          NA           NA           NA           NA           NA         1099 
TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 
          NA           NA           NA           NA           NA           NA 
TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 
          NA           NA           NA           NA           NA           NA 
TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 
          NA           NA           NA           NA           NA           NA 
TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 
          NA           NA           NA           NA           NA         4335 
TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A461 
          NA           NA           NA          851           NA           NA 
TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CX-7082 TCGA-CX-7085 
          NA          750           NA          717          317          321 
TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 
         237          828           NA          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-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 
         112          104         1778         1081          516         1030 
TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 
         548           NA          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          564          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-A622 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 
          14           13           NA            6           NA          407 
TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-7753 
          58          133          414          403            2            5 
TCGA-HD-7754 TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 
          25           NA           NA           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-A61I TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L 
         360          412           NA          440           NA          351 
TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A 
         360          224          210           14           34          392 
TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5Q6 
          56          111          112          254          910           NA 
TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 
        1652          721           NA         1120           NA          578 
TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 
        1917           NA           NA           NA           NA           NA 
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-A6IJ TCGA-UF-A7JV 
         225           64           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=147,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=267,	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=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=7,	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=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=22,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=49,	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=81,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'YEAROFTOBACCOSMOKINGONSET':	nDistinctValues=57,	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=18,	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 417 columns, 1 survival variables, and 12 non-survival variables.
AGE, nv=60, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=5, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
 40 108  85 131 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
 40 108  85 131 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
 T1  T2  T3  T4 
 40 108  85 131 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
 40 108  85 131 
PATHOLOGY.N.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
136  56 129   7 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
136  56 129   7 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
 N0  N1  N2  N3 
136  56 129   7 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
136  56 129   7 
PATHOLOGY.M.STAGE, nv=2, 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=81, 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    27  16
  1P GAIN WILD-TYPE 230  82
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               43               312 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               16                82 
$`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          452         1330         1980           98 
TCGA-CN-6989 TCGA-CQ-7067 TCGA-CR-6478 TCGA-CR-6482 TCGA-CR-7379 TCGA-CR-7388 
         611          509         1969          345         1036         1951 
TCGA-CV-5431 TCGA-CV-5442 TCGA-CV-5444 TCGA-CV-5973 TCGA-CV-5977 TCGA-CV-7091 
         522         2327         2437         2641         1840         1959 
TCGA-CV-7095 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7235 TCGA-CV-7422 TCGA-CV-A461 
        1970         1939         1945         1724         1957         1954 
TCGA-CV-A6JE TCGA-CX-7082 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7596 
         750          317         1081          516         1965          340 
TCGA-F7-8298 TCGA-H7-7774 TCGA-IQ-A61O TCGA-KU-A66T TCGA-P3-A5Q5 TCGA-P3-A6SW 
         490          407          360          210          910         1120 
TCGA-P3-A6SX 
        1954 

$`1P GAIN 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-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-6871 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A6D8 
         190          644           63          236          895          513 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 
         351          216          182          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-C9-A480 
         687          638         1153          428          436            4 
TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 
         799          721          485          142          613          392 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 
         462          993          642          369          395          240 
TCGA-CN-4738 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 
        1960          811         1268         1988          488          512 
TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 
         173         1081         1977         1980         1966         1966 
TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 
        1975          413          290          630          424          629 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6021 
         433          594          629           45          432         1970 
TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6992 TCGA-CN-6994 
         202          424          224          318          394          119 
TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63T 
         432          429           46          443          447          225 
TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 TCGA-CQ-5323 
         526          484          348          175          367         1466 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 
        1207          654         1660         1422          896         1399 
TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 
         317          341          129          870         1000         1057 
TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 
         985         1959         1959          815         1461         1378 
TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 
        1007         1309          901          877          968         1960 
TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG 
         613         1963          545          548          393          391 
TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 
         303          608         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-6480 TCGA-CR-6481 TCGA-CR-6484 TCGA-CR-6487 
        1971          514          362          311          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-7382 TCGA-CR-7383 
         889           30          972         1968          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-7399 
         908          898          930          216          156          181 
TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5434 
        1077          911         1472         1955         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-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5976 TCGA-CV-5978 TCGA-CV-5979 
         519          406          701         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-7097 TCGA-CV-7099 
        1957         1969         1959         3837         1970         1936 
TCGA-CV-7100 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 
        1959         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-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-7435 TCGA-CV-7440 TCGA-CV-A45O 
        1937         1984         1958         1959         1981          851 
TCGA-CV-A45Q TCGA-CV-A6JD TCGA-CV-A6JN TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 
        1945         1970          717          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-DQ-5624 
         568          106          128          112          104         1778 
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-F7-7848 TCGA-F7-8489 TCGA-F7-A50G 
         369          368          324          564          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-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-A61L TCGA-KU-A66S TCGA-MT-A51W TCGA-MT-A51X 
         412          440          351          224           14           34 
TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A5QA 
         392           56          111          112          254         1652 
TCGA-P3-A5QE TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A64Z 
         721          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           64 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                5                 2 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             2641              3837 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            910.0             622.5 
[1] "5.0 - 2641.0 (910.0)" "2.0 - 3837.0 (622.5)"
[1] "hr=" "1"  
D1V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  1P GAIN MUTATED         3        6         6        26         1
  1P GAIN WILD-TYPE      21       57        65       166         8
D1V3, multiclass
           clus
vv          1P GAIN MUTATED 1P GAIN WILD-TYPE
  STAGE I                 3                21
  STAGE II                6                57
  STAGE III               6                65
  STAGE IVA              26               166
  STAGE IVB               1                 8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  1P GAIN MUTATED     3  12  12  15
  1P GAIN WILD-TYPE  37  96  73 116
D1V4, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  T1               3                37
  T2              12                96
  T3              12                73
  T4              15               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
  1P GAIN MUTATED    11   8  17   1
  1P GAIN WILD-TYPE 125  48 112   6
D1V5, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  N0              11               125
  N1               8                48
  N2              17               112
  N3               1                 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"
D1V6, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     6   9
  1P GAIN WILD-TYPE 102  39
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      6    9
  1P GAIN WILD-TYPE  102   39
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  M0               6               102
  MX               9                39
[1] 2 2
[1] FALSE
D1V7, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    18  35
  1P GAIN WILD-TYPE 103 261
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     18   35
  1P GAIN WILD-TYPE  103  261
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE              18               103
  MALE                35               261
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  1P GAIN MUTATED                                      50
  1P GAIN WILD-TYPE                                   360
                   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                                                     2
  1P GAIN WILD-TYPE                                                   4
D1V8, multiclass
                                                             clus
vv                                                            1P GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    50
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       2
                                                             clus
vv                                                            1P GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     360
  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"
D1V9, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    11  42
  1P GAIN WILD-TYPE  68 296
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     11   42
  1P GAIN WILD-TYPE   68  296
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  NO               11                68
  YES              42               296
[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                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1P GAIN MUTATED                           7    43
  1P GAIN WILD-TYPE                        26   318
D1V12, multiclass
                                  clus
vv                                 1P GAIN MUTATED 1P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      7                26
  WHITE                                         43               318
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V13, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     4  48
  1P GAIN WILD-TYPE  14 333
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      4   48
  1P GAIN WILD-TYPE   14  333
                        clus
vv                       1P GAIN MUTATED 1P GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                14
  NOT HISPANIC OR LATINO              48               333
[1] 2 2
[1] FALSE

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                 0   1
  1Q GAIN MUTATED    54  23
  1Q GAIN WILD-TYPE 203  75
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               77               278 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               23                75 
$`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          452 
TCGA-CN-4728 TCGA-CN-4739 TCGA-CN-5359 TCGA-CN-5367 TCGA-CN-5374 TCGA-CN-6010 
         613         1330         1980         1966          290          630 
TCGA-CN-6013 TCGA-CN-6020 TCGA-CN-6023 TCGA-CN-6997 TCGA-CN-A63U TCGA-CQ-7064 
         433           98          424          429          526         1378 
TCGA-CQ-7067 TCGA-CQ-A4C9 TCGA-CQ-A4CD TCGA-CQ-A4CI TCGA-CR-6478 TCGA-CR-6482 
         509          613          548          608         1969          345 
TCGA-CR-7370 TCGA-CR-7379 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CV-5430 
         105         1036         1951          392          907         1955 
TCGA-CV-5431 TCGA-CV-5434 TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5444 TCGA-CV-5977 
         522         3295         1978         2327         2437         1840 
TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-7091 
         215         1315         1969         1952         1959         1959 
TCGA-CV-7095 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7235 TCGA-CV-7243 TCGA-CV-7250 
        1970         1939         1945         1724          954         1960 
TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7422 TCGA-CV-7440 TCGA-CV-A461 TCGA-CV-A6JE 
        1976         1099         1957         1981         1954          750 
TCGA-CX-7082 TCGA-CX-7086 TCGA-D6-6827 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-7589 
         317          237          568         1081          516          575 
TCGA-DQ-7596 TCGA-F7-8298 TCGA-H7-7774 TCGA-HD-7754 TCGA-HD-7917 TCGA-HL-7533 
         340          490          407           25           37         1057 
TCGA-IQ-A61H TCGA-IQ-A61O TCGA-KU-A66T TCGA-P3-A5Q5 TCGA-P3-A6SW 
         412          360          210          910         1120 

$`1Q 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-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6873 TCGA-BA-A4IF TCGA-BA-A6D8 
        1747          190          644          113          895          513 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4225 
         351          216          182          187         2878          140 
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-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 
         436            5            4          799          721          485 
TCGA-CN-4726 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 
         142          392          462          993          642          369 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 
         395          240         1960          811         1268         1988 
TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 
         488          512          173         1081         1977         1980 
TCGA-CN-5366 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6016 
        1966         1975          413          424          629          594 
TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6024 
         629           45          432         1970          202          224 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6998 
         318          611          394          119          432           46 
TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y 
         443          447          225          484          348          175 
TCGA-CN-A641 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 
         367         1466         1207          654         1660         1422 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 
         896         1399          317          341          129          870 
TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 
        1000         1057          985         1959         1959          815 
TCGA-CQ-7063 TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 
        1461         1007         1309          901          877          968 
TCGA-CQ-A4C7 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH 
        1960         1963          545          393          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-6477 
        1521         1966         1050         1125         1971          514 
TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 
         362          311          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-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 
        1960         1979          759          889           30          972 
TCGA-CR-7377 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7391 
        1968          796         1954          997         1430          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-5432 TCGA-CV-5435 
         181         1077          911         1472         1950         1438 
TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5441 TCGA-CV-5443 TCGA-CV-5966 TCGA-CV-5970 
         584          546         2886         1958          519          406 
TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 
         701         2641         1478         1665          641         1899 
TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6952 
        1970         1948         3835         1948         1969         1966 
TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7097 TCGA-CV-7099 
        1957         1969         1959         3837         1970         1936 
TCGA-CV-7100 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7245 
        1959         1987         1979         1444         1095          797 
TCGA-CV-7248 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7424 TCGA-CV-7427 
        1967         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-A45O TCGA-CV-A45Q TCGA-CV-A6JD TCGA-CV-A6JN TCGA-CX-7085 TCGA-CX-7219 
         851         1945         1970          717          321          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-A4Z9 TCGA-D6-A4ZB TCGA-DQ-5624 TCGA-DQ-5630 
         106          128          112          104         1778         1030 
TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 
         548         1965          775          622          299          369 
TCGA-DQ-7594 TCGA-DQ-7595 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I 
         368          324          564          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-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-7753 
          58          133          414          403            2            5 
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-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 
          10          111           33          485          122          441 
TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61J TCGA-IQ-A61L TCGA-KU-A66S TCGA-MT-A51W 
         588          360          440          351          224           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-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T4 
        1652          721         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-A6IJ 
         225           64 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               25                 2 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             3295              3837 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              624               629 
[1] "25.0 - 3295.0 (624.0)" "2.0 - 3837.0 (629.0)" 
[1] "hr=" "1.1"
D2V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  1Q GAIN MUTATED         4       12        12        48         3
  1Q GAIN WILD-TYPE      20       51        59       144         6
D2V3, multiclass
           clus
vv          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  STAGE I                 4                20
  STAGE II               12                51
  STAGE III              12                59
  STAGE IVA              48               144
  STAGE IVB               3                 6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  1Q GAIN MUTATED    5 25 16 33
  1Q GAIN WILD-TYPE 35 83 69 98
D2V4, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T1               5                35
  T2              25                83
  T3              16                69
  T4              33                98
[1] 4 2
[1] 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    21  12  32   3
  1Q GAIN WILD-TYPE 115  44  97   4
D2V5, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  N0              21               115
  N1              12                44
  N2              32                97
  N3               3                 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"
D2V6, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED   14 10
  1Q GAIN WILD-TYPE 94 38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     14   10
  1Q GAIN WILD-TYPE   94   38
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  M0              14                94
  MX              10                38
[1] 2 2
[1] FALSE
D2V7, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    25  70
  1Q GAIN WILD-TYPE  96 226
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     25   70
  1Q GAIN WILD-TYPE   96  226
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE              25                96
  MALE                70               226
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  1Q GAIN MUTATED                                      91
  1Q GAIN WILD-TYPE                                   319
                   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                                                     3
  1Q GAIN WILD-TYPE                                                   3
D2V8, multiclass
                                                             clus
vv                                                            1Q GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    91
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       3
                                                             clus
vv                                                            1Q GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     319
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                 0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V9, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    22  73
  1Q GAIN WILD-TYPE  57 265
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     22   73
  1Q GAIN WILD-TYPE   57  265
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO               22                57
  YES              73               265
[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                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1Q GAIN MUTATED                          13    79
  1Q GAIN WILD-TYPE                        20   282
D2V12, multiclass
                                  clus
vv                                 1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                     13                20
  WHITE                                         79               282
[1] 4 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     6  85
  1Q GAIN WILD-TYPE  12 296
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      6   85
  1Q GAIN WILD-TYPE   12  296
                        clus
vv                       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   6                12
  NOT HISPANIC OR LATINO              85               296
[1] 2 2
[1] FALSE

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                 0   1
  2P GAIN MUTATED    44  10
  2P GAIN WILD-TYPE 213  88
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               54               301 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               10                88 
$`2P GAIN MUTATED`
TCGA-BA-4075 TCGA-BA-5555 TCGA-BA-A4IF TCGA-BB-8596 TCGA-CN-4727 TCGA-CN-4742 
         283          520          895         1955          452         1988 
TCGA-CN-5356 TCGA-CN-5359 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6012 TCGA-CN-6023 
         512         1980          290          630          629          424 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-A63T TCGA-CQ-5329 TCGA-CQ-5332 
         318          611          119          225         1422          317 
TCGA-CR-5247 TCGA-CR-6477 TCGA-CR-7365 TCGA-CR-7372 TCGA-CR-7383 TCGA-CR-7398 
         358          514         1191          759         1954          156 
TCGA-CR-7399 TCGA-CV-5430 TCGA-CV-5440 TCGA-CV-6941 TCGA-CV-7090 TCGA-CV-7091 
         181         1955         1978         1959         3837         1959 
TCGA-CV-7235 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7250 TCGA-CV-7254 
        1724         1095          954          797         1960         1976 
TCGA-CV-7261 TCGA-CV-7422 TCGA-CV-7435 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 
        1099         1957         1959          237          828          773 
TCGA-D6-6823 TCGA-D6-8569 TCGA-D6-A4ZB TCGA-DQ-5629 TCGA-DQ-7589 TCGA-DQ-7592 
         701          128          104          516          575          299 
TCGA-F7-A620 TCGA-HD-A633 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-IQ-A61E TCGA-IQ-A61H 
          13           49          111           33          588          412 

$`2P 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-5557 TCGA-BA-5558 TCGA-BA-5559 
        1288         1762          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-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BB-4217 
         236          513          351          216          182          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-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 
         485          142          613          392          462          993 
TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 
         642          369          395          240         1960         1330 
TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5363 
         811         1268          488          173         1081         1977 
TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6011 
        1980         1966         1966         1975          413          424 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 
         433          594          629           45          432           98 
TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6996 TCGA-CN-6997 
        1970          202          224          394          432          429 
TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W 
          46          443          447          526          484          348 
TCGA-CN-A63Y TCGA-CN-A641 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 
         175          367         1466         1207          654         1660 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 
         896         1399          341          129          870         1000 
TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 
        1057          985         1959         1959          815         1461 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 
        1378         1007          509         1309          901          877 
TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD 
         968         1960          613         1963          545          548 
TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5248 
         393          391          303          608         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-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-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-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 
         911         1472          522         1950         3295         1438 
TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 
         584          546         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-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-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-7095 TCGA-CV-7097 
        1966         1957         1969         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-7238 TCGA-CV-7248 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7424 
        1444         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-7440 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A461 TCGA-CV-A6JD TCGA-CV-A6JE 
        1981          851         1945         1954         1970          750 
TCGA-CV-A6JN TCGA-CX-7082 TCGA-CX-7085 TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 
         717          317          321          292           77          491 
TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-DQ-5624 TCGA-DQ-5625 
         154          568          106          112         1778         1081 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7593 
        1030          548         1965          775          622          369 
TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 
         368          324          340          564          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-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-A634 TCGA-HL-7533 TCGA-IQ-7630 
          24           25           11           10         1057          485 
TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61G TCGA-IQ-A61J TCGA-IQ-A61L TCGA-IQ-A61O 
         122          441          360          440          351          360 
TCGA-KU-A66S TCGA-KU-A66T TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D 
         224          210           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         1652          721 
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 
          64 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               13                 2 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             3837              3835 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              620               629 
[1] "13.0 - 3837.0 (620.0)" "2.0 - 3835.0 (629.0)" 
[1] "hr=" "1.7"
D3V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  2P GAIN MUTATED         4       13        14        34         2
  2P GAIN WILD-TYPE      20       50        57       158         7
D3V3, multiclass
           clus
vv          2P GAIN MUTATED 2P GAIN WILD-TYPE
  STAGE I                 4                20
  STAGE II               13                50
  STAGE III              14                57
  STAGE IVA              34               158
  STAGE IVB               2                 7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  2P GAIN MUTATED     4  18  19  26
  2P GAIN WILD-TYPE  36  90  66 105
D3V4, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  T1               4                36
  T2              18                90
  T3              19                66
  T4              26               105
[1] 4 2
[1] 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    30   8  21   1
  2P GAIN WILD-TYPE 106  48 108   6
D3V5, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  N0              30               106
  N1               8                48
  N2              21               108
  N3               1                 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"
D3V6, binary
                   cls
clus                 0  1
  2P GAIN MUTATED   12  8
  2P GAIN WILD-TYPE 96 40
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     12    8
  2P GAIN WILD-TYPE   96   40
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  M0              12                96
  MX               8                40
[1] 2 2
[1] FALSE
D3V7, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    15  58
  2P GAIN WILD-TYPE 106 238
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     15   58
  2P GAIN WILD-TYPE  106  238
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE              15               106
  MALE                58               238
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  2P GAIN MUTATED                                      73
  2P GAIN WILD-TYPE                                   337
                   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                                                     0
  2P GAIN WILD-TYPE                                                   6
D3V8, multiclass
                                                             clus
vv                                                            2P GAIN 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                       0
                                                             clus
vv                                                            2P GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     337
  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"
D3V9, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    15  58
  2P GAIN WILD-TYPE  64 280
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     15   58
  2P GAIN WILD-TYPE   64  280
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  NO               15                64
  YES              58               280
[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                                0    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2P GAIN MUTATED                           7    64
  2P GAIN WILD-TYPE                        26   297
D3V12, multiclass
                                  clus
vv                                 2P GAIN MUTATED 2P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      7                26
  WHITE                                         64               297
[1] 4 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  66
  2P GAIN WILD-TYPE  14 315
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      4   66
  2P GAIN WILD-TYPE   14  315
                        clus
vv                       2P GAIN MUTATED 2P GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                14
  NOT HISPANIC OR LATINO              66               315
[1] 2 2
[1] FALSE

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                 0   1
  2Q GAIN MUTATED    33  13
  2Q GAIN WILD-TYPE 224  85
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               46               309 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               13                85 
$`2Q GAIN MUTATED`
TCGA-BA-4075 TCGA-BA-A4IF TCGA-BB-8596 TCGA-CN-4727 TCGA-CN-4742 TCGA-CN-5356 
         283          895         1955          452         1988          512 
TCGA-CN-5359 TCGA-CN-5374 TCGA-CN-6012 TCGA-CN-6994 TCGA-CN-A63T TCGA-CQ-5329 
        1980          290          629          119          225         1422 
TCGA-CQ-5332 TCGA-CQ-6224 TCGA-CQ-6228 TCGA-CR-5247 TCGA-CR-6477 TCGA-CR-7365 
         317          985         1959          358          514         1191 
TCGA-CR-7383 TCGA-CV-5430 TCGA-CV-5434 TCGA-CV-5440 TCGA-CV-6941 TCGA-CV-7091 
        1954         1955         3295         1978         1959         1959 
TCGA-CV-7235 TCGA-CV-7242 TCGA-CV-7245 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 
        1724         1095          797         1960         1976         1099 
TCGA-CV-7422 TCGA-CV-7435 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6823 TCGA-D6-8569 
        1957         1959          237          828          701          128 
TCGA-D6-A4ZB TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7592 TCGA-HD-A6HZ 
         104          516         1965          575          299          111 
TCGA-HD-A6I0 TCGA-IQ-A61E TCGA-IQ-A61H TCGA-MT-A67D 
          33          588          412           56 

$`2Q 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-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-6871 TCGA-BA-6872 
        1747          190          644          451           63          384 
TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE 
         113          236          513          351          216          182 
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-8601 TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 
         428          436          624            5            4          799 
TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 
         721          485          142          613          392          462 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 
         993          642          369          395          240         1960 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5360 
        1330          811         1268          488          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          413 
TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 
         630          424          433          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          424          224 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 
         318          611          394          432          429           46 
TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y 
         443          447          526          484          348          175 
TCGA-CN-A641 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5330 
         367         1466         1207          654         1660          896 
TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 
        1399          341          129          870         1000         1057 
TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 
        1959          815         1461         1378         1007          509 
TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
        1309          901          877          968         1960          613 
TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH 
        1963          545          548          393          391          303 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 
         608         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-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-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-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-5435 TCGA-CV-5436 
         911         1472          522         1950         1438          584 
TCGA-CV-5439 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 
         546         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-7095 TCGA-CV-7097 
        1957         1969         1959         3837         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-7238 TCGA-CV-7243 TCGA-CV-7248 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 
        1444          954         1967         1974         1948         1955 
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-A461 TCGA-CV-A6JD 
        1958         1981          851         1945         1954         1970 
TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CX-7082 TCGA-CX-7085 TCGA-D6-6516 TCGA-D6-6517 
         750          717          317          321          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          112 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 
        1778         1081         1030          548          775          622 
TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 
         369          368          324          340          564          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-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-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61G 
          10         1057          485          122          441          360 
TCGA-IQ-A61J TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-MT-A51W 
         440          351          360          224          210           14 
TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A5Q5 
          34          392          111          112          254          910 
TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 
        1652          721         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 
         228          225           64 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               33                 2 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             3295              3837 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            812.5             622.0 
[1] "33.0 - 3295.0 (812.5)" "2.0 - 3837.0 (622.0)" 
[1] "hr=" "1.3"
D4V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  2Q GAIN MUTATED         2       10        11        28         0
  2Q GAIN WILD-TYPE      22       53        60       164         9
D4V3, multiclass
           clus
vv          2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  STAGE I                 2                22
  STAGE II               10                53
  STAGE III              11                60
  STAGE IVA              28               164
  STAGE IVB               0                 9
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  2Q GAIN MUTATED     3  15  13  20
  2Q GAIN WILD-TYPE  37  93  72 111
D4V4, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  T1               3                37
  T2              15                93
  T3              13                72
  T4              20               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
  2Q GAIN MUTATED    25   5  16   0
  2Q GAIN WILD-TYPE 111  51 113   7
D4V5, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  N0              25               111
  N1               5                51
  N2              16               113
  N3               0                 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"
D4V6, binary
                   cls
clus                 0  1
  2Q GAIN MUTATED    9  8
  2Q GAIN WILD-TYPE 99 40
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      9    8
  2Q GAIN WILD-TYPE   99   40
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  M0               9                99
  MX               8                40
[1] 2 2
[1] FALSE
D4V7, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    14  44
  2Q GAIN WILD-TYPE 107 252
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     14   44
  2Q GAIN WILD-TYPE  107  252
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE              14               107
  MALE                44               252
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  2Q GAIN MUTATED                                      58
  2Q GAIN WILD-TYPE                                   352
                   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                                                   6
D4V8, multiclass
                                                             clus
vv                                                            2Q GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    58
  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                                     352
  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"
D4V9, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    14  44
  2Q GAIN WILD-TYPE  65 294
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     14   44
  2Q GAIN WILD-TYPE   65  294
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  NO               14                65
  YES              44               294
[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                                0    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2Q GAIN MUTATED                           6    51
  2Q GAIN WILD-TYPE                        27   310
D4V12, multiclass
                                  clus
vv                                 2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      6                27
  WHITE                                         51               310
[1] 4 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  53
  2Q GAIN WILD-TYPE  14 328
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      4   53
  2Q GAIN WILD-TYPE   14  328
                        clus
vv                       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                14
  NOT HISPANIC OR LATINO              53               328
[1] 2 2
[1] FALSE

Clustering(5) Variable = 3P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                 0   1
  3P GAIN MUTATED    45  10
  3P GAIN WILD-TYPE 212  88
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               55               300 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               10                88 
$`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          462 
TCGA-CN-4731 TCGA-CN-5356 TCGA-CN-6013 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6023 
         993          512          433           98         1970          424 
TCGA-CN-6988 TCGA-CN-6994 TCGA-CQ-5323 TCGA-CQ-6223 TCGA-CR-6467 TCGA-CR-6470 
         318          119         1466         1057         1777         1521 
TCGA-CR-6474 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6492 TCGA-CR-7365 
        1971          354          234          379          479         1191 
TCGA-CR-7368 TCGA-CR-7389 TCGA-CR-7397 TCGA-CV-5431 TCGA-CV-5442 TCGA-CV-5977 
        1245          392          216          522         2327         1840 
TCGA-CV-6433 TCGA-CV-7097 TCGA-CV-7243 TCGA-CV-7261 TCGA-DQ-5624 TCGA-DQ-7595 
         641         1970          954         1099         1778          324 
TCGA-DQ-7596 TCGA-F7-8489 TCGA-F7-A623 TCGA-HD-7917 TCGA-HD-8314 TCGA-HD-8634 
         340          658            6           37           44           24 
TCGA-HD-A634 TCGA-IQ-A61E TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A6SX TCGA-P3-A6T8 
          10          588          112          254         1954          400 
TCGA-QK-A6IJ 
          64 

$`3P GAIN WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 
         462          283          415          248          722         1288 
TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 
         520          725         1636          644          451           63 
TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE 
         384          236          513          351          216          182 
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-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-4725 
        1955          624            5            4          799          485 
TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4733 TCGA-CN-4735 
         142          452          613          392          642          369 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 
         395          240         1960         1330          811         1268 
TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 
        1988          488          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          413          290 
TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 
         630          424          629          594          629           45 
TCGA-CN-6019 TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6996 
         432          202          224          611          394          432 
TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63U 
         429           46          443          447          225          526 
TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 TCGA-CQ-5324 TCGA-CQ-5325 
         484          348          175          367         1207          654 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 
        1660         1422          896         1399          317          341 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 
         129          870         1000          985         1959         1959 
TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 
         815         1461         1378         1007          509         1309 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CA 
         901          877          968         1960          613         1963 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI 
         545          548          393          391          303          608 
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-7238 
        1939         1945         1987         1979         1724         1444 
TCGA-CV-7242 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7406 
        1095          797         1967         1960         1976         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-A461 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN 
         851         1945         1954         1970          750          717 
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-D6-6826 TCGA-D6-6827 TCGA-D6-8568 
         701           77          491          154          568          106 
TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 
         128          112          104         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-7593 TCGA-DQ-7594 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-A50G TCGA-F7-A50I 
         369          368          564          490           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-HD-7229 TCGA-HD-7753 
          58          133          414          403            2            5 
TCGA-HD-7754 TCGA-HD-8224 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A6HZ 
          25           55           25           11           49          111 
TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61G 
          33         1057          485          122          441          360 
TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T 
         412          440          351          360          224          210 
TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-P3-A5Q5 
          14           34          392           56          111          910 
TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T4 
        1652          721         1120          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 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                6                 2 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             2878              3837 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
              512               640 
[1] "6.0 - 2878.0 (512.0)" "2.0 - 3837.0 (640.0)"
[1] "hr=" "1.4"
D5V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  3P GAIN MUTATED         3        9        12        31         1
  3P GAIN WILD-TYPE      21       54        59       161         8
D5V3, multiclass
           clus
vv          3P GAIN MUTATED 3P GAIN WILD-TYPE
  STAGE I                 3                21
  STAGE II                9                54
  STAGE III              12                59
  STAGE IVA              31               161
  STAGE IVB               1                 8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  3P GAIN MUTATED     7  20   9  21
  3P GAIN WILD-TYPE  33  88  76 110
D5V4, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  T1               7                33
  T2              20                88
  T3               9                76
  T4              21               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
  3P GAIN MUTATED    19  11  22   1
  3P GAIN WILD-TYPE 117  45 107   6
D5V5, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  N0              19               117
  N1              11                45
  N2              22               107
  N3               1                 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"
D5V6, binary
                   cls
clus                 0  1
  3P GAIN MUTATED   15  9
  3P GAIN WILD-TYPE 93 39
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     15    9
  3P GAIN WILD-TYPE   93   39
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  M0              15                93
  MX               9                39
[1] 2 2
[1] FALSE
D5V7, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    16  52
  3P GAIN WILD-TYPE 105 244
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     16   52
  3P GAIN WILD-TYPE  105  244
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE              16               105
  MALE                52               244
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  3P GAIN MUTATED                                      67
  3P GAIN WILD-TYPE                                   343
                   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                                                   5
D5V8, multiclass
                                                             clus
vv                                                            3P 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                       1
                                                             clus
vv                                                            3P GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     343
  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"
D5V9, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    15  53
  3P GAIN WILD-TYPE  64 285
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     15   53
  3P GAIN WILD-TYPE   64  285
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  NO               15                64
  YES              53               285
[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                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3P GAIN MUTATED                           5    59
  3P GAIN WILD-TYPE                        28   302
D5V12, multiclass
                                  clus
vv                                 3P GAIN MUTATED 3P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      5                28
  WHITE                                         59               302
[1] 4 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     3  63
  3P GAIN WILD-TYPE  15 318
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      3   63
  3P GAIN WILD-TYPE   15  318
                        clus
vv                       3P GAIN MUTATED 3P GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                15
  NOT HISPANIC OR LATINO              63               318
[1] 2 2
[1] FALSE

Clustering(6) Variable = 3Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                 0   1
  3Q GAIN MUTATED   126  50
  3Q GAIN WILD-TYPE 131  48
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              176               179 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               50                48 
$`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-A6D8 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 
         895          513         2878          278          140          133 
TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 
         423          687          428          436         1955          624 
TCGA-C9-A47Z TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 
           5          721          485          142          452          613 
TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4739 
         392          462          993          395          240         1330 
TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 
         811         1268         1988          512          173         1980 
TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5367 TCGA-CN-5373 TCGA-CN-5374 
        1081         1977         1980         1966          413          290 
TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 
         629          433          594          432           98         1970 
TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6998 
         424          224          318          611          119           46 
TCGA-CN-A49B TCGA-CN-A63T TCGA-CQ-5323 TCGA-CQ-5329 TCGA-CQ-6223 TCGA-CQ-6228 
         447          225         1466         1422         1057         1959 
TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7067 TCGA-CQ-7069 TCGA-CQ-A4C6 TCGA-CQ-A4C9 
         815         1378          509          901          968          613 
TCGA-CQ-A4CA TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CR-5243 TCGA-CR-5249 TCGA-CR-6467 
        1963          393          391         2562         1152         1777 
TCGA-CR-6470 TCGA-CR-6474 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6484 TCGA-CR-6487 
        1521         1971         1969          362          354          234 
TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-7365 TCGA-CR-7368 TCGA-CR-7369 
         379          350          479         1191         1245         1960 
TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7377 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 
        1979          759         1968          997         1430         1951 
TCGA-CR-7389 TCGA-CR-7397 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 
         392          216          911         1472         1955          522 
TCGA-CV-5432 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5444 
        1950          584          546         1978         2327         2437 
TCGA-CV-5973 TCGA-CV-5977 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6935 TCGA-CV-6936 
        2641         1840         1665          641         1969         1952 
TCGA-CV-6945 TCGA-CV-6954 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7097 TCGA-CV-7101 
        1969         1957         3837         1959         1970         1939 
TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 
        1945         1987         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-7424 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-A461 TCGA-CX-7086 TCGA-CX-7219 
        1947         1958         1959         1954          237          828 
TCGA-D6-8569 TCGA-D6-A4ZB TCGA-DQ-5624 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7589 
         128          104         1778         1030          548          575 
TCGA-DQ-7592 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G 
         299          324          340          490          658           15 
TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61V TCGA-F7-A623 TCGA-HD-7754 TCGA-HD-7917 
          92          585          384            6           25           37 
TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-A634 TCGA-HL-7533 TCGA-IQ-A61E 
          55           44           24           10         1057          588 
TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J TCGA-KU-A66T TCGA-MT-A67G TCGA-MZ-A6I9 
         360          412          440          210          112          254 
TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T4 TCGA-P3-A6T8 
         910         1652         1120         1954         1968          400 
TCGA-QK-A652 TCGA-QK-A6IJ 
         357           64 

$`3Q GAIN WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-5152 TCGA-BA-5555 TCGA-BA-5556 
         462          283          415         1288          520          725 
TCGA-BA-5558 TCGA-BA-6869 TCGA-BA-6871 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE 
        1636          644           63          351          216          182 
TCGA-BB-4217 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7866 TCGA-BB-7870 
         187          558          310          536          638         1153 
TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4738 TCGA-CN-5355 
           4          799          642          369         1960          488 
TCGA-CN-5366 TCGA-CN-5370 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6017 TCGA-CN-6018 
        1966         1975          630          424          629           45 
TCGA-CN-6022 TCGA-CN-6992 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-A498 TCGA-CN-A63U 
         202          394          432          429          443          526 
TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 TCGA-CQ-5324 TCGA-CQ-5325 
         484          348          175          367         1207          654 
TCGA-CQ-5327 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 
        1660          896         1399          317          341          129 
TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-7063 TCGA-CQ-7065 
         870         1000          985         1959         1461         1007 
TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-A4C7 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CH 
        1309          877         1960          545          548          303 
TCGA-CQ-A4CI TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5250 TCGA-CR-6471 TCGA-CR-6472 
         608          358         1663          799         1966         1050 
TCGA-CR-6473 TCGA-CR-6477 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6493 TCGA-CR-7364 
        1125          514          311          345         1956         1435 
TCGA-CR-7367 TCGA-CR-7370 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7379 
        1440          105          889           30          972         1036 
TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
         796         1954          907          913          946          908 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CV-5434 
         898          930          156          181         1077         3295 
TCGA-CV-5435 TCGA-CV-5441 TCGA-CV-5443 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 
        1438         2886         1958          519          406          701 
TCGA-CV-5976 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 
        1478          215         1315         1899         1970         1948 
TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6952 TCGA-CV-6960 TCGA-CV-6961 
        1959         3835         1948         1966         1969         1959 
TCGA-CV-7095 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7418 
        1970         1936         1959         1979         1724         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-7440 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN 
        1981          851         1945         1970          750          717 
TCGA-CX-7082 TCGA-CX-7085 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 
         317          321          773          292          701           77 
TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-DQ-5625 
         491          154          568          106          112         1081 
TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7593 TCGA-DQ-7594 
         516         1965          775          622          369          368 
TCGA-F7-7848 TCGA-F7-A61S TCGA-F7-A61W TCGA-F7-A620 TCGA-H7-7774 TCGA-H7-8501 
         564            3           14           13          407           58 
TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-8635 
         133          414          403            2            5           25 
TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-IQ-7630 TCGA-IQ-7631 
          11           49          111           33          485          122 
TCGA-IQ-7632 TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-MT-A51W TCGA-MT-A51X 
         441          351          360          224           14           34 
TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-P3-A5QE TCGA-P3-A6T0 TCGA-P3-A6T2 
         392           56          111          721          578         1917 
TCGA-QK-A64Z TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II 
         553          245          218          228          225 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                5                 2 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             3837              3835 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            649.5             608.0 
[1] "5.0 - 3837.0 (649.5)" "2.0 - 3835.0 (608.0)"
[1] "hr=" "1.3"
D6V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  3Q GAIN MUTATED        10       29        34       101         5
  3Q GAIN WILD-TYPE      14       34        37        91         4
D6V3, multiclass
           clus
vv          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  STAGE I                10                14
  STAGE II               29                34
  STAGE III              34                37
  STAGE IVA             101                91
  STAGE IVB               5                 4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  3Q GAIN MUTATED   18 56 42 66
  3Q GAIN WILD-TYPE 22 52 43 65
D6V4, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  T1              18                22
  T2              56                52
  T3              42                43
  T4              66                65
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  3Q GAIN MUTATED   58 30 73  5
  3Q GAIN WILD-TYPE 78 26 56  2
D6V5, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  N0              58                78
  N1              30                26
  N2              73                56
  N3               5                 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"
D6V6, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED   52 24
  3Q GAIN WILD-TYPE 56 24
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     52   24
  3Q GAIN WILD-TYPE   56   24
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  M0              52                56
  MX              24                24
[1] 2 2
[1] FALSE
D6V7, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    51 156
  3Q GAIN WILD-TYPE  70 140
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     51  156
  3Q GAIN WILD-TYPE   70  140
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE              51                70
  MALE               156               140
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  3Q GAIN MUTATED                                     204
  3Q GAIN WILD-TYPE                                   206
                   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                                                     3
  3Q GAIN WILD-TYPE                                                   3
D6V8, multiclass
                                                             clus
vv                                                            3Q GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                   204
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       3
                                                             clus
vv                                                            3Q GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     206
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                 1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V9, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    47 160
  3Q GAIN WILD-TYPE  32 178
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     47  160
  3Q GAIN WILD-TYPE   32  178
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  NO               47                32
  YES             160               178
[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                                0     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3Q GAIN MUTATED                          16   177
  3Q GAIN WILD-TYPE                        17   184
D6V12, multiclass
                                  clus
vv                                 3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          5                 5
  BLACK OR AFRICAN AMERICAN                     16                17
  WHITE                                        177               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"
D6V13, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    10 186
  3Q GAIN WILD-TYPE   8 195
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     10  186
  3Q GAIN WILD-TYPE    8  195
                        clus
vv                       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  HISPANIC OR LATINO                  10                 8
  NOT HISPANIC OR LATINO             186               195
[1] 2 2
[1] FALSE

Clustering(7) Variable = 4P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                 0   1
  4P GAIN MUTATED    21   8
  4P GAIN WILD-TYPE 236  90
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               29               326 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                8                90 
$`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          452          240 
TCGA-CN-4740 TCGA-CQ-6224 TCGA-CQ-7069 TCGA-CR-5247 TCGA-CR-7389 TCGA-CV-5430 
         811          985          901          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-7433 TCGA-DQ-5625 TCGA-DQ-7592 
        3837         1945         1987         1984         1081          299 
TCGA-F7-A623 TCGA-HD-7753 TCGA-IQ-A61L TCGA-MT-A67D TCGA-P3-A6T4 
           6            5          351           56         1968 

$`4P 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-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-A4IF TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BB-4217 
         895          513          351          216          182          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-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 
         485          142          613          392          462          993 
TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4741 
         642          369          395         1960         1330         1268 
TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 
        1988          488          512          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          413 
TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 
         290          630          424          629          433          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-6994 
         424          224          318          611          394          119 
TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63T 
         432          429           46          443          447          225 
TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 TCGA-CQ-5323 
         526          484          348          175          367         1466 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 
        1207          654         1660         1422          896         1399 
TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 
         317          341          129          870         1000         1057 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 
        1959         1959          815         1461         1378         1007 
TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
         509         1309          877          968         1960          613 
TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH 
        1963          545          548          393          391          303 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 
         608         2562         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-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-7402 TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5432 
         181         1077          911         1472          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-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-6952 
        1969         1952         1959         3835         1948         1966 
TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 
        1969         1959         1959         1970         1970         1936 
TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7242 
        1959         1939         1979         1724         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-A461 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN 
         851         1945         1954         1970          750          717 
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-D6-6826 TCGA-D6-6827 TCGA-D6-8568 
         701           77          491          154          568          106 
TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-DQ-5624 TCGA-DQ-5629 TCGA-DQ-5630 
         128          112          104         1778          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-F7-8298 TCGA-F7-8489 
         368          324          340          564          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-HD-7229 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 
           2           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-MT-A51W 
         412          440          360          224          210           14 
TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A5Q5 
          34          392          111          112          254          910 
TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 
        1652          721         1120         1954          578         1917 
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-A6IJ 
         225           64 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                5                 2 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             3837              3835 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            901.0             623.5 
[1] "5.0 - 3837.0 (901.0)" "2.0 - 3835.0 (623.5)"
[1] "hr=" "1.7"
D7V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  4P GAIN MUTATED         1        6         3        18         0
  4P GAIN WILD-TYPE      23       57        68       174         9
D7V3, multiclass
           clus
vv          4P GAIN MUTATED 4P GAIN WILD-TYPE
  STAGE I                 1                23
  STAGE II                6                57
  STAGE III               3                68
  STAGE IVA              18               174
  STAGE IVB               0                 9
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  4P GAIN MUTATED     2  10   3  13
  4P GAIN WILD-TYPE  38  98  82 118
D7V4, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  T1               2                38
  T2              10                98
  T3               3                82
  T4              13               118
[1] 4 2
[1] 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  11   0
  4P GAIN WILD-TYPE 128  52 118   7
D7V5, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  N0               8               128
  N1               4                52
  N2              11               118
  N3               0                 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"
D7V6, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     5   2
  4P GAIN WILD-TYPE 103  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      5    2
  4P GAIN WILD-TYPE  103   46
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  M0               5               103
  MX               2                46
[1] 2 2
[1] FALSE
D7V7, binary
                   cls
clus                  0   1
  4P GAIN MUTATED    10  24
  4P GAIN WILD-TYPE 111 272
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     10   24
  4P GAIN WILD-TYPE  111  272
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE              10               111
  MALE                24               272
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  4P GAIN MUTATED                                      34
  4P GAIN WILD-TYPE                                   376
                   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                                                   6
D7V8, multiclass
                                                             clus
vv                                                            4P 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                       0
                                                             clus
vv                                                            4P 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                         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"
D7V9, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     8  26
  4P GAIN WILD-TYPE  71 312
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      8   26
  4P GAIN WILD-TYPE   71  312
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  NO                8                71
  YES              26               312
[1] 2 2
[1] FALSE
D7V10, continuous
D7V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4P GAIN MUTATED                                  1     0
  4P GAIN WILD-TYPE                                0    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4P GAIN MUTATED                           5    27
  4P GAIN WILD-TYPE                        28   334
D7V12, multiclass
                                  clus
vv                                 4P GAIN MUTATED 4P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      5                28
  WHITE                                         27               334
[1] 4 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     3  27
  4P GAIN WILD-TYPE  15 354
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      3   27
  4P GAIN WILD-TYPE   15  354
                        clus
vv                       4P GAIN MUTATED 4P GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                15
  NOT HISPANIC OR LATINO              27               354
[1] 2 2
[1] FALSE

Clustering(8) Variable = 4Q GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                 0   1
  4Q GAIN MUTATED    16   9
  4Q GAIN WILD-TYPE 241  89
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               25               330 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                9                89 
$`4Q GAIN MUTATED`
TCGA-BA-6872 TCGA-BB-4225 TCGA-CN-4727 TCGA-CN-4740 TCGA-CN-5363 TCGA-CQ-7069 
         384          140          452          811         1977          901 
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 
        1968 

$`4Q 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-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-7269 TCGA-BA-A4IF TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB 
         113          236          895          513          351          216 
TCGA-BA-A6DE TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-4228 
         182          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          485          142          613          392 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 
         462          993          642          369          395          240 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 
        1960         1330         1268         1988          488          512 
TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 
         173         1980         1081         1980         1966         1966 
TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 
        1975          413          290          630          424          629 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 
         433          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          424          224          318          611 
TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 
         394          119          432          429           46          443 
TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y 
         447          225          526          484          348          175 
TCGA-CN-A641 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 
         367         1466         1207          654         1660         1422 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 
         896         1399          317          341          129          870 
TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 
        1000         1057          985         1959         1959          815 
TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7071 
        1461         1378         1007          509         1309          877 
TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD 
         968         1960          613         1963          545          548 
TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5248 
         393          391          303          608         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-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-6488 TCGA-CR-6492 TCGA-CR-6493 
         345          354          234          379          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-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5439 
        1955          522         1950         3295         1438          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-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-6952 TCGA-CV-6954 
        1952         1959         3835         1948         1966         1957 
TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 
        1969         1959         1959         1970         1970         1936 
TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 
        1959         1939         1987         1979         1724         1444 
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-7434 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45O 
        1972         1937         1958         1959         1981          851 
TCGA-CV-A45Q TCGA-CV-A461 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CX-7082 
        1945         1954         1970          750          717          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-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 
          77          491          568          106          128          112 
TCGA-D6-A4ZB TCGA-DQ-5624 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 
         104         1778          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          564          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-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-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-MT-A51W TCGA-MT-A51X 
         440          360          224          210           14           34 
TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QA 
         392          111          112          254          910         1652 
TCGA-P3-A5QE TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T8 TCGA-QK-A64Z 
         721         1954          578         1917          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           64 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                5                 2 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
             3837              3835 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            797.0             626.5 
[1] "5.0 - 3837.0 (797.0)" "2.0 - 3835.0 (626.5)"
[1] "hr=" "1"  
D8V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  4Q GAIN MUTATED         1        6         0        15         2
  4Q GAIN WILD-TYPE      23       57        71       177         7
D8V3, multiclass
           clus
vv          4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  STAGE I                 1                23
  STAGE II                6                57
  STAGE III               0                71
  STAGE IVA              15               177
  STAGE IVB               2                 7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  4Q GAIN MUTATED     2   6   4  12
  4Q GAIN WILD-TYPE  38 102  81 119
D8V4, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  T1               2                38
  T2               6               102
  T3               4                81
  T4              12               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 GAIN MUTATED     8   1  10   2
  4Q GAIN WILD-TYPE 128  55 119   5
D8V5, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  N0               8               128
  N1               1                55
  N2              10               119
  N3               2                 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"
D8V6, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     6   2
  4Q GAIN WILD-TYPE 102  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      6    2
  4Q GAIN WILD-TYPE  102   46
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  M0               6               102
  MX               2                46
[1] 2 2
[1] FALSE
D8V7, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     8  21
  4Q GAIN WILD-TYPE 113 275
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      8   21
  4Q GAIN WILD-TYPE  113  275
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE               8               113
  MALE                21               275
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  4Q GAIN MUTATED                                      28
  4Q GAIN WILD-TYPE                                   382
                   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                                                   5
D8V8, multiclass
                                                             clus
vv                                                            4Q GAIN 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                                                            4Q GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     382
  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"
D8V9, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     3  26
  4Q GAIN WILD-TYPE  76 312
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      3   26
  4Q GAIN WILD-TYPE   76  312
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  NO                3                76
  YES              26               312
[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                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4Q GAIN MUTATED                           6    22
  4Q GAIN WILD-TYPE                        27   339
D8V12, multiclass
                                  clus
vv                                 4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      6                27
  WHITE                                         22               339
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V13, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     3  23
  4Q GAIN WILD-TYPE  15 358
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      3   23
  4Q GAIN WILD-TYPE   15  358
                        clus
vv                       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                15
  NOT HISPANIC OR LATINO              23               358
[1] 2 2
[1] FALSE

Clustering(9) Variable = 5P GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                 0   1
  5P GAIN MUTATED   101  40
  5P GAIN WILD-TYPE 156  58
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              141               214 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               40                58 
$`5P GAIN MUTATED`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4078 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 
         462          283          276          520          725         1636 
TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 
        1747          190          644          451          384          113 
TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A6D8 TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BB-4217 
         236          895          513          216          182          187 
TCGA-BB-4223 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7864 TCGA-BB-7870 
        2878          133          558          310          687         1153 
TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A47Z TCGA-CN-4723 TCGA-CN-4727 TCGA-CN-4729 
        1955          624            5          721          452          392 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 
         462          993          395          240         1960         1330 
TCGA-CN-4742 TCGA-CN-5359 TCGA-CN-5363 TCGA-CN-5366 TCGA-CN-6010 TCGA-CN-6011 
        1988         1980         1977         1966          630          424 
TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6023 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6997 
         432           98          424          394          119          429 
TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63W TCGA-CQ-5330 TCGA-CQ-6221 TCGA-CQ-6224 
         443          447          348          896         1000          985 
TCGA-CQ-7064 TCGA-CQ-7067 TCGA-CQ-A4CA TCGA-CQ-A4CD TCGA-CR-5243 TCGA-CR-6467 
        1378          509         1963          548         2562         1777 
TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6484 TCGA-CR-6488 
        1966         1125         1971          514          354          379 
TCGA-CR-6492 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7383 
         479         1191         1440         1245         1960         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-A6JE 
        1945         1987         1724          797         1947          750 
TCGA-CX-7086 TCGA-D6-8568 TCGA-D6-8569 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 
         237          106          128          516         1030          548 
TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7592 TCGA-DQ-7596 TCGA-F7-A50J TCGA-F7-A61S 
         575          775          299          340          585            3 
TCGA-F7-A620 TCGA-H7-8502 TCGA-HD-7753 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8635 
          13          133            5           37           55           25 
TCGA-HD-A6HZ TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-A61E TCGA-IQ-A61J TCGA-IQ-A61O 
         111         1057          485          588          440          360 
TCGA-KU-A66S TCGA-KU-A66T TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67D TCGA-P3-A5QA 
         224          210           14           34           56         1652 
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-A6IG TCGA-QK-A6IJ 
         357          218           64 

$`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-A6DA TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-7862 
         623           63          351          278          140          536 
TCGA-BB-7863 TCGA-BB-7866 TCGA-BB-7871 TCGA-BB-7872 TCGA-C9-A480 TCGA-CN-4722 
         423          638          428          436            4          799 
TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4740 
         485          142          613          642          369          811 
TCGA-CN-4741 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5365 
        1268          488          512          173         1081         1980 
TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6012 TCGA-CN-6013 
        1966         1975          413          290          629          433 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6024 
         594          629           45         1970          202          224 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A63T TCGA-CN-A63U 
         318          611          432           46          225          526 
TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A641 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
         484          175          367         1466         1207          654 
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-6223 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 
         870         1057         1959         1959          815         1461 
TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 
        1007         1309          901          877          968         1960 
TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI 
         613          545          393          391          303          608 
TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6470 TCGA-CR-6472 
         358         1663         1152          799         1521         1050 
TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6491 
        1969          362          311          345          234          350 
TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 
        1956         1435          105         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-7390 TCGA-CR-7391 TCGA-CR-7393 TCGA-CR-7394 
        1430         1951          907          913          908          898 
TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7401 TCGA-CR-7402 TCGA-CV-5430 TCGA-CV-5432 
         930          216         1077          911         1955         1950 
TCGA-CV-5434 TCGA-CV-5436 TCGA-CV-5441 TCGA-CV-5443 TCGA-CV-5971 TCGA-CV-5973 
        3295          584         2886         1958          701         2641 
TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 
        1478         1840         1315         1665          641         1899 
TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6952 TCGA-CV-6960 
        1948         1969         3835         1948         1966         1969 
TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7183 TCGA-CV-7238 TCGA-CV-7242 
        1970         1936         1959         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-7427 TCGA-CV-7428 TCGA-CV-7430 
        1948         1955         1957         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-A461 TCGA-CV-A6JD TCGA-CV-A6JN TCGA-CX-7082 TCGA-CX-7085 
        1945         1954         1970          717          317          321 
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-A4Z9 TCGA-D6-A4ZB TCGA-DQ-5624 TCGA-DQ-5625 
         154          568          112          104         1778         1081 
TCGA-DQ-7588 TCGA-DQ-7591 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-F7-7848 
        1965          622          369          368          324          564 
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-A623 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-HD-7229 
           6          407           58          414          403            2 
TCGA-HD-7754 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 
          25           44           24           11           49           10 
TCGA-HD-A6I0 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61L 
          33          122          441          360          412          351 
TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QE 
         392          111          112          254          910          721 
TCGA-P3-A6T0 TCGA-QK-A6IF TCGA-QK-A6IH TCGA-QK-A6II 
         578          245          228          225 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                3                 2 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             3837              3835 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              548               701 
[1] "3.0 - 3837.0 (548.0)" "2.0 - 3835.0 (701.0)"
[1] "hr=" "1"  
D9V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  5P GAIN MUTATED         7       19        31        75         5
  5P GAIN WILD-TYPE      17       44        40       117         4
D9V3, multiclass
           clus
vv          5P GAIN MUTATED 5P GAIN WILD-TYPE
  STAGE I                 7                17
  STAGE II               19                44
  STAGE III              31                40
  STAGE IVA              75               117
  STAGE IVB               5                 4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  5P GAIN MUTATED   13 41 32 53
  5P GAIN WILD-TYPE 27 67 53 78
D9V4, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  T1              13                27
  T2              41                67
  T3              32                53
  T4              53                78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  5P GAIN MUTATED   44 27 49  4
  5P GAIN WILD-TYPE 92 29 80  3
D9V5, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  N0              44                92
  N1              27                29
  N2              49                80
  N3               4                 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"
D9V6, binary
                   cls
clus                 0  1
  5P GAIN MUTATED   41 24
  5P GAIN WILD-TYPE 67 24
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     41   24
  5P GAIN WILD-TYPE   67   24
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  M0              41                67
  MX              24                24
[1] 2 2
[1] FALSE
D9V7, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    38 122
  5P GAIN WILD-TYPE  83 174
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     38  122
  5P GAIN WILD-TYPE   83  174
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE              38                83
  MALE               122               174
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  5P GAIN MUTATED                                     157
  5P GAIN WILD-TYPE                                   253
                   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                                                   4
D9V8, multiclass
                                                             clus
vv                                                            5P GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                   157
  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                                     253
  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"
D9V9, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    39 121
  5P GAIN WILD-TYPE  40 217
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     39  121
  5P GAIN WILD-TYPE   40  217
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  NO               39                40
  YES             121               217
[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                                0     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5P GAIN MUTATED                          16   134
  5P GAIN WILD-TYPE                        17   227
D9V12, multiclass
                                  clus
vv                                 5P GAIN MUTATED 5P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          3                 7
  BLACK OR AFRICAN AMERICAN                     16                17
  WHITE                                        134               227
[1] 4 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     9 146
  5P GAIN WILD-TYPE   9 235
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      9  146
  5P GAIN WILD-TYPE    9  235
                        clus
vv                       5P GAIN MUTATED 5P GAIN WILD-TYPE
  HISPANIC OR LATINO                   9                 9
  NOT HISPANIC OR LATINO             146               235
[1] 2 2
[1] FALSE

Clustering(10) Variable = 5Q GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                 0   1
  5Q GAIN MUTATED    33  15
  5Q GAIN WILD-TYPE 224  83
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               48               307 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               15                83 
$`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-BB-4223 TCGA-BB-7861 TCGA-BB-7864 TCGA-CN-4738 TCGA-CN-5363 TCGA-CN-6011 
        2878          310          687         1960         1977          424 
TCGA-CN-6023 TCGA-CN-6997 TCGA-CN-A49B TCGA-CQ-6224 TCGA-CQ-7067 TCGA-CR-5243 
         424          429          447          985          509         2562 
TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6484 TCGA-CR-7389 TCGA-CV-5431 TCGA-CV-5439 
        1966         1125          354          392          522          546 
TCGA-CV-5442 TCGA-CV-5444 TCGA-CV-6441 TCGA-CV-6936 TCGA-CV-6945 TCGA-CV-6954 
        2327         2437         1970         1952         1969         1957 
TCGA-CV-7102 TCGA-CV-7235 TCGA-CV-7245 TCGA-D6-8569 TCGA-DQ-5629 TCGA-DQ-5630 
        1945         1724          797          128          516         1030 
TCGA-DQ-7590 TCGA-F7-A50J TCGA-F7-A61S TCGA-HD-8635 TCGA-HD-A6HZ TCGA-IQ-A61O 
         775          585            3           25          111          360 
TCGA-MT-A51W TCGA-P3-A5QA TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A6IG 
          14         1652         1917         1968          400          218 

$`5Q GAIN WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5151 TCGA-BA-5152 
         283          415         1983          276          722         1288 
TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 
        1762          520          623         1636         1747          190 
TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A6D8 TCGA-BA-A6DA 
          63          384          113          236          513          351 
TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BB-4217 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 
         216          182          187          278          140          133 
TCGA-BB-4228 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 
         558          536          423          638         1153          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-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 
         721          485          142          452          613          392 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 
         462          993          642          369          395          240 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 
        1330          811         1268         1988          488          512 
TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 
         173         1980         1081         1980         1966         1966 
TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6012 TCGA-CN-6013 
        1975          413          290          630          629          433 
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-6994 
         202          224          318          611          394          119 
TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V 
         432           46          443          225          526          484 
TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
         348          175          367         1466         1207          654 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 
        1660         1422          896         1399          317          341 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6227 TCGA-CQ-6228 
         129          870         1000         1057         1959         1959 
TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7069 
         815         1461         1378         1007         1309          901 
TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB 
         877          968         1960          613         1963          545 
TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5247 
         548          393          391          303          608          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-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-5443 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 
        1958          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-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6952 
        1948         1969         1959         3835         1948         1966 
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-7180 TCGA-CV-7183 TCGA-CV-7238 
        1936         1959         1939         1987         1979         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-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-A461 TCGA-CV-A6JD TCGA-CV-A6JE 
        1981          851         1945         1954         1970          750 
TCGA-CV-A6JN TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 
         717          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-A4Z9 TCGA-D6-A4ZB TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5631 
         106          112          104         1778         1081          548 
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-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G 
         324          340          564          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-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-7753 
          58          133          414          403            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-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-KU-A66S TCGA-KU-A66T TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F 
         224          210           34          392           56          111 
TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX 
         112          254          910          721         1120         1954 
TCGA-P3-A6T0 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IH TCGA-QK-A6II 
         578          553          357          245          228          225 
TCGA-QK-A6IJ 
          64 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                3                 2 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             2878              3837 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            665.5             624.0 
[1] "3.0 - 2878.0 (665.5)" "2.0 - 3837.0 (624.0)"
[1] "hr=" "1.2"
D10V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  5Q GAIN MUTATED         3        3        10        28         1
  5Q GAIN WILD-TYPE      21       60        61       164         8
D10V3, multiclass
           clus
vv          5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  STAGE I                 3                21
  STAGE II                3                60
  STAGE III              10                61
  STAGE IVA              28               164
  STAGE IVB               1                 8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  5Q GAIN MUTATED     5  11  13  16
  5Q GAIN WILD-TYPE  35  97  72 115
D10V4, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T1               5                35
  T2              11                97
  T3              13                72
  T4              16               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
  5Q GAIN MUTATED    13   9  19   1
  5Q GAIN WILD-TYPE 123  47 110   6
D10V5, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  N0              13               123
  N1               9                47
  N2              19               110
  N3               1                 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"
D10V6, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED   11 10
  5Q GAIN WILD-TYPE 97 38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     11   10
  5Q GAIN WILD-TYPE   97   38
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  M0              11                97
  MX              10                38
[1] 2 2
[1] FALSE
D10V7, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    11  42
  5Q GAIN WILD-TYPE 110 254
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     11   42
  5Q GAIN WILD-TYPE  110  254
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE              11               110
  MALE                42               254
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  5Q GAIN MUTATED                                      52
  5Q GAIN WILD-TYPE                                   358
                   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                                                   6
D10V8, multiclass
                                                             clus
vv                                                            5Q GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    52
  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                                     358
  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"
D10V9, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    15  38
  5Q GAIN WILD-TYPE  64 300
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     15   38
  5Q GAIN WILD-TYPE   64  300
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  NO               15                64
  YES              38               300
[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                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5Q GAIN MUTATED                           5    45
  5Q GAIN WILD-TYPE                        28   316
D10V12, multiclass
                                  clus
vv                                 5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      5                28
  WHITE                                         45               316
[1] 4 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     5  46
  5Q GAIN WILD-TYPE  13 335
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      5   46
  5Q GAIN WILD-TYPE   13  335
                        clus
vv                       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   5                13
  NOT HISPANIC OR LATINO              46               335
[1] 2 2
[1] FALSE

Clustering(11) Variable = 6P GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                 0   1
  6P GAIN MUTATED    42  12
  6P GAIN WILD-TYPE 215  86
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               54               301 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               12                86 
$`6P GAIN MUTATED`
TCGA-BA-4075 TCGA-BA-5555 TCGA-BA-6870 TCGA-BA-6873 TCGA-BB-4224 TCGA-BB-7870 
         283          520          451          113          278         1153 
TCGA-C9-A47Z TCGA-CN-4723 TCGA-CN-5356 TCGA-CN-5363 TCGA-CN-5367 TCGA-CN-6020 
           5          721          512         1977         1966           98 
TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6989 TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A641 
         202          424          611          526          348          367 
TCGA-CQ-5329 TCGA-CQ-5331 TCGA-CQ-5334 TCGA-CQ-7067 TCGA-CQ-A4C7 TCGA-CQ-A4CA 
        1422         1399          129          509         1960         1963 
TCGA-CQ-A4CE TCGA-CR-5247 TCGA-CR-6487 TCGA-CR-7368 TCGA-CR-7389 TCGA-CR-7402 
         393          358          234         1245          392          911 
TCGA-CV-5430 TCGA-CV-5442 TCGA-CV-5977 TCGA-CV-6003 TCGA-CV-6954 TCGA-CV-7235 
        1955         2327         1840         1665         1957         1724 
TCGA-CV-7243 TCGA-CV-7250 TCGA-CV-7440 TCGA-CV-A6JE TCGA-DQ-5625 TCGA-F7-A50I 
         954         1960         1981          750         1081           92 
TCGA-H7-8502 TCGA-HD-7753 TCGA-HD-7917 TCGA-HD-A6I0 TCGA-IQ-A61E TCGA-IQ-A61L 
         133            5           37           33          588          351 
TCGA-KU-A66T TCGA-MT-A51W TCGA-MT-A67D TCGA-P3-A6SW TCGA-P3-A6T4 TCGA-QK-A6IG 
         210           14           56         1120         1968          218 

$`6P 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-5557 TCGA-BA-5558 TCGA-BA-5559 
        1288         1762          725          623         1636         1747 
TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A4IF 
         190          644           63          384          236          895 
TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BB-4217 TCGA-BB-4223 
         513          351          216          182          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-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 
         687          638          428          436         1955          624 
TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 
           4          799          485          142          452          613 
TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 
         392          462          993          642          369          395 
TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 
         240         1960         1330          811         1268         1988 
TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5365 TCGA-CN-5366 
         488          173         1980         1081         1980         1966 
TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 
        1975          413          290          630          424          629 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6021 
         433          594          629           45          432         1970 
TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 
         224          318          394          119          432          429 
TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63Y 
          46          443          447          225          484          175 
TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5330 TCGA-CQ-5332 
        1466         1207          654         1660          896          317 
TCGA-CQ-5333 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 
         341          870         1000         1057          985         1959 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7068 
        1959          815         1461         1378         1007         1309 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD 
         901          877          968          613          545          548 
TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 
         391          303          608         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-A461 TCGA-CV-A6JD TCGA-CV-A6JN 
        1959          851         1945         1954         1970          717 
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-D6-6826 TCGA-D6-6827 TCGA-D6-8568 
         701           77          491          154          568          106 
TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-DQ-5624 TCGA-DQ-5629 TCGA-DQ-5630 
         128          112          104         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          564          490 
TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W 
         658           15          585            3          384           14 
TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-A6C4 TCGA-H7-A6C5 
          13            6          407           58          414          403 
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-A6HZ TCGA-HL-7533 TCGA-IQ-7630 
          11           49           10          111         1057          485 
TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61O 
         122          441          360          412          440          360 
TCGA-KU-A66S TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 
         224           34          392          111          112          254 
TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 
         910         1652          721         1954          578         1917 
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 
          64 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                5                 2 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             2327              3837 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              516               641 
[1] "5.0 - 2327.0 (516.0)" "2.0 - 3837.0 (641.0)"
[1] "hr=" "1.1"
D11V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  6P GAIN MUTATED         4       10        12        28         2
  6P GAIN WILD-TYPE      20       53        59       164         7
D11V3, multiclass
           clus
vv          6P GAIN MUTATED 6P GAIN WILD-TYPE
  STAGE I                 4                20
  STAGE II               10                53
  STAGE III              12                59
  STAGE IVA              28               164
  STAGE IVB               2                 7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  6P GAIN MUTATED     4  18  15  20
  6P GAIN WILD-TYPE  36  90  70 111
D11V4, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  T1               4                36
  T2              18                90
  T3              15                70
  T4              20               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
  6P GAIN MUTATED    23  11  17   2
  6P GAIN WILD-TYPE 113  45 112   5
D11V5, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  N0              23               113
  N1              11                45
  N2              17               112
  N3               2                 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"
D11V6, binary
                   cls
clus                 0  1
  6P GAIN MUTATED   16 10
  6P GAIN WILD-TYPE 92 38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     16   10
  6P GAIN WILD-TYPE   92   38
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  M0              16                92
  MX              10                38
[1] 2 2
[1] FALSE
D11V7, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    17  46
  6P GAIN WILD-TYPE 104 250
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     17   46
  6P GAIN WILD-TYPE  104  250
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE              17               104
  MALE                46               250
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  6P GAIN MUTATED                                      62
  6P GAIN WILD-TYPE                                   348
                   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                                                     1
  6P GAIN WILD-TYPE                                                   5
D11V8, multiclass
                                                             clus
vv                                                            6P GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    62
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       1
                                                             clus
vv                                                            6P GAIN 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                         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"
D11V9, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     6  57
  6P GAIN WILD-TYPE  73 281
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      6   57
  6P GAIN WILD-TYPE   73  281
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  NO                6                73
  YES              57               281
[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                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6P GAIN MUTATED                           9    50
  6P GAIN WILD-TYPE                        24   311
D11V12, multiclass
                                  clus
vv                                 6P GAIN MUTATED 6P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      9                24
  WHITE                                         50               311
[1] 4 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     3  56
  6P GAIN WILD-TYPE  15 325
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      3   56
  6P GAIN WILD-TYPE   15  325
                        clus
vv                       6P GAIN MUTATED 6P GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                15
  NOT HISPANIC OR LATINO              56               325
[1] 2 2
[1] FALSE

Clustering(12) Variable = 6Q GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                 0   1
  6Q GAIN MUTATED    30   8
  6Q GAIN WILD-TYPE 227  90
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               38               317 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                8                90 
$`6Q GAIN MUTATED`
TCGA-BA-4075 TCGA-BA-6873 TCGA-BB-7870 TCGA-C9-A47Z TCGA-CN-4723 TCGA-CN-5356 
         283          113         1153            5          721          512 
TCGA-CN-5363 TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-A63U TCGA-CN-A63W TCGA-CQ-5331 
        1977           98          202          526          348         1399 
TCGA-CQ-5334 TCGA-CQ-7067 TCGA-CQ-A4CA TCGA-CQ-A4CE TCGA-CR-5247 TCGA-CR-7389 
         129          509         1963          393          358          392 
TCGA-CV-5430 TCGA-CV-5442 TCGA-CV-5973 TCGA-CV-5977 TCGA-CV-6003 TCGA-CV-7434 
        1955         2327         2641         1840         1665         1958 
TCGA-CV-7440 TCGA-CX-7219 TCGA-DQ-5625 TCGA-F7-A50I TCGA-HD-7753 TCGA-HD-7917 
        1981          828         1081           92            5           37 
TCGA-HD-A6I0 TCGA-IQ-A61E TCGA-IQ-A61L TCGA-KU-A66T TCGA-MT-A51W TCGA-MT-A67D 
          33          588          351          210           14           56 
TCGA-P3-A6T4 TCGA-QK-A6IG 
        1968          218 

$`6Q 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-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-6871 TCGA-BA-6872 
        1747          190          644          451           63          384 
TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE 
         236          895          513          351          216          182 
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-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4725 
         436         1955          624            4          799          485 
TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 
         142          452          613          392          462          993 
TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 
         642          369          395          240         1960         1330 
TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5359 
         811         1268         1988          488          173         1980 
TCGA-CN-5360 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 
        1081         1980         1966         1966         1975          413 
TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 
         290          630          424          629          433          594 
TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6021 TCGA-CN-6023 TCGA-CN-6024 
         629           45          432         1970          424          224 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 
         318          611          394          119          432          429 
TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63Y 
          46          443          447          225          484          175 
TCGA-CN-A641 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 
         367         1466         1207          654         1660         1422 
TCGA-CQ-5330 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 
         896          317          341          870         1000         1057 
TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 
         985         1959         1959          815         1461         1378 
TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 
        1007         1309          901          877          968         1960 
TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI 
         613          545          548          391          303          608 
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         1724         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-A461 
        1937         1984         1959          851         1945         1954 
TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 
        1970          750          717          317          321          237 
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-DQ-5624 
         568          106          128          112          104         1778 
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-A50G TCGA-F7-A50J TCGA-F7-A61S 
         564          490          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-HD-7229 TCGA-HD-7754 TCGA-HD-8224 
         133          414          403            2           25           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-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61G 
         111         1057          485          122          441          360 
TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61O TCGA-KU-A66S TCGA-MT-A51X TCGA-MT-A67A 
         412          440          360          224           34          392 
TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE 
         111          112          254          910         1652          721 
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-A6IH TCGA-QK-A6II TCGA-QK-A6IJ 
         357          245          228          225           64 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                5                 2 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
             2641              3837 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
              451               641 
[1] "5.0 - 2641.0 (451.0)" "2.0 - 3837.0 (641.0)"
[1] "hr=" "1.5"
D12V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  6Q GAIN MUTATED         3        6        11        21         2
  6Q GAIN WILD-TYPE      21       57        60       171         7
D12V3, multiclass
           clus
vv          6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  STAGE I                 3                21
  STAGE II                6                57
  STAGE III              11                60
  STAGE IVA              21               171
  STAGE IVB               2                 7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  6Q GAIN MUTATED     3  12  10  19
  6Q GAIN WILD-TYPE  37  96  75 112
D12V4, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  T1               3                37
  T2              12                96
  T3              10                75
  T4              19               112
[1] 4 2
[1] 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    19  10  11   1
  6Q GAIN WILD-TYPE 117  46 118   6
D12V5, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  N0              19               117
  N1              10                46
  N2              11               118
  N3               1                 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"
D12V6, binary
                   cls
clus                 0  1
  6Q GAIN MUTATED   11  7
  6Q GAIN WILD-TYPE 97 41
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     11    7
  6Q GAIN WILD-TYPE   97   41
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  M0              11                97
  MX               7                41
[1] 2 2
[1] FALSE
D12V7, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    14  34
  6Q GAIN WILD-TYPE 107 262
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     14   34
  6Q GAIN WILD-TYPE  107  262
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE              14               107
  MALE                34               262
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  6Q GAIN MUTATED                                      48
  6Q GAIN WILD-TYPE                                   362
                   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                                                     0
  6Q GAIN WILD-TYPE                                                   6
D12V8, multiclass
                                                             clus
vv                                                            6Q 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                       0
                                                             clus
vv                                                            6Q GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     362
  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"
D12V9, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     3  45
  6Q GAIN WILD-TYPE  76 293
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      3   45
  6Q GAIN WILD-TYPE   76  293
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  NO                3                76
  YES              45               293
[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                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6Q GAIN MUTATED                           7    37
  6Q GAIN WILD-TYPE                        26   324
D12V12, multiclass
                                  clus
vv                                 6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      7                26
  WHITE                                         37               324
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V13, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     4  41
  6Q GAIN WILD-TYPE  14 340
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      4   41
  6Q GAIN WILD-TYPE   14  340
                        clus
vv                       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                14
  NOT HISPANIC OR LATINO              41               340
[1] 2 2
[1] FALSE

Clustering(13) Variable = 7P GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                 0   1
  7P GAIN MUTATED    82  41
  7P GAIN WILD-TYPE 175  57
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              123               232 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               41                57 
$`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-BB-4224 TCGA-BB-7863 TCGA-BB-7870 TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A47Z 
         278          423         1153         1955          624            5 
TCGA-CN-4722 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4737 TCGA-CN-4738 
         799          392          462          993          240         1960 
TCGA-CN-4739 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5363 TCGA-CN-5365 
        1330          512          173         1980         1977         1980 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6020 
        1966         1966          424          629          433           98 
TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6997 
         202          424          224          318          611          429 
TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A641 TCGA-CQ-5329 TCGA-CQ-5334 TCGA-CQ-7067 
         225          484          367         1422          129          509 
TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CH 
        1309          901         1960          613         1963          303 
TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6484 TCGA-CR-7364 TCGA-CR-7365 
        1971          514         1969          354         1435         1191 
TCGA-CR-7367 TCGA-CR-7370 TCGA-CR-7377 TCGA-CR-7382 TCGA-CR-7389 TCGA-CR-7390 
        1440          105         1968          796          392          907 
TCGA-CR-7398 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5439 
         156         1955          522         1950         3295          546 
TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5444 TCGA-CV-5978 TCGA-CV-6935 TCGA-CV-6936 
        1978         2327         2437          215         1969         1952 
TCGA-CV-6945 TCGA-CV-6954 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7101 TCGA-CV-7180 
        1969         1957         3837         1959         1939         1987 
TCGA-CV-7235 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7254 TCGA-CV-7261 
        1724          954          797         1967         1976         1099 
TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7435 TCGA-CV-7440 TCGA-CX-7086 TCGA-CX-7219 
        1957         1947         1959         1981          237          828 
TCGA-D6-6516 TCGA-D6-6823 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8569 TCGA-DQ-5625 
         773          701          154          568          128         1081 
TCGA-DQ-5629 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7592 TCGA-F7-8298 
         516          548         1965          575          299          490 
TCGA-F7-A50I TCGA-F7-A61S TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7917 
          92            3          403            2            5           37 
TCGA-HD-8634 TCGA-HD-A633 TCGA-IQ-7631 TCGA-IQ-A61H TCGA-IQ-A61O TCGA-KU-A66T 
          24           49          122          412          360          210 
TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67G TCGA-P3-A6SX TCGA-P3-A6T4 
          14           34          392          112         1954         1968 
TCGA-P3-A6T8 TCGA-QK-A6IG TCGA-QK-A6II 
         400          218          225 

$`7P GAIN 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-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-A6D8 TCGA-BA-A6DA 
         384          113          236          895          513          351 
TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-4227 
         216          182          187         2878          140          133 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7871 
         558          310          536          687          638          428 
TCGA-BB-7872 TCGA-C9-A480 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 
         436            4          721          485          142          452 
TCGA-CN-4728 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4740 TCGA-CN-4741 
         613          642          369          395          811         1268 
TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5360 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 
        1988          488         1081         1975          413          290 
TCGA-CN-6010 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6021 
         630          594          629           45          432         1970 
TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49B 
         394          119          432           46          443          447 
TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A63Y TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
         526          348          175         1466         1207          654 
TCGA-CQ-5327 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-6218 
        1660          896         1399          317          341          870 
TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 
        1000         1057          985         1959         1959          815 
TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4CB 
        1461         1378         1007          877          968          545 
TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 
         548          393          391          608         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-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 
        1050         1125          362          311          345          234 
TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7368 TCGA-CR-7369 
         379          350          479         1956         1245         1960 
TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7379 
        1979          759          889           30          972         1036 
TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7391 TCGA-CR-7392 
        1954          997         1430         1951          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-5435 TCGA-CV-5436 TCGA-CV-5441 TCGA-CV-5443 
         911         1472         1438          584         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-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 
        1315         1665          641         1899         1970         1948 
TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6952 TCGA-CV-6960 TCGA-CV-6961 
        1959         3835         1948         1966         1969         1959 
TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7183 
        1970         1970         1936         1959         1945         1979 
TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7250 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 
        1444         1095         1960         1974         1948         1955 
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-A461 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN 
         851         1945         1954         1970          750          717 
TCGA-CX-7082 TCGA-CX-7085 TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-8568 
         317          321          292           77          491          106 
TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-DQ-5624 TCGA-DQ-5630 TCGA-DQ-7590 TCGA-DQ-7591 
         112          104         1778         1030          775          622 
TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 
         369          368          324          340          564          658 
TCGA-F7-A50G TCGA-F7-A50J TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 
          15          585          384           14           13            6 
TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-HD-7754 TCGA-HD-8224 
         407           58          133          414           25           55 
TCGA-HD-8314 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 
          44           25           11           10          111           33 
TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61J 
        1057          485          441          588          360          440 
TCGA-IQ-A61L TCGA-KU-A66S TCGA-MT-A67D TCGA-MT-A67F TCGA-MZ-A6I9 TCGA-P3-A5Q5 
         351          224           56          111          254          910 
TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-QK-A64Z 
        1652          721         1120          578         1917          553 
TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IH TCGA-QK-A6IJ 
         357          245          228           64 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                2                 4 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             3837              3835 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              548               649 
[1] "2.0 - 3837.0 (548.0)" "4.0 - 3835.0 (649.0)"
[1] "hr=" "1"  
D13V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  7P GAIN MUTATED         9       25        24        76         5
  7P GAIN WILD-TYPE      15       38        47       116         4
D13V3, multiclass
           clus
vv          7P GAIN MUTATED 7P GAIN WILD-TYPE
  STAGE I                 9                15
  STAGE II               25                38
  STAGE III              24                47
  STAGE IVA              76               116
  STAGE IVB               5                 4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  7P GAIN MUTATED   11 41 33 54
  7P GAIN WILD-TYPE 29 67 52 77
D13V4, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  T1              11                29
  T2              41                67
  T3              33                52
  T4              54                77
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  7P GAIN MUTATED   50 18 50  4
  7P GAIN WILD-TYPE 86 38 79  3
D13V5, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  N0              50                86
  N1              18                38
  N2              50                79
  N3               4                 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"
D13V6, binary
                   cls
clus                 0  1
  7P GAIN MUTATED   35 19
  7P GAIN WILD-TYPE 73 29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     35   19
  7P GAIN WILD-TYPE   73   29
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  M0              35                73
  MX              19                29
[1] 2 2
[1] FALSE
D13V7, binary
                   cls
clus                  0   1
  7P GAIN MUTATED    40 112
  7P GAIN WILD-TYPE  81 184
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     40  112
  7P GAIN WILD-TYPE   81  184
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE              40                81
  MALE               112               184
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  7P GAIN MUTATED                                     151
  7P GAIN WILD-TYPE                                   259
                   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                                                     0
  7P GAIN WILD-TYPE                                                   6
D13V8, multiclass
                                                             clus
vv                                                            7P GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                   151
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       0
                                                             clus
vv                                                            7P GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     259
  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"
D13V9, binary
                   cls
clus                  0   1
  7P GAIN MUTATED    31 121
  7P GAIN WILD-TYPE  48 217
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     31  121
  7P GAIN WILD-TYPE   48  217
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  NO               31                48
  YES             121               217
[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                                0     6
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7P GAIN MUTATED                          17   127
  7P GAIN WILD-TYPE                        16   234
D13V12, multiclass
                                  clus
vv                                 7P GAIN MUTATED 7P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          4                 6
  BLACK OR AFRICAN AMERICAN                     17                16
  WHITE                                        127               234
[1] 4 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     7 139
  7P GAIN WILD-TYPE  11 242
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      7  139
  7P GAIN WILD-TYPE   11  242
                        clus
vv                       7P GAIN MUTATED 7P GAIN WILD-TYPE
  HISPANIC OR LATINO                   7                11
  NOT HISPANIC OR LATINO             139               242
[1] 2 2
[1] FALSE

Clustering(14) Variable = 7Q GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                 0   1
  7Q GAIN MUTATED    55  29
  7Q GAIN WILD-TYPE 202  69
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               84               271 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               29                69 
$`7Q GAIN MUTATED`
TCGA-BA-6870 TCGA-BB-7870 TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A47Z TCGA-CN-4722 
         451         1153         1955          624            5          799 
TCGA-CN-4727 TCGA-CN-4729 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-5356 TCGA-CN-5358 
         452          392         1960         1330          512          173 
TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5367 TCGA-CN-6012 TCGA-CN-6013 
        1081         1977         1980         1966          629          433 
TCGA-CN-6020 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6997 
          98          424          224          318          611          429 
TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A641 TCGA-CQ-7067 TCGA-CQ-7069 TCGA-CQ-A4C7 
         225          484          367          509          901         1960 
TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CR-6478 TCGA-CR-7370 TCGA-CR-7389 TCGA-CR-7390 
         613         1963         1969          105          392          907 
TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5439 
        1955          522         1950         3295         1438          546 
TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5978 TCGA-CV-6935 TCGA-CV-6941 TCGA-CV-6945 
        1978         2327          215         1969         1959         1969 
TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7101 TCGA-CV-7235 TCGA-CV-7245 TCGA-CV-7248 
        3837         1959         1939         1724          797         1967 
TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7435 TCGA-CX-7086 
        1976         1099         1957         1947         1959          237 
TCGA-D6-6516 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8569 TCGA-DQ-5625 TCGA-DQ-5629 
         773          154          568          128         1081          516 
TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7592 TCGA-F7-8298 TCGA-F7-A50I 
         548         1965          575          299          490           92 
TCGA-F7-A61S TCGA-HD-7753 TCGA-HD-7917 TCGA-IQ-7631 TCGA-IQ-A61H TCGA-IQ-A61O 
           3            5           37          122          412          360 
TCGA-MT-A51W TCGA-MT-A67A TCGA-MT-A67G TCGA-P3-A6SX TCGA-P3-A6T4 TCGA-QK-A6II 
          14          392          112         1954         1968          225 

$`7Q 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-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-A4IF TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB 
         113          236          895          513          351          216 
TCGA-BA-A6DE TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 
         182          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-C9-A480 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 
         428          436            4          721          485          142 
TCGA-CN-4728 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 
         613          462          993          642          369          395 
TCGA-CN-4737 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5359 
         240          811         1268         1988          488         1980 
TCGA-CN-5366 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 
        1966         1975          413          290          630          424 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6021 TCGA-CN-6022 
         594          629           45          432         1970          202 
TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49B 
         394          119          432           46          443          447 
TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A63Y TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
         526          348          175         1466         1207          654 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 
        1660         1422          896         1399          317          341 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 
         129          870         1000         1057          985         1959 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7068 
        1959          815         1461         1378         1007         1309 
TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG 
         877          968          545          548          393          391 
TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 
         303          608         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-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 
        1971          514          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-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-7391 TCGA-CR-7392 
        1954          997         1430         1951          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-5436 TCGA-CV-5441 TCGA-CV-5443 
        1077          911         1472          584         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-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-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-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 
        1969         1959         1970         1970         1936         1959 
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-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-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7440 TCGA-CV-A45O 
        1972         1937         1984         1958         1981          851 
TCGA-CV-A45Q TCGA-CV-A461 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CX-7082 
        1945         1954         1970          750          717          317 
TCGA-CX-7085 TCGA-CX-7219 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 
         321          828          292          701           77          491 
TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-DQ-5624 TCGA-DQ-5630 TCGA-DQ-7590 
         106          112          104         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          564 
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-A6C5 
           6          407           58          133          414          403 
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-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 
          11           49           10          111           33         1057 
TCGA-IQ-7630 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61J TCGA-IQ-A61L 
         485          441          588          360          440          351 
TCGA-KU-A66S TCGA-KU-A66T TCGA-MT-A51X TCGA-MT-A67D TCGA-MT-A67F TCGA-MZ-A6I9 
         224          210           34           56          111          254 
TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6T0 TCGA-P3-A6T2 
         910         1652          721         1120          578         1917 
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-A6IJ 
          64 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                3                 2 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             3837              3835 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              612               638 
[1] "3.0 - 3837.0 (612.0)" "2.0 - 3835.0 (638.0)"
[1] "hr=" "1"  
D14V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  7Q GAIN MUTATED         8       16        16        49         3
  7Q GAIN WILD-TYPE      16       47        55       143         6
D14V3, multiclass
           clus
vv          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  STAGE I                 8                16
  STAGE II               16                47
  STAGE III              16                55
  STAGE IVA              49               143
  STAGE IVB               3                 6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  7Q GAIN MUTATED    9 24 23 36
  7Q GAIN WILD-TYPE 31 84 62 95
D14V4, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T1               9                31
  T2              24                84
  T3              23                62
  T4              36                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
  7Q GAIN MUTATED    34  11  32   3
  7Q GAIN WILD-TYPE 102  45  97   4
D14V5, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  N0              34               102
  N1              11                45
  N2              32                97
  N3               3                 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"
D14V6, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED   20 13
  7Q GAIN WILD-TYPE 88 35
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     20   13
  7Q GAIN WILD-TYPE   88   35
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  M0              20                88
  MX              13                35
[1] 2 2
[1] FALSE
D14V7, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED    27  76
  7Q GAIN WILD-TYPE  94 220
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     27   76
  7Q GAIN WILD-TYPE   94  220
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE              27                94
  MALE                76               220
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  7Q GAIN MUTATED                                     102
  7Q GAIN WILD-TYPE                                   308
                   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                                                     0
  7Q GAIN WILD-TYPE                                                   6
D14V8, multiclass
                                                             clus
vv                                                            7Q GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                   102
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       0
                                                             clus
vv                                                            7Q 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                         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"
D14V9, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED    22  81
  7Q GAIN WILD-TYPE  57 257
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     22   81
  7Q GAIN WILD-TYPE   57  257
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NO               22                57
  YES              81               257
[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                                0     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7Q GAIN MUTATED                          11    86
  7Q GAIN WILD-TYPE                        22   275
D14V12, multiclass
                                  clus
vv                                 7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          2                 8
  BLACK OR AFRICAN AMERICAN                     11                22
  WHITE                                         86               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"
D14V13, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED     6  92
  7Q GAIN WILD-TYPE  12 289
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      6   92
  7Q GAIN WILD-TYPE   12  289
                        clus
vv                       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   6                12
  NOT HISPANIC OR LATINO              92               289
[1] 2 2
[1] FALSE

Clustering(15) Variable = 8P GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                 0   1
  8P GAIN MUTATED    74  29
  8P GAIN WILD-TYPE 183  69
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              103               252 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               29                69 
$`8P GAIN MUTATED`
TCGA-BA-4075 TCGA-BA-5555 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6871 
         283          520          623         1747          190           63 
TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-7861 TCGA-BB-7864 
         187         2878          278          140          310          687 
TCGA-BB-7870 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-CN-4722 TCGA-CN-4723 
        1153          436         1955          624          799          721 
TCGA-CN-4729 TCGA-CN-4731 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-5355 
         392          993         1960         1330          811          488 
TCGA-CN-5356 TCGA-CN-5359 TCGA-CN-5366 TCGA-CN-6010 TCGA-CN-6012 TCGA-CN-6022 
         512         1980         1966          630          629          202 
TCGA-CN-6024 TCGA-CN-6994 TCGA-CN-6998 TCGA-CN-A63T TCGA-CN-A63V TCGA-CQ-5324 
         224          119           46          225          484         1207 
TCGA-CQ-5325 TCGA-CQ-5330 TCGA-CQ-6224 TCGA-CQ-7068 TCGA-CQ-A4C9 TCGA-CQ-A4CE 
         654          896          985         1309          613          393 
TCGA-CQ-A4CG TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6477 
         391          608         2562         1777         1521          514 
TCGA-CR-6478 TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6493 TCGA-CR-7365 TCGA-CR-7367 
        1969          345          234         1956         1191         1440 
TCGA-CR-7370 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7389 TCGA-CV-5430 
         105         1036          796         1954          392         1955 
TCGA-CV-5431 TCGA-CV-5435 TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5976 TCGA-CV-5977 
         522         1438         1978         2327         1478         1840 
TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6934 TCGA-CV-6936 TCGA-CV-6943 TCGA-CV-6945 
        1665          641         1948         1952         1948         1969 
TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7180 TCGA-CV-7243 TCGA-CV-7254 
        1959         1970         1970         1987          954         1976 
TCGA-CV-7424 TCGA-CV-7428 TCGA-CV-A461 TCGA-CV-A6JE TCGA-CX-7086 TCGA-D6-6516 
        1947         1973         1954          750          237          773 
TCGA-D6-6823 TCGA-D6-8568 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-F7-7848 
         701          106          516         1965          575          564 
TCGA-F7-A61S TCGA-H7-A6C4 TCGA-HD-7917 TCGA-HD-8314 TCGA-HD-A634 TCGA-IQ-A61O 
           3          414           37           44           10          360 
TCGA-KU-A66S TCGA-MT-A51W TCGA-MT-A67D TCGA-MT-A67G TCGA-P3-A5QE TCGA-QK-A6IG 
         224           14           56          112          721          218 
TCGA-QK-A6IJ 
          64 

$`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          513          351 
TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7862 TCGA-BB-7863 
         216          182          133          558          536          423 
TCGA-BB-7866 TCGA-BB-7871 TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4725 TCGA-CN-4726 
         638          428            5            4          485          142 
TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4730 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 
         452          613          462          642          369          395 
TCGA-CN-4737 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5363 
         240         1268         1988          173         1081         1977 
TCGA-CN-5365 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6011 
        1980         1966         1975          413          290          424 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 
         433          594          629           45          432           98 
TCGA-CN-6021 TCGA-CN-6023 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6996 
        1970          424          318          611          394          432 
TCGA-CN-6997 TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A63Y 
         429          443          447          526          348          175 
TCGA-CN-A641 TCGA-CQ-5323 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5331 TCGA-CQ-5332 
         367         1466         1660         1422         1399          317 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6227 
         341          129          870         1000         1057         1959 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 
        1959          815         1461         1378         1007          509 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CA TCGA-CQ-A4CB 
         901          877          968         1960         1963          545 
TCGA-CQ-A4CD TCGA-CQ-A4CH TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 
         548          303          358         1663         1152          799 
TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6480 TCGA-CR-6481 
        1966         1050         1125         1971          362          311 
TCGA-CR-6484 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-7364 TCGA-CR-7368 
         354          379          350          479         1435         1245 
TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 
        1960         1979          759          889           30          972 
TCGA-CR-7377 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7390 TCGA-CR-7391 
        1968          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-7402 TCGA-CR-7404 TCGA-CV-5432 TCGA-CV-5434 
         181         1077          911         1472         1950         3295 
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-5978 TCGA-CV-5979 TCGA-CV-6436 
         406          701         2641          215         1315         1899 
TCGA-CV-6441 TCGA-CV-6935 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6952 TCGA-CV-6954 
        1970         1969         1959         3835         1966         1957 
TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 
        1969         1959         3837         1936         1959         1939 
TCGA-CV-7102 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7245 
        1945         1979         1724         1444         1095          797 
TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 
        1967         1960         1099         1974         1948         1955 
TCGA-CV-7422 TCGA-CV-7427 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 
        1957         1937         1972         1937         1984         1958 
TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A6JD TCGA-CV-A6JN 
        1959         1981          851         1945         1970          717 
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-DQ-5624 
         154          568          128          112          104         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-F7-8298 TCGA-F7-8489 
         369          368          324          340          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-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C5 TCGA-HD-7229 
           6          407           58          133          403            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-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 
          49          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-A66T TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67F TCGA-MZ-A6I9 TCGA-P3-A5Q5 
         210           34          392          111          254          910 
TCGA-P3-A5QA TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T4 
        1652         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 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                3                 2 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             2878              3837 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              687               591 
[1] "3.0 - 2878.0 (687.0)" "2.0 - 3837.0 (591.0)"
[1] "hr=" "1.1"
D15V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  8P GAIN MUTATED         7       18        22        52         2
  8P GAIN WILD-TYPE      17       45        49       140         7
D15V3, multiclass
           clus
vv          8P GAIN MUTATED 8P GAIN WILD-TYPE
  STAGE I                 7                17
  STAGE II               18                45
  STAGE III              22                49
  STAGE IVA              52               140
  STAGE IVB               2                 7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  8P GAIN MUTATED   12 35 21 33
  8P GAIN WILD-TYPE 28 73 64 98
D15V4, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  T1              12                28
  T2              35                73
  T3              21                64
  T4              33                98
[1] 4 2
[1] 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    35  18  36   2
  8P GAIN WILD-TYPE 101  38  93   5
D15V5, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  N0              35               101
  N1              18                38
  N2              36                93
  N3               2                 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"
D15V6, binary
                   cls
clus                 0  1
  8P GAIN MUTATED   28 12
  8P GAIN WILD-TYPE 80 36
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     28   12
  8P GAIN WILD-TYPE   80   36
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  M0              28                80
  MX              12                36
[1] 2 2
[1] FALSE
D15V7, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    26  90
  8P GAIN WILD-TYPE  95 206
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     26   90
  8P GAIN WILD-TYPE   95  206
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE              26                95
  MALE                90               206
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  8P GAIN MUTATED                                     111
  8P GAIN WILD-TYPE                                   299
                   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                                                     4
  8P GAIN WILD-TYPE                                                   2
D15V8, multiclass
                                                             clus
vv                                                            8P GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                   111
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       4
                                                             clus
vv                                                            8P GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     299
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                 0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V9, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    25  91
  8P GAIN WILD-TYPE  54 247
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     25   91
  8P GAIN WILD-TYPE   54  247
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  NO               25                54
  YES              91               247
[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                                1     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8P GAIN MUTATED                          13    97
  8P GAIN WILD-TYPE                        20   264
D15V12, multiclass
                                  clus
vv                                 8P GAIN MUTATED 8P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 8
  BLACK OR AFRICAN AMERICAN                     13                20
  WHITE                                         97               264
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V13, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     5 106
  8P GAIN WILD-TYPE  13 275
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      5  106
  8P GAIN WILD-TYPE   13  275
                        clus
vv                       8P GAIN MUTATED 8P GAIN WILD-TYPE
  HISPANIC OR LATINO                   5                13
  NOT HISPANIC OR LATINO             106               275
[1] 2 2
[1] FALSE

Clustering(16) Variable = 8Q GAIN MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                 0   1
  8Q GAIN MUTATED   147  58
  8Q GAIN WILD-TYPE 110  40
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              205               150 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               58                40 
$`8Q GAIN MUTATED`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-5152 TCGA-BA-5555 TCGA-BA-5557 
         283         1983          248         1288          520          623 
TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 
        1636         1747          190          451           63          384 
TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A6DA TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 
         113          236          351          187         2878          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-7870 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A47Z TCGA-C9-A480 
        1153          436         1955          624            5            4 
TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4731 TCGA-CN-4736 
         799          721          613          392          993          395 
TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4742 TCGA-CN-5355 
         240         1960         1330          811         1988          488 
TCGA-CN-5356 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5370 TCGA-CN-5373 
         512         1977         1980         1966         1975          413 
TCGA-CN-6012 TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6992 
         629           98          202          224          318          394 
TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63T 
         119          432           46          443          447          225 
TCGA-CN-A63V TCGA-CN-A63W TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5329 TCGA-CQ-5330 
         484          348         1207          654         1422          896 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 
         129          870          985         1959         1959          815 
TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-A4C6 TCGA-CQ-A4C7 
        1007          509         1309          901          968         1960 
TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CI TCGA-CR-5243 
         613          545          393          391          608         2562 
TCGA-CR-5247 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6473 TCGA-CR-6477 TCGA-CR-6478 
         358         1777         1521         1125          514         1969 
TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6493 TCGA-CR-7365 
         345          354          234          379         1956         1191 
TCGA-CR-7367 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7372 TCGA-CR-7376 TCGA-CR-7377 
        1440         1960          105          759          972         1968 
TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 
        1036          796         1954         1430         1951          392 
TCGA-CR-7397 TCGA-CR-7399 TCGA-CR-7401 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 
         216          181         1077         1955          522         1950 
TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5444 
        1438          584         1978         2886         2327         2437 
TCGA-CV-5966 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-6003 TCGA-CV-6433 
         519         1478         1840          215         1665          641 
TCGA-CV-6436 TCGA-CV-6934 TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 
        1899         1948         1952         1959         3835         1948 
TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 
        1969         1966         3837         1959         1970         1970 
TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7243 
        1945         1987         1979         1724         1444          954 
TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7254 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7428 
         797         1967         1976         1947         1937         1973 
TCGA-CV-7434 TCGA-CV-A461 TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CX-7082 TCGA-CX-7086 
        1958         1954          750          717          317          237 
TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6826 TCGA-D6-8568 
         828          773          292          701          154          106 
TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 
         128          112          104         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          564          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-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 
         414           37           55           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-P3-A5QA 
         210           14           34           56          112         1652 
TCGA-P3-A5QE TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II 
         721          553          357          218          228          225 
TCGA-QK-A6IJ 
          64 

$`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-BB-7862 
         644          895          513          216          182          536 
TCGA-BB-7866 TCGA-BB-7871 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4730 
         638          428          485          142          452          462 
TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4741 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 
         642          369         1268          173         1980         1081 
TCGA-CN-5367 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6016 
        1966          290          630          424          433          594 
TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6021 TCGA-CN-6023 TCGA-CN-6989 
         629           45          432         1970          424          611 
TCGA-CN-6997 TCGA-CN-A63U TCGA-CN-A63Y TCGA-CN-A641 TCGA-CQ-5323 TCGA-CQ-5327 
         429          526          175          367         1466         1660 
TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-7063 
        1399          317          341         1000         1057         1461 
TCGA-CQ-7064 TCGA-CQ-7071 TCGA-CQ-A4CA TCGA-CQ-A4CD TCGA-CQ-A4CH TCGA-CR-5248 
        1378          877         1963          548          303         1663 
TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6474 TCGA-CR-6480 
        1152          799         1966         1050         1971          362 
TCGA-CR-6481 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-7364 TCGA-CR-7368 TCGA-CR-7371 
         311          350          479         1435         1245         1979 
TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7385 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 
         889           30          997          907          913          946 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7398 TCGA-CR-7402 TCGA-CR-7404 
         908          898          930          156          911         1472 
TCGA-CV-5434 TCGA-CV-5439 TCGA-CV-5443 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 
        3295          546         1958          406          701         2641 
TCGA-CV-5979 TCGA-CV-6441 TCGA-CV-6935 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 
        1315         1970         1969         1957         1969         1959 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7242 TCGA-CV-7250 TCGA-CV-7261 
        1936         1959         1939         1095         1960         1099 
TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7430 TCGA-CV-7432 
        1974         1948         1955         1957         1972         1937 
TCGA-CV-7433 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A6JD 
        1984         1959         1981          851         1945         1970 
TCGA-CX-7085 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6827 TCGA-DQ-5631 TCGA-DQ-7590 
         321           77          491          568          548          775 
TCGA-DQ-7591 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-A50G 
         622          369          368          324          340           15 
TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8502 TCGA-H7-A6C5 
         384           14            6          407          133          403 
TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A6HZ 
           2            5           25           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-MT-A67A TCGA-MT-A67F TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A6SW 
         440          392          111          254          910         1120 
TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A6IF 
        1954          578         1917         1968          400          245 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                3                 2 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             3837              3295 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            624.0             629.5 
[1] "3.0 - 3837.0 (624.0)" "2.0 - 3295.0 (629.5)"
[1] "hr=" "1.1"
D16V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  8Q GAIN MUTATED        15       35        47       111         8
  8Q GAIN WILD-TYPE       9       28        24        81         1
D16V3, multiclass
           clus
vv          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  STAGE I                15                 9
  STAGE II               35                28
  STAGE III              47                24
  STAGE IVA             111                81
  STAGE IVB               8                 1
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  8Q GAIN MUTATED   26 62 53 76
  8Q GAIN WILD-TYPE 14 46 32 55
D16V4, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T1              26                14
  T2              62                46
  T3              53                32
  T4              76                55
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  8Q GAIN MUTATED   74 34 81  6
  8Q GAIN WILD-TYPE 62 22 48  1
D16V5, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  N0              74                62
  N1              34                22
  N2              81                48
  N3               6                 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"
D16V6, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED   66 24
  8Q GAIN WILD-TYPE 42 24
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     66   24
  8Q GAIN WILD-TYPE   42   24
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  M0              66                42
  MX              24                24
[1] 2 2
[1] FALSE
D16V7, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED    75 170
  8Q GAIN WILD-TYPE  46 126
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     75  170
  8Q GAIN WILD-TYPE   46  126
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE              75                46
  MALE               170               126
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  8Q GAIN MUTATED                                     240
  8Q GAIN WILD-TYPE                                   170
                   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                                                     4
  8Q GAIN WILD-TYPE                                                   2
D16V8, multiclass
                                                             clus
vv                                                            8Q GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                   240
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       4
                                                             clus
vv                                                            8Q GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     170
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                 0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V9, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED    45 200
  8Q GAIN WILD-TYPE  34 138
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     45  200
  8Q GAIN WILD-TYPE   34  138
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NO               45                34
  YES             200               138
[1] 2 2
[1] FALSE
D16V10, continuous
D16V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8Q GAIN MUTATED                                  1     7
  8Q GAIN WILD-TYPE                                0     3
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8Q GAIN MUTATED                          22   205
  8Q GAIN WILD-TYPE                        11   156
D16V12, multiclass
                                  clus
vv                                 8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          7                 3
  BLACK OR AFRICAN AMERICAN                     22                11
  WHITE                                        205               156
[1] 4 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    12 223
  8Q GAIN WILD-TYPE   6 158
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     12  223
  8Q GAIN WILD-TYPE    6  158
                        clus
vv                       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  HISPANIC OR LATINO                  12                 6
  NOT HISPANIC OR LATINO             223               158
[1] 2 2
[1] FALSE

Clustering(17) Variable = 9P GAIN MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                 0   1
  9P GAIN MUTATED    51  16
  9P GAIN WILD-TYPE 206  82
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               67               288 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               16                82 
$`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-BB-7870 TCGA-CN-5355 TCGA-CN-5359 TCGA-CN-5363 TCGA-CN-5370 TCGA-CN-6010 
        1153          488         1980         1977         1975          630 
TCGA-CN-6011 TCGA-CN-6023 TCGA-CN-6994 TCGA-CN-6996 TCGA-CQ-5325 TCGA-CQ-5329 
         424          424          119          432          654         1422 
TCGA-CQ-5330 TCGA-CQ-6223 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C6 
         896         1057          815         1461         1309          968 
TCGA-CQ-A4C7 TCGA-CQ-A4CD TCGA-CR-6467 TCGA-CR-6487 TCGA-CR-7370 TCGA-CR-7371 
        1960          548         1777          234          105         1979 
TCGA-CR-7373 TCGA-CR-7395 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5966 
         889          930         1978         2886         2327          519 
TCGA-CV-5977 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6941 TCGA-CV-6952 TCGA-CV-7099 
        1840          641         1899         1959         1966         1936 
TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7427 TCGA-CV-A45Q 
        1724         1444         1976         1099         1937         1945 
TCGA-CV-A6JD TCGA-CX-7219 TCGA-D6-6516 TCGA-DQ-5625 TCGA-F7-A61S TCGA-H7-7774 
        1970          828          773         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 
         218 

$`9P GAIN 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-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 
        1288         1762          520         1636          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          513 
TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 
         216          182          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-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          485          142          452 
TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 
         613          392          462          993          642          369 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 
         395          240         1960         1330          811         1268 
TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5365 TCGA-CN-5366 
        1988          512          173         1081         1980         1966 
TCGA-CN-5367 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 
        1966          413          290          629          433          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-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-6998 
         224          318          611          394          429           46 
TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W 
         443          447          225          526          484          348 
TCGA-CN-A63Y TCGA-CN-A641 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5327 TCGA-CQ-5331 
         175          367         1466         1207         1660         1399 
TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6224 
         317          341          129          870         1000          985 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7069 
        1959         1959         1378         1007          509          901 
TCGA-CQ-7071 TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CE TCGA-CQ-A4CG 
         877          613         1963          545          393          391 
TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 
         303          608         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-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 
         514         1969          362          311          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-7372 TCGA-CR-7374 TCGA-CR-7376 
        1440         1245         1960          759           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-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 
         898          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-5443 TCGA-CV-5444 TCGA-CV-5970 TCGA-CV-5971 
         584          546         1958         2437          406          701 
TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6441 
        2641         1478          215         1315         1665         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-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-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7183 
        1970         1959         1939         1945         1987         1979 
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-7428 TCGA-CV-7430 
        1948         1955         1957         1947         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-A461 TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 
        1954          750          717          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-DQ-5624 TCGA-DQ-5629 
         106          128          112          104         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          564 
TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61V 
         490          658           15           92          585          384 
TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-8501 TCGA-H7-A6C4 TCGA-H7-A6C5 
          14           13            6           58          414          403 
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-MT-A51X TCGA-MT-A67D TCGA-MZ-A6I9 TCGA-P3-A5Q5 
         224          210           34           56          254          910 
TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T4 TCGA-P3-A6T8 
        1652          721         1954          578         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           64 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                3                 2 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
             2886              3837 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            896.0             586.5 
[1] "3.0 - 2886.0 (896.0)" "2.0 - 3837.0 (586.5)"
[1] "hr=" "1.4"
D17V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  9P GAIN MUTATED         6       17        11        39         4
  9P GAIN WILD-TYPE      18       46        60       153         5
D17V3, multiclass
           clus
vv          9P GAIN MUTATED 9P GAIN WILD-TYPE
  STAGE I                 6                18
  STAGE II               17                46
  STAGE III              11                60
  STAGE IVA              39               153
  STAGE IVB               4                 5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  9P GAIN MUTATED     8  19  19  31
  9P GAIN WILD-TYPE  32  89  66 100
D17V4, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  T1               8                32
  T2              19                89
  T3              19                66
  T4              31               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 GAIN MUTATED    31   9  24   4
  9P GAIN WILD-TYPE 105  47 105   3
D17V5, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  N0              31               105
  N1               9                47
  N2              24               105
  N3               4                 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"
D17V6, binary
                   cls
clus                 0  1
  9P GAIN MUTATED   22 10
  9P GAIN WILD-TYPE 86 38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     22   10
  9P GAIN WILD-TYPE   86   38
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  M0              22                86
  MX              10                38
[1] 2 2
[1] FALSE
D17V7, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    30  53
  9P GAIN WILD-TYPE  91 243
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     30   53
  9P GAIN WILD-TYPE   91  243
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE              30                91
  MALE                53               243
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  9P GAIN MUTATED                                      82
  9P GAIN WILD-TYPE                                   328
                   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                                                   5
D17V8, multiclass
                                                             clus
vv                                                            9P GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    82
  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                                     328
  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"
D17V9, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    11  72
  9P GAIN WILD-TYPE  68 266
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     11   72
  9P GAIN WILD-TYPE   68  266
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  NO               11                68
  YES              72               266
[1] 2 2
[1] FALSE
D17V10, continuous
D17V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9P GAIN MUTATED                                  0     1
  9P GAIN WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9P GAIN MUTATED                           5    75
  9P GAIN WILD-TYPE                        28   286
D17V12, multiclass
                                  clus
vv                                 9P GAIN MUTATED 9P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      5                28
  WHITE                                         75               286
[1] 4 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     4  77
  9P GAIN WILD-TYPE  14 304
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      4   77
  9P GAIN WILD-TYPE   14  304
                        clus
vv                       9P GAIN MUTATED 9P GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                14
  NOT HISPANIC OR LATINO              77               304
[1] 2 2
[1] FALSE

Clustering(18) Variable = 9Q GAIN MUTATION ANALYSIS
D18V1, survival
                   sevent
clus2                 0   1
  9Q GAIN MUTATED    65  24
  9Q GAIN WILD-TYPE 192  74
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               89               266 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               24                74 
$`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-BB-4224 TCGA-BB-7864 TCGA-BB-7870 TCGA-CN-4723 TCGA-CN-4727 
         351          278          687         1153          721          452 
TCGA-CN-4728 TCGA-CN-4741 TCGA-CN-5355 TCGA-CN-5359 TCGA-CN-5363 TCGA-CN-5367 
         613         1268          488         1980         1977         1966 
TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6021 TCGA-CN-6023 TCGA-CN-6994 TCGA-CN-6996 
         630          424         1970          424          119          432 
TCGA-CN-A63T TCGA-CQ-5323 TCGA-CQ-5325 TCGA-CQ-5330 TCGA-CQ-6223 TCGA-CQ-6229 
         225         1466          654          896         1057          815 
TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CA TCGA-CQ-A4CD 
        1461         1309          968         1960         1963          548 
TCGA-CQ-A4CG TCGA-CR-6467 TCGA-CR-6477 TCGA-CR-7368 TCGA-CR-7373 TCGA-CR-7379 
         391         1777          514         1245          889         1036 
TCGA-CR-7389 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5442 
         392         1950         3295          546         1978         2327 
TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5977 TCGA-CV-6433 TCGA-CV-6436 
        2437          519          406         1840          641         1899 
TCGA-CV-6941 TCGA-CV-6952 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7235 TCGA-CV-7238 
        1959         1966         1936         1959         1724         1444 
TCGA-CV-7245 TCGA-CV-7261 TCGA-CV-7422 TCGA-CV-7427 TCGA-CV-7432 TCGA-CV-7434 
         797         1099         1957         1937         1937         1958 
TCGA-CV-A45Q TCGA-CV-A461 TCGA-CV-A6JD TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-8569 
        1945         1954         1970          828          773          128 
TCGA-DQ-5625 TCGA-F7-A61S TCGA-H7-7774 TCGA-H7-8502 TCGA-HD-7917 TCGA-HD-8314 
        1081            3          407          133           37           44 
TCGA-HD-A634 TCGA-HD-A6I0 TCGA-IQ-7630 TCGA-IQ-A61L TCGA-MT-A51W TCGA-MT-A67A 
          10           33          485          351           14          392 
TCGA-MT-A67G TCGA-P3-A6SW TCGA-P3-A6T2 TCGA-QK-A64Z TCGA-QK-A6IG 
         112         1120         1917          553          218 

$`9Q GAIN 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-5152 TCGA-BA-5153 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 
        1288         1762         1636          190          644          451 
TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A6D8 TCGA-BA-A6DB 
          63          384          236          895          513          216 
TCGA-BA-A6DE TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 
         182          187         2878          140          133          558 
TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7866 TCGA-BB-7871 TCGA-BB-7872 
         310          536          423          638          428          436 
TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4725 
        1955          624            5            4          799          485 
TCGA-CN-4726 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 
         142          392          462          993          642          369 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4742 
         395          240         1960         1330          811         1988 
TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5370 
         512          173         1081         1980         1966         1975 
TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 
         413          290          629          433          594          629 
TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6988 
          45          432           98          202          224          318 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49B 
         611          394          429           46          443          447 
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-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-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-7064 
         870         1000          985         1959         1959         1378 
TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C9 TCGA-CQ-A4CB 
        1007          509          901          877          613          545 
TCGA-CQ-A4CE TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 
         393          303          608         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-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 
        1971         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-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 
        1191         1440         1960          105         1979          759 
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-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-5435 TCGA-CV-5436 
         911         1472         1955          522         1438          584 
TCGA-CV-5441 TCGA-CV-5443 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5978 
        2886         1958          701         2641         1478          215 
TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 
        1315         1665         1970         1948         1969         1952 
TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 
        3835         1948         1969         1957         1969         1959 
TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7101 TCGA-CV-7102 
        3837         1959         1970         1970         1939         1945 
TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7248 TCGA-CV-7250 
        1987         1979         1095          954         1967         1960 
TCGA-CV-7254 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7424 TCGA-CV-7428 
        1976         1974         1948         1955         1947         1973 
TCGA-CV-7430 TCGA-CV-7433 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A6JE 
        1972         1984         1959         1981          851          750 
TCGA-CV-A6JN TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-D6-6517 TCGA-D6-6823 
         717          317          321          237          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          112 
TCGA-D6-A4ZB TCGA-DQ-5624 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 
         104         1778          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          564          490          658           15 
TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 
          92          585          384           14           13            6 
TCGA-H7-8501 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 
          58          414          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-HL-7533 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H 
        1057          122          441          588          360          412 
TCGA-IQ-A61J TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-MT-A51X TCGA-MT-A67D 
         440          360          224          210           34           56 
TCGA-MT-A67F TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SX 
         111          254          910         1652          721         1954 
TCGA-P3-A6T0 TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IH 
         578         1968          400          357          245          228 
TCGA-QK-A6II TCGA-QK-A6IJ 
         225           64 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                3                 2 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             3295              3837 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            815.0             584.5 
[1] "3.0 - 3295.0 (815.0)" "2.0 - 3837.0 (584.5)"
[1] "hr=" "1.1"
D18V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  9Q GAIN MUTATED         6       20        14        57         5
  9Q GAIN WILD-TYPE      18       43        57       135         4
D18V3, multiclass
           clus
vv          9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  STAGE I                 6                18
  STAGE II               20                43
  STAGE III              14                57
  STAGE IVA              57               135
  STAGE IVB               5                 4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  9Q GAIN MUTATED    9 25 23 45
  9Q GAIN WILD-TYPE 31 83 62 86
D18V4, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  T1               9                31
  T2              25                83
  T3              23                62
  T4              45                86
[1] 4 2
[1] 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   41 13 33  4
  9Q GAIN WILD-TYPE 95 43 96  3
D18V5, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  N0              41                95
  N1              13                43
  N2              33                96
  N3               4                 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"
D18V6, binary
                   cls
clus                 0  1
  9Q GAIN MUTATED   25 11
  9Q GAIN WILD-TYPE 83 37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     25   11
  9Q GAIN WILD-TYPE   83   37
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  M0              25                83
  MX              11                37
[1] 2 2
[1] FALSE
D18V7, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    32  78
  9Q GAIN WILD-TYPE  89 218
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     32   78
  9Q GAIN WILD-TYPE   89  218
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE              32                89
  MALE                78               218
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  9Q GAIN MUTATED                                     108
  9Q GAIN WILD-TYPE                                   302
                   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                                                     2
  9Q GAIN WILD-TYPE                                                   4
D18V8, multiclass
                                                             clus
vv                                                            9Q GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                   108
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       2
                                                             clus
vv                                                            9Q GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     302
  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"
D18V9, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    19  91
  9Q GAIN WILD-TYPE  60 247
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     19   91
  9Q GAIN WILD-TYPE   60  247
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  NO               19                60
  YES              91               247
[1] 2 2
[1] FALSE
D18V10, continuous
D18V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9Q GAIN MUTATED                                  0     1
  9Q GAIN WILD-TYPE                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9Q GAIN MUTATED                          10    96
  9Q GAIN WILD-TYPE                        23   265
D18V12, multiclass
                                  clus
vv                                 9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                     10                23
  WHITE                                         96               265
[1] 4 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     7  98
  9Q GAIN WILD-TYPE  11 283
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      7   98
  9Q GAIN WILD-TYPE   11  283
                        clus
vv                       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   7                11
  NOT HISPANIC OR LATINO              98               283
[1] 2 2
[1] FALSE

Clustering(19) Variable = 10P GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                  0   1
  10P GAIN MUTATED    23   4
  10P GAIN WILD-TYPE 234  94
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                27                328 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 4                 94 
$`10P GAIN MUTATED`
TCGA-BA-5151 TCGA-BA-5555 TCGA-BA-6869 TCGA-BA-6872 TCGA-BB-7861 TCGA-CN-4727 
         722          520          644          384          310          452 
TCGA-CN-5356 TCGA-CN-6013 TCGA-CN-6994 TCGA-CN-A63T TCGA-CQ-7067 TCGA-CR-5247 
         512          433          119          225          509          358 
TCGA-CR-6488 TCGA-CR-7399 TCGA-CV-5441 TCGA-CV-6003 TCGA-CV-6934 TCGA-CV-7091 
         379          181         2886         1665         1948         1959 
TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7435 TCGA-DQ-7589 TCGA-F7-7848 TCGA-HD-7917 
        1960         1976         1959          575          564           37 
TCGA-HD-A6HZ TCGA-P3-A5QE TCGA-QK-A6IG 
         111          721          218 

$`10P 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-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-6870 TCGA-BA-6871 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF 
         190          451           63          113          236          895 
TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BB-4217 TCGA-BB-4223 
         513          351          216          182          187         2878 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7862 TCGA-BB-7863 
         278          140          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          485 
TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
         142          613          392          462          993          642 
TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 
         369          395          240         1960         1330          811 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 
        1268         1988          488          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          413 
TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6016 TCGA-CN-6017 
         290          630          424          629          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          424 
TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6996 TCGA-CN-6997 
         224          318          611          394          432          429 
TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W 
          46          443          447          526          484          348 
TCGA-CN-A63Y TCGA-CN-A641 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 
         175          367         1466         1207          654         1660 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 
        1422          896         1399          317          341          129 
TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 
         870         1000         1057          985         1959         1959 
TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7069 
         815         1461         1378         1007         1309          901 
TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB 
         877          968         1960          613         1963          545 
TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 
         548          393          391          303          608         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-6484 TCGA-CR-6487 TCGA-CR-6491 TCGA-CR-6492 
         311          345          354          234          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-7401 TCGA-CR-7402 
         898          930          216          156         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-5442 TCGA-CV-5443 TCGA-CV-5444 
         584          546         1978         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-6935 
         215         1315          641         1899         1970         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-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 
        1724         1444         1095          954          797         1967 
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-7440 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A461 TCGA-CV-A6JD TCGA-CV-A6JE 
        1981          851         1945         1954         1970          750 
TCGA-CV-A6JN TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 
         717          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-DQ-5624 TCGA-DQ-5625 
         106          128          112          104         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-F7-8298 
         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-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-8224 
         414          403            2            5           25           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-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F 
         210           14           34          392           56          111 
TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A6SW TCGA-P3-A6SX 
         112          254          910         1652         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 
         245          228          225           64 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                37                  2 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              2886               3837 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             512.0              639.5 
[1] "37.0 - 2886.0 (512.0)" "2.0 - 3837.0 (639.5)" 
[1] "hr=" "1.8"
D19V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  10P GAIN MUTATED         2        4         7        13         0
  10P GAIN WILD-TYPE      22       59        64       179         9
D19V3, multiclass
           clus
vv          10P GAIN MUTATED 10P GAIN WILD-TYPE
  STAGE I                  2                 22
  STAGE II                 4                 59
  STAGE III                7                 64
  STAGE IVA               13                179
  STAGE IVB                0                  9
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  10P GAIN MUTATED     3   8   7   8
  10P GAIN WILD-TYPE  37 100  78 123
D19V4, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  T1                3                 37
  T2                8                100
  T3                7                 78
  T4                8                123
[1] 4 2
[1] 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    12   6   7   0
  10P GAIN WILD-TYPE 124  50 122   7
D19V5, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  N0               12                124
  N1                6                 50
  N2                7                122
  N3                0                  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"
D19V6, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     3   3
  10P GAIN WILD-TYPE 105  45
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      3    3
  10P GAIN WILD-TYPE  105   45
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  M0                3                105
  MX                3                 45
[1] 2 2
[1] FALSE
D19V7, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     7  23
  10P GAIN WILD-TYPE 114 273
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      7   23
  10P GAIN WILD-TYPE  114  273
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE                7                114
  MALE                 23                273
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  10P GAIN MUTATED                                      29
  10P GAIN WILD-TYPE                                   381
                    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                                                   5
D19V8, multiclass
                                                             clus
vv                                                            10P GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     29
  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                                      381
  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"
D19V9, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     6  24
  10P GAIN WILD-TYPE  73 314
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      6   24
  10P GAIN WILD-TYPE   73  314
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  NO                 6                 73
  YES               24                314
[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                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10P GAIN MUTATED                           2    28
  10P GAIN WILD-TYPE                        31   333
D19V12, multiclass
                                  clus
vv                                 10P GAIN MUTATED 10P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 10
  BLACK OR AFRICAN AMERICAN                       2                 31
  WHITE                                          28                333
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V13, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     0  30
  10P GAIN WILD-TYPE  18 351
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      0   30
  10P GAIN WILD-TYPE   18  351
                        clus
vv                       10P GAIN MUTATED 10P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 18
  NOT HISPANIC OR LATINO               30                351
[1] 2 2
[1] FALSE

Clustering(20) Variable = 10Q GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                  0   1
  10Q GAIN MUTATED    20   5
  10Q GAIN WILD-TYPE 237  93
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                25                330 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 5                 93 
$`10Q GAIN MUTATED`
TCGA-BA-5151 TCGA-BA-6872 TCGA-BA-6873 TCGA-CN-4727 TCGA-CN-6013 TCGA-CN-6023 
         722          384          113          452          433          424 
TCGA-CN-6994 TCGA-CN-A63T TCGA-CQ-5329 TCGA-CQ-7067 TCGA-CQ-A4C7 TCGA-CR-7390 
         119          225         1422          509         1960          907 
TCGA-CR-7399 TCGA-CV-5441 TCGA-CV-5966 TCGA-CV-6003 TCGA-CV-6441 TCGA-CV-7091 
         181         2886          519         1665         1970         1959 
TCGA-CV-7435 TCGA-D6-6825 TCGA-DQ-5629 TCGA-F7-A620 TCGA-HD-7917 TCGA-HD-A6HZ 
        1959          491          516           13           37          111 
TCGA-QK-A6IG 
         218 

$`10Q 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-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-6871 TCGA-BA-7269 
        1747          190          644          451           63          236 
TCGA-BA-A4IF TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BB-4217 
         895          513          351          216          182          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-A47Z TCGA-C9-A480 TCGA-CN-4722 
         436         1955          624            5            4          799 
TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 
         721          485          142          613          392          462 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 
         993          642          369          395          240         1960 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 
        1330          811         1268         1988          488          512 
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          413          290          630          424 
TCGA-CN-6012 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 
         629          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-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63U 
         432          429           46          443          447          526 
TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 TCGA-CQ-5323 TCGA-CQ-5324 
         484          348          175          367         1466         1207 
TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 
         654         1660          896         1399          317          341 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 
         129          870         1000         1057          985         1959 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7068 
        1959          815         1461         1378         1007         1309 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB 
         901          877          968          613         1963          545 
TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 
         548          393          391          303          608         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-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-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-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-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 
        2437          406          701         2641         1478         1840 
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-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-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 
        1724         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-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-7440 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A461 
        1984         1958         1981          851         1945         1954 
TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 
        1970          750          717          317          321          237 
TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6826 
         828          773          292          701           77          154 
TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-DQ-5624 
         568          106          128          112          104         1778 
TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 
        1081         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-A50G TCGA-F7-A50I TCGA-F7-A50J 
         564          490          658           15           92          585 
TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8501 
           3          384           14            6          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-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-IQ-A61L TCGA-IQ-A61O 
         588          360          412          440          351          360 
TCGA-KU-A66S TCGA-KU-A66T TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D 
         224          210           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         1652          721 
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           64 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                13                  2 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              2886               3837 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
             491.0              639.5 
[1] "13.0 - 2886.0 (491.0)" "2.0 - 3837.0 (639.5)" 
[1] "hr=" "1.3"
D20V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  10Q GAIN MUTATED         3        3         6        14         0
  10Q GAIN WILD-TYPE      21       60        65       178         9
D20V3, multiclass
           clus
vv          10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  STAGE I                  3                 21
  STAGE II                 3                 60
  STAGE III                6                 65
  STAGE IVA               14                178
  STAGE IVB                0                  9
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  10Q GAIN MUTATED     3   7   7   9
  10Q GAIN WILD-TYPE  37 101  78 122
D20V4, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  T1                3                 37
  T2                7                101
  T3                7                 78
  T4                9                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
  10Q GAIN MUTATED    11   6   9   0
  10Q GAIN WILD-TYPE 125  50 120   7
D20V5, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  N0               11                125
  N1                6                 50
  N2                9                120
  N3                0                  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"
D20V6, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     6   3
  10Q GAIN WILD-TYPE 102  45
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      6    3
  10Q GAIN WILD-TYPE  102   45
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  M0                6                102
  MX                3                 45
[1] 2 2
[1] FALSE
D20V7, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     7  21
  10Q GAIN WILD-TYPE 114 275
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      7   21
  10Q GAIN WILD-TYPE  114  275
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FEMALE                7                114
  MALE                 21                275
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  10Q GAIN MUTATED                                      28
  10Q GAIN WILD-TYPE                                   382
                    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                                                   6
D20V8, multiclass
                                                             clus
vv                                                            10Q GAIN 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                        0
                                                             clus
vv                                                            10Q GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      382
  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"
D20V9, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     7  21
  10Q GAIN WILD-TYPE  72 317
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      7   21
  10Q GAIN WILD-TYPE   72  317
     clus
vv    10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  NO                 7                 72
  YES               21                317
[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                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10Q GAIN MUTATED                           0    27
  10Q GAIN WILD-TYPE                        33   334
D20V12, multiclass
                                  clus
vv                                 10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 10
  BLACK OR AFRICAN AMERICAN                       0                 33
  WHITE                                          27                334
[1] 4 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  26
  10Q GAIN WILD-TYPE  16 355
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      2   26
  10Q GAIN WILD-TYPE   16  355
                        clus
vv                       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                 16
  NOT HISPANIC OR LATINO               26                355
[1] 2 2
[1] FALSE

Clustering(21) Variable = 11P GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                  0   1
  11P GAIN MUTATED    35  10
  11P GAIN WILD-TYPE 222  88
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                45                310 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                10                 88 
$`11P GAIN MUTATED`
TCGA-BA-4075 TCGA-BA-5556 TCGA-BA-6868 TCGA-BB-4225 TCGA-BB-7861 TCGA-C9-A47Z 
         283          725          190          140          310            5 
TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5367 TCGA-CN-6994 
         240         1960         1988          488         1966          119 
TCGA-CN-6997 TCGA-CQ-5323 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-7063 TCGA-CQ-7065 
         429         1466          341          129         1461         1007 
TCGA-CQ-7069 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CR-6484 
         901          968         1960          393          391          354 
TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7382 TCGA-CV-5440 TCGA-CV-6003 TCGA-CV-6433 
        1191         1440          796         1978         1665          641 
TCGA-CV-7254 TCGA-CV-7261 TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6827 TCGA-D6-8569 
        1976         1099          828          773          568          128 
TCGA-DQ-7588 TCGA-F7-A50J TCGA-HD-7229 TCGA-IQ-7630 TCGA-IQ-A61L TCGA-P3-A5QA 
        1965          585            2          485          351         1652 
TCGA-P3-A6T2 TCGA-QK-A6IG TCGA-QK-A6IJ 
        1917          218           64 

$`11P 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-5555 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 
        1288         1762          520          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-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BB-4217 
         895          513          351          216          182          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-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 
         624            4          799          721          485          142 
TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
         452          613          392          462          993          642 
TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-5356 
         369          395         1330          811         1268          512 
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-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 
        1975          413          290          630          424          629 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 
         433          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          424          224          318          611 
TCGA-CN-6992 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63T 
         394          432           46          443          447          225 
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-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 
         654         1660         1422          896         1399          317 
TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 
         870         1000         1057          985         1959         1959 
TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-A4C9 
         815         1378          509         1309          877          613 
TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 
        1963          545          548          303          608         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-7368 TCGA-CR-7369 TCGA-CR-7370 
         479         1956         1435         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-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 
        1036         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-5435 TCGA-CV-5436 
        1955          522         1950         3295         1438          584 
TCGA-CV-5439 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 
         546         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-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 
        1315         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 
        1724         1444         1095          954          797         1967 
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-A461 TCGA-CV-A6JD 
        1959         1981          851         1945         1954         1970 
TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-D6-6517 
         750          717          317          321          237          292 
TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-8568 TCGA-D6-A4Z9 
         701           77          491          154          106          112 
TCGA-D6-A4ZB TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 
         104         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-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G 
         324          340          564          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-HD-7753 
         407           58          133          414          403            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-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-A66T TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A 
         360          224          210           14           34          392 
TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QE 
          56          111          112          254          910          721 
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 
         357          245          228          225 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 2                  3 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              1988               3837 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             641.0              626.5 
[1] "2.0 - 1988.0 (641.0)" "3.0 - 3837.0 (626.5)"
[1] "hr=" "1.1"
D21V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  11P GAIN MUTATED         5       12        12        23         1
  11P GAIN WILD-TYPE      19       51        59       169         8
D21V3, multiclass
           clus
vv          11P GAIN MUTATED 11P GAIN WILD-TYPE
  STAGE I                  5                 19
  STAGE II                12                 51
  STAGE III               12                 59
  STAGE IVA               23                169
  STAGE IVB                1                  8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  11P GAIN MUTATED     6  18  13  16
  11P GAIN WILD-TYPE  34  90  72 115
D21V4, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  T1                6                 34
  T2               18                 90
  T3               13                 72
  T4               16                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 GAIN MUTATED    27   7  13   1
  11P GAIN WILD-TYPE 109  49 116   6
D21V5, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  N0               27                109
  N1                7                 49
  N2               13                116
  N3                1                  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"
D21V6, binary
                    cls
clus                  0  1
  11P GAIN MUTATED   23  4
  11P GAIN WILD-TYPE 85 44
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     23    4
  11P GAIN WILD-TYPE   85   44
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  M0               23                 85
  MX                4                 44
[1] 2 2
[1] FALSE
D21V7, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    17  39
  11P GAIN WILD-TYPE 104 257
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     17   39
  11P GAIN WILD-TYPE  104  257
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE               17                104
  MALE                 39                257
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  11P GAIN MUTATED                                      56
  11P GAIN WILD-TYPE                                   354
                    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                                                   6
D21V8, multiclass
                                                             clus
vv                                                            11P 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                        0
                                                             clus
vv                                                            11P GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      354
  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"
D21V9, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    12  44
  11P GAIN WILD-TYPE  67 294
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     12   44
  11P GAIN WILD-TYPE   67  294
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  NO                12                 67
  YES               44                294
[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                                1     6
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11P GAIN MUTATED                           5    45
  11P GAIN WILD-TYPE                        28   316
D21V12, multiclass
                                  clus
vv                                 11P GAIN MUTATED 11P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           4                  6
  BLACK OR AFRICAN AMERICAN                       5                 28
  WHITE                                          45                316
[1] 4 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  52
  11P GAIN WILD-TYPE  16 329
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      2   52
  11P GAIN WILD-TYPE   16  329
                        clus
vv                       11P GAIN MUTATED 11P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                 16
  NOT HISPANIC OR LATINO               52                329
[1] 2 2
[1] FALSE

Clustering(22) Variable = 11Q GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                  0   1
  11Q GAIN MUTATED    32  13
  11Q GAIN WILD-TYPE 225  85
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                45                310 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                13                 85 
$`11Q GAIN MUTATED`
TCGA-BA-4075 TCGA-BA-5556 TCGA-BA-5558 TCGA-BB-4225 TCGA-BB-7861 TCGA-CN-4731 
         283          725         1636          140          310          993 
TCGA-CN-4737 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5367 TCGA-CN-6018 TCGA-CN-6994 
         240         1988          488         1966           45          119 
TCGA-CN-6997 TCGA-CN-A63U TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-7063 TCGA-CQ-7065 
         429          526          341          129         1461         1007 
TCGA-CQ-7069 TCGA-CQ-A4C7 TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CR-6484 TCGA-CR-7365 
         901         1960          393          391          354         1191 
TCGA-CR-7367 TCGA-CR-7372 TCGA-CR-7383 TCGA-CV-5440 TCGA-CV-6003 TCGA-CV-6960 
        1440          759         1954         1978         1665         1969 
TCGA-CV-7248 TCGA-CV-7261 TCGA-CV-7440 TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6826 
        1967         1099         1981          828          773          154 
TCGA-D6-6827 TCGA-D6-A4ZB TCGA-DQ-5631 TCGA-F7-A50J TCGA-HD-7229 TCGA-IQ-7630 
         568          104          548          585            2          485 
TCGA-P3-A5QA TCGA-QK-A6IG TCGA-QK-A6IJ 
        1652          218           64 

$`11Q 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-5555 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6868 
        1288         1762          520          623         1747          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-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BB-4217 
         895          513          351          216          182          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          485 
TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4733 
         142          452          613          392          462          642 
TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 
         369          395         1960         1330          811         1268 
TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 
         512          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          413          290          630          424 
TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6020 
         629          433          594          629          432           98 
TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 
        1970          202          424          224          318          611 
TCGA-CN-6992 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63T 
         394          432           46          443          447          225 
TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 TCGA-CQ-5323 TCGA-CQ-5324 
         484          348          175          367         1466         1207 
TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 
         654         1660         1422          896         1399          317 
TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 
         870         1000         1057          985         1959         1959 
TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-A4C6 
         815         1378          509         1309          877          968 
TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CH TCGA-CQ-A4CI 
         613         1963          545          548          303          608 
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-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 
         546         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-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-6961 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 
        1957         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-7250 
        1724         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-A461 TCGA-CV-A6JD TCGA-CV-A6JE 
        1959          851         1945         1954         1970          750 
TCGA-CV-A6JN TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-D6-6517 TCGA-D6-6823 
         717          317          321          237          292          701 
TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-DQ-5624 
          77          491          106          128          112         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-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A61S 
         564          490          658           15           92            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-HD-7753 TCGA-HD-7754 TCGA-HD-7917 
         133          414          403            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-A61L TCGA-IQ-A61O 
         588          360          412          440          351          360 
TCGA-KU-A66S TCGA-KU-A66T TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D 
         224          210           14           34          392           56 
TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A6SW 
         111          112          254          910          721         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-A6IH TCGA-QK-A6II 
         357          245          228          225 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 2                  3 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              1988               3837 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
               585                629 
[1] "2.0 - 1988.0 (585.0)" "3.0 - 3837.0 (629.0)"
[1] "hr=" "1.1"
D22V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  11Q GAIN MUTATED         6        9        13        27         0
  11Q GAIN WILD-TYPE      18       54        58       165         9
D22V3, multiclass
           clus
vv          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  STAGE I                  6                 18
  STAGE II                 9                 54
  STAGE III               13                 58
  STAGE IVA               27                165
  STAGE IVB                0                  9
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  11Q GAIN MUTATED     7  14  15  19
  11Q GAIN WILD-TYPE  33  94  70 112
D22V4, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T1                7                 33
  T2               14                 94
  T3               15                 70
  T4               19                112
[1] 4 2
[1] 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    25   6  18   0
  11Q GAIN WILD-TYPE 111  50 111   7
D22V5, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  N0               25                111
  N1                6                 50
  N2               18                111
  N3                0                  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"
D22V6, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED   20  5
  11Q GAIN WILD-TYPE 88 43
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     20    5
  11Q GAIN WILD-TYPE   88   43
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  M0               20                 88
  MX                5                 43
[1] 2 2
[1] FALSE
D22V7, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    20  38
  11Q GAIN WILD-TYPE 101 258
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     20   38
  11Q GAIN WILD-TYPE  101  258
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE               20                101
  MALE                 38                258
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  11Q GAIN MUTATED                                      58
  11Q GAIN WILD-TYPE                                   352
                    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                                                   6
D22V8, multiclass
                                                             clus
vv                                                            11Q GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     58
  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                                      352
  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"
D22V9, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     9  49
  11Q GAIN WILD-TYPE  70 289
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      9   49
  11Q GAIN WILD-TYPE   70  289
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  NO                 9                 70
  YES               49                289
[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                                1     8
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11Q GAIN MUTATED                           5    49
  11Q GAIN WILD-TYPE                        28   312
D22V12, multiclass
                                  clus
vv                                 11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           2                  8
  BLACK OR AFRICAN AMERICAN                       5                 28
  WHITE                                          49                312
[1] 4 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     1  54
  11Q GAIN WILD-TYPE  17 327
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      1   54
  11Q GAIN WILD-TYPE   17  327
                        clus
vv                       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 17
  NOT HISPANIC OR LATINO               54                327
[1] 2 2
[1] FALSE

Clustering(23) Variable = 12P GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                  0   1
  12P GAIN MUTATED    74  23
  12P GAIN WILD-TYPE 183  75
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                97                258 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                23                 75 
$`12P GAIN MUTATED`
TCGA-BA-5555 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IF TCGA-BB-4223 TCGA-BB-4224 
         520         1747           63          895         2878          278 
TCGA-BB-4225 TCGA-BB-7862 TCGA-BB-7870 TCGA-C9-A47Z TCGA-CN-4725 TCGA-CN-4728 
         140          536         1153            5          485          613 
TCGA-CN-4729 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-5356 TCGA-CN-5359 
         392          240         1960         1330          512         1980 
TCGA-CN-5366 TCGA-CN-6012 TCGA-CN-6018 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 
        1966          629           45          424          224          318 
TCGA-CN-6994 TCGA-CN-A49B TCGA-CN-A63T TCGA-CQ-5329 TCGA-CQ-5332 TCGA-CQ-6224 
         119          447          225         1422          317          985 
TCGA-CQ-7067 TCGA-CQ-A4CE TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-6467 TCGA-CR-6487 
         509          393         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-CX-7086 TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6823 TCGA-DQ-5624 
        1981          237          828          773          701         1778 
TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-F7-7848 
         516         1965          575          622          299          564 
TCGA-F7-A50J TCGA-F7-A61S TCGA-H7-7774 TCGA-H7-8501 TCGA-HD-7753 TCGA-HD-7754 
         585            3          407           58            5           25 
TCGA-HD-7917 TCGA-HD-A6HZ TCGA-KU-A66T TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A 
          37          111          210           14           34          392 
TCGA-MT-A67D TCGA-MT-A67G TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-QK-A64Z TCGA-QK-A6IF 
          56          112         1917         1968          553          245 
TCGA-QK-A6IG 
         218 

$`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-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BB-4217 TCGA-BB-4227 
         513          351          216          182          187          133 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7871 
         558          310          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-4726 TCGA-CN-4727 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 
         142          452          462          993          642          369 
TCGA-CN-4736 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 
         395          811         1268         1988          488          173 
TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 
        1081         1977         1980         1966         1975          413 
TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 
         290          630          424          433          594          629 
TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6989 TCGA-CN-6992 
         432           98         1970          202          611          394 
TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A63U TCGA-CN-A63V 
         432          429           46          443          526          484 
TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
         348          175          367         1466         1207          654 
TCGA-CQ-5327 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 
        1660          896         1399          341          129          870 
TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 
        1000         1057         1959         1959          815         1461 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 
        1378         1007         1309          901          877          968 
TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CG 
        1960          613         1963          545          548          391 
TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6470 
         303          608         1663         1152          799         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-6491 TCGA-CR-6492 
         362          311          345          354          350          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-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-7391 TCGA-CR-7392 TCGA-CR-7393 
        1430         1951          392          913          946          908 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5435 
         898          930         1077          911         1472         1438 
TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 
         584          546         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-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-6942 TCGA-CV-6943 TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6960 
        1952         3835         1948         1966         1957         1969 
TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 
        1959         3837         1970         1970         1936         1959 
TCGA-CV-7101 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7250 
        1939         1987         1979         1724         1444         1960 
TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 
        1974         1948         1947         1937         1973         1972 
TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A461 
        1937         1984         1958          851         1945         1954 
TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CX-7082 TCGA-CX-7085 TCGA-D6-6517 
        1970          750          717          317          321          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-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7590 
         112          104         1081         1030          548          775 
TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-8298 TCGA-F7-8489 
         369          368          324          340          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-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-8224 TCGA-HD-8314 
         133          414          403            2           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-MT-A67F 
         412          440          351          360          224          111 
TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX 
         254          910         1652          721         1120         1954 
TCGA-P3-A6T0 TCGA-P3-A6T8 TCGA-QK-A652 TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ 
         578          400          357          228          225           64 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 3                  2 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              3295               3837 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             575.0              641.5 
[1] "3.0 - 3295.0 (575.0)" "2.0 - 3837.0 (641.5)"
[1] "hr=" "1.2"
D23V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  12P GAIN MUTATED         9       17        21        55         2
  12P GAIN WILD-TYPE      15       46        50       137         7
D23V3, multiclass
           clus
vv          12P GAIN MUTATED 12P GAIN WILD-TYPE
  STAGE I                  9                 15
  STAGE II                17                 46
  STAGE III               21                 50
  STAGE IVA               55                137
  STAGE IVB                2                  7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  12P GAIN MUTATED   11 32 26 35
  12P GAIN WILD-TYPE 29 76 59 96
D23V4, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  T1               11                 29
  T2               32                 76
  T3               26                 59
  T4               35                 96
[1] 4 2
[1] 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   42 15 36  2
  12P GAIN WILD-TYPE 94 41 93  5
D23V5, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  N0               42                 94
  N1               15                 41
  N2               36                 93
  N3                2                  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"
D23V6, binary
                    cls
clus                  0  1
  12P GAIN MUTATED   26 13
  12P GAIN WILD-TYPE 82 35
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     26   13
  12P GAIN WILD-TYPE   82   35
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  M0               26                 82
  MX               13                 35
[1] 2 2
[1] FALSE
D23V7, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    31  87
  12P GAIN WILD-TYPE  90 209
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     31   87
  12P GAIN WILD-TYPE   90  209
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE               31                 90
  MALE                 87                209
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  12P GAIN MUTATED                                     118
  12P GAIN WILD-TYPE                                   292
                    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                                                     0
  12P GAIN WILD-TYPE                                                   6
D23V8, multiclass
                                                             clus
vv                                                            12P GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    118
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        0
                                                             clus
vv                                                            12P GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      292
  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"
D23V9, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    23  95
  12P GAIN WILD-TYPE  56 243
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     23   95
  12P GAIN WILD-TYPE   56  243
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  NO                23                 56
  YES               95                243
[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                                0     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12P GAIN MUTATED                          10   104
  12P GAIN WILD-TYPE                        23   257
D23V12, multiclass
                                  clus
vv                                 12P GAIN MUTATED 12P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           1                  9
  BLACK OR AFRICAN AMERICAN                      10                 23
  WHITE                                         104                257
[1] 4 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     4 111
  12P GAIN WILD-TYPE  14 270
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      4  111
  12P GAIN WILD-TYPE   14  270
                        clus
vv                       12P GAIN MUTATED 12P GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                 14
  NOT HISPANIC OR LATINO              111                270
[1] 2 2
[1] FALSE

Clustering(24) Variable = 12Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                  0   1
  12Q GAIN MUTATED    46  14
  12Q GAIN WILD-TYPE 211  84
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                60                295 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                14                 84 
$`12Q GAIN MUTATED`
TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IF TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-7870 
        1747           63          895         2878          140         1153 
TCGA-C9-A47Z TCGA-CN-4725 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4737 TCGA-CN-4739 
           5          485          452          613          240         1330 
TCGA-CN-5356 TCGA-CN-5359 TCGA-CN-5366 TCGA-CN-6010 TCGA-CN-6012 TCGA-CN-6023 
         512         1980         1966          630          629          424 
TCGA-CN-6988 TCGA-CN-A49B TCGA-CN-A63T TCGA-CQ-5332 TCGA-CQ-6224 TCGA-CQ-7067 
         318          447          225          317          985          509 
TCGA-CQ-A4CE TCGA-CR-5247 TCGA-CR-6467 TCGA-CR-7365 TCGA-CR-7379 TCGA-CR-7383 
         393          358         1777         1191         1036         1954 
TCGA-CR-7399 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5434 TCGA-CV-6941 TCGA-CV-7102 
         181         1955          522         3295         1959         1945 
TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7422 TCGA-CV-7435 
        1095          954          797         1967         1957         1959 
TCGA-CV-7440 TCGA-D6-6516 TCGA-D6-6823 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7591 
        1981          773          701         1965          575          622 
TCGA-F7-A50J TCGA-F7-A61S TCGA-H7-7774 TCGA-HD-7753 TCGA-HD-A6HZ TCGA-KU-A66T 
         585            3          407            5          111          210 
TCGA-MT-A51W TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67G TCGA-P3-A6T4 TCGA-QK-A6IF 
          14          392           56          112         1968          245 

$`12Q 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-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-6872 TCGA-BA-6873 
        1636          190          644          451          384          113 
TCGA-BA-7269 TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BB-4217 
         236          513          351          216          182          187 
TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 
         278          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-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4729 TCGA-CN-4730 
           4          799          721          142          392          462 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4740 
         993          642          369          395         1960          811 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5363 
        1268         1988          488          173         1081         1977 
TCGA-CN-5365 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6011 
        1980         1966         1975          413          290          424 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 
         433          594          629           45          432           98 
TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 
        1970          202          224          611          394          119 
TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A63U TCGA-CN-A63V 
         432          429           46          443          526          484 
TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
         348          175          367         1466         1207          654 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 
        1660         1422          896         1399          341          129 
TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 
         870         1000         1057         1959         1959          815 
TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 
        1461         1378         1007         1309          901          877 
TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD 
         968         1960          613         1963          545          548 
TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 
         391          303          608         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 
        1724         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-A461 
        1937         1984         1958          851         1945         1954 
TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 
        1970          750          717          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-DQ-5624 TCGA-DQ-5625 
         106          128          112          104         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          564          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-HD-7229 TCGA-HD-7754 
          58          133          414          403            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-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-MT-A51X TCGA-MT-A67F TCGA-MZ-A6I9 TCGA-P3-A5Q5 
         360          224           34          111          254          910 
TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 
        1652          721         1120         1954          578         1917 
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 
          64 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 3                  2 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              3295               3837 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             617.5              638.0 
[1] "3.0 - 3295.0 (617.5)" "2.0 - 3837.0 (638.0)"
[1] "hr=" "1.3"
D24V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  12Q GAIN MUTATED         6        8        14        33         0
  12Q GAIN WILD-TYPE      18       55        57       159         9
D24V3, multiclass
           clus
vv          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  STAGE I                  6                 18
  STAGE II                 8                 55
  STAGE III               14                 57
  STAGE IVA               33                159
  STAGE IVB                0                  9
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  12Q GAIN MUTATED     7  16  17  21
  12Q GAIN WILD-TYPE  33  92  68 110
D24V4, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T1                7                 33
  T2               16                 92
  T3               17                 68
  T4               21                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
  12Q GAIN MUTATED    29   8  20   0
  12Q GAIN WILD-TYPE 107  48 109   7
D24V5, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  N0               29                107
  N1                8                 48
  N2               20                109
  N3                0                  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"
D24V6, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED   16  8
  12Q GAIN WILD-TYPE 92 40
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     16    8
  12Q GAIN WILD-TYPE   92   40
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  M0               16                 92
  MX                8                 40
[1] 2 2
[1] FALSE
D24V7, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    21  49
  12Q GAIN WILD-TYPE 100 247
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     21   49
  12Q GAIN WILD-TYPE  100  247
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE               21                100
  MALE                 49                247
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  12Q GAIN MUTATED                                      70
  12Q GAIN WILD-TYPE                                   340
                    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                                                     0
  12Q GAIN WILD-TYPE                                                   6
D24V8, multiclass
                                                             clus
vv                                                            12Q GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     70
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        0
                                                             clus
vv                                                            12Q 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                          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"
D24V9, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    20  50
  12Q GAIN WILD-TYPE  59 288
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     20   50
  12Q GAIN WILD-TYPE   59  288
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  NO                20                 59
  YES               50                288
[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                                1     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12Q GAIN MUTATED                           4    64
  12Q GAIN WILD-TYPE                        29   297
D24V12, multiclass
                                  clus
vv                                 12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  9
  BLACK OR AFRICAN AMERICAN                       4                 29
  WHITE                                          64                297
[1] 4 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     4  64
  12Q GAIN WILD-TYPE  14 317
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      4   64
  12Q GAIN WILD-TYPE   14  317
                        clus
vv                       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                 14
  NOT HISPANIC OR LATINO               64                317
[1] 2 2
[1] FALSE

Clustering(25) Variable = 13Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                  0   1
  13Q GAIN MUTATED    29  10
  13Q GAIN WILD-TYPE 228  88
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                39                316 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                10                 88 
$`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          613 
TCGA-CN-4729 TCGA-CN-4737 TCGA-CN-4742 TCGA-CN-5370 TCGA-CN-6013 TCGA-CN-6989 
         392          240         1988         1975          433          611 
TCGA-CN-6996 TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CQ-A4CH TCGA-CR-5247 
         432          484          348          175          303          358 
TCGA-CR-6484 TCGA-CR-6488 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7370 TCGA-CR-7390 
         354          379         1191         1440          105          907 
TCGA-CV-5440 TCGA-CV-6003 TCGA-CV-7090 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7243 
        1978         1665         3837         1970         1970          954 
TCGA-D6-6823 TCGA-D6-8569 TCGA-DQ-5629 TCGA-DQ-5631 TCGA-F7-A50J TCGA-IQ-A61G 
         701          128          516          548          585          360 
TCGA-MT-A51W TCGA-MT-A51X TCGA-QK-A6IH 
          14           34          228 

$`13Q 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-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-6871 TCGA-BA-6872 TCGA-BA-6873 
        1747          190          644           63          384          113 
TCGA-BA-7269 TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BB-4217 
         236          513          351          216          182          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-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-4727 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 
         485          452          462          993          642          369 
TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-5355 
         395         1960         1330          811         1268          488 
TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 
         512          173         1980         1081         1977         1980 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 
        1966         1966          413          290          630          424 
TCGA-CN-6012 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 
         629          594          629           45          432           98 
TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6992 
        1970          202          424          224          318          394 
TCGA-CN-6994 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63T 
         119          429           46          443          447          225 
TCGA-CN-A63U TCGA-CN-A641 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 
         526          367         1466         1207          654         1660 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 
        1422          896         1399          317          341          129 
TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 
         870         1000         1057          985         1959         1959 
TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 
         815         1461         1378         1007          509         1309 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CA 
         901          877          968         1960          613         1963 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CI TCGA-CR-5243 
         545          548          393          391          608         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         1724         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-A461 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CX-7082 TCGA-CX-7085 
        1954         1970          750          717          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-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-DQ-5624 
         154          568          106          112          104         1778 
TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 
        1081         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          564 
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-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-A61H TCGA-IQ-A61J TCGA-IQ-A61L TCGA-IQ-A61O 
         441          588          412          440          351          360 
TCGA-KU-A66S TCGA-KU-A66T TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G 
         224          210          392           56          111          112 
TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX 
         254          910         1652          721         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 
         245          218          225           64 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                14                  2 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              3837               3835 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
               451                649 
[1] "14.0 - 3837.0 (451.0)" "2.0 - 3835.0 (649.0)" 
[1] "hr=" "1.2"
D25V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  13Q GAIN MUTATED         1       10         9        20         2
  13Q GAIN WILD-TYPE      23       53        62       172         7
D25V3, multiclass
           clus
vv          13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  STAGE I                  1                 23
  STAGE II                10                 53
  STAGE III                9                 62
  STAGE IVA               20                172
  STAGE IVB                2                  7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  13Q GAIN MUTATED     2  14  10  16
  13Q GAIN WILD-TYPE  38  94  75 115
D25V4, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  T1                2                 38
  T2               14                 94
  T3               10                 75
  T4               16                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
  13Q GAIN MUTATED    14   7  15   0
  13Q GAIN WILD-TYPE 122  49 114   7
D25V5, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  N0               14                122
  N1                7                 49
  N2               15                114
  N3                0                  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"
D25V6, binary
                    cls
clus                  0  1
  13Q GAIN MUTATED   13  6
  13Q GAIN WILD-TYPE 95 42
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     13    6
  13Q GAIN WILD-TYPE   95   42
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  M0               13                 95
  MX                6                 42
[1] 2 2
[1] FALSE
D25V7, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED    15  34
  13Q GAIN WILD-TYPE 106 262
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     15   34
  13Q GAIN WILD-TYPE  106  262
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE               15                106
  MALE                 34                262
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  13Q GAIN MUTATED                                      49
  13Q GAIN WILD-TYPE                                   361
                    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                                                     0
  13Q GAIN WILD-TYPE                                                   6
D25V8, multiclass
                                                             clus
vv                                                            13Q GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     49
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        0
                                                             clus
vv                                                            13Q GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      361
  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"
D25V9, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED    14  35
  13Q GAIN WILD-TYPE  65 303
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     14   35
  13Q GAIN WILD-TYPE   65  303
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  NO                14                 65
  YES               35                303
[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                                1     8
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  13Q GAIN MUTATED                           3    41
  13Q GAIN WILD-TYPE                        30   320
D25V12, multiclass
                                  clus
vv                                 13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           2                  8
  BLACK OR AFRICAN AMERICAN                       3                 30
  WHITE                                          41                320
[1] 4 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     3  44
  13Q GAIN WILD-TYPE  15 337
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      3   44
  13Q GAIN WILD-TYPE   15  337
                        clus
vv                       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                 15
  NOT HISPANIC OR LATINO               44                337
[1] 2 2
[1] FALSE

Clustering(26) Variable = 14Q GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                  0   1
  14Q GAIN MUTATED    68  34
  14Q GAIN WILD-TYPE 189  64
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
               102                253 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                34                 64 
$`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-BB-8601 TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4723 TCGA-CN-4730 
         351          624            5            4          721          462 
TCGA-CN-4738 TCGA-CN-4740 TCGA-CN-5356 TCGA-CN-5363 TCGA-CN-5366 TCGA-CN-5367 
        1960          811          512         1977         1966         1966 
TCGA-CN-6021 TCGA-CN-6994 TCGA-CN-A63T TCGA-CN-A63W TCGA-CQ-5323 TCGA-CQ-5329 
        1970          119          225          348         1466         1422 
TCGA-CQ-5330 TCGA-CQ-5334 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7067 
         896          129          985         1959          815          509 
TCGA-CQ-7069 TCGA-CQ-A4C6 TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CR-6474 TCGA-CR-6477 
         901          968          393          391         1971          514 
TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7370 TCGA-CR-7372 
         379          350         1191         1440          105          759 
TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7383 TCGA-CR-7388 TCGA-CR-7390 TCGA-CV-5432 
        1968         1036         1954         1951          907         1950 
TCGA-CV-5434 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5444 TCGA-CV-5970 TCGA-CV-5973 
        3295          546         1978         2437          406         2641 
TCGA-CV-5977 TCGA-CV-6003 TCGA-CV-6934 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6945 
        1840         1665         1948         1959         3835         1969 
TCGA-CV-6954 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7101 TCGA-CV-7180 
        1957         3837         1959         1970         1939         1987 
TCGA-CV-7238 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7254 TCGA-CV-7418 
        1444          954          797         1967         1976         1955 
TCGA-CV-7434 TCGA-CV-7440 TCGA-CV-A45Q TCGA-CV-A6JE TCGA-CX-7086 TCGA-CX-7219 
        1958         1981         1945          750          237          828 
TCGA-D6-6516 TCGA-D6-6823 TCGA-D6-6825 TCGA-D6-A4Z9 TCGA-DQ-5625 TCGA-DQ-5629 
         773          701          491          112         1081          516 
TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-F7-A50I TCGA-F7-A50J 
        1965          575          299          369           92          585 
TCGA-HD-7753 TCGA-HD-7917 TCGA-HD-A6HZ TCGA-IQ-A61E TCGA-IQ-A61J TCGA-IQ-A61L 
           5           37          111          588          440          351 
TCGA-KU-A66T TCGA-MT-A51W TCGA-MT-A51X TCGA-P3-A6SX TCGA-P3-A6T4 TCGA-QK-A6IG 
         210           14           34         1954         1968          218 

$`14Q 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-5557 TCGA-BA-5558 TCGA-BA-5559 
        1288         1762          725          623         1636         1747 
TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-A6D8 TCGA-BA-A6DB 
         190          644          451           63          513          216 
TCGA-BA-A6DE TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 
         182          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          485 
TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4731 TCGA-CN-4733 
         142          452          613          392          993          642 
TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4739 TCGA-CN-4741 TCGA-CN-4742 
         369          395          240         1330         1268         1988 
TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5365 TCGA-CN-5370 
         488          173         1980         1081         1980         1975 
TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 
         413          290          630          424          629          433 
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 
         424          224          318          611          394          432 
TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63U TCGA-CN-A63V 
         429           46          443          447          526          484 
TCGA-CN-A63Y TCGA-CN-A641 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5331 
         175          367         1207          654         1660         1399 
TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6228 
         317          341          870         1000         1057         1959 
TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-A4C7 
        1461         1378         1007         1309          877         1960 
TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CH TCGA-CQ-A4CI 
         613         1963          545          548          303          608 
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-6478 TCGA-CR-6480 
        1521         1966         1050         1125         1969          362 
TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6492 TCGA-CR-6493 
         311          345          354          234          479         1956 
TCGA-CR-7364 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7373 TCGA-CR-7374 
        1435         1245         1960         1979          889           30 
TCGA-CR-7376 TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7389 TCGA-CR-7391 
         972          796          997         1430          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-5435 TCGA-CV-5436 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5966 
        1438          584         2886         2327         1958          519 
TCGA-CV-5971 TCGA-CV-5976 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6436 
         701         1478          215         1315          641         1899 
TCGA-CV-6441 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6943 TCGA-CV-6952 TCGA-CV-6960 
        1970         1969         1952         1948         1966         1969 
TCGA-CV-6961 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7183 
        1959         1970         1936         1959         1945         1979 
TCGA-CV-7235 TCGA-CV-7242 TCGA-CV-7250 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 
        1724         1095         1960         1099         1974         1948 
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-7435 TCGA-CV-A45O TCGA-CV-A461 TCGA-CV-A6JD TCGA-CV-A6JN 
        1984         1959          851         1954         1970          717 
TCGA-CX-7082 TCGA-CX-7085 TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6826 TCGA-D6-6827 
         317          321          292           77          154          568 
TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4ZB TCGA-DQ-5624 TCGA-DQ-5630 TCGA-DQ-5631 
         106          128          104         1778         1030          548 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 
         775          622          368          324          340          564 
TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W 
         490          658           15            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-HD-7229 TCGA-HD-7754 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 
         403            2           25           55           44           24 
TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 
          25           11           49           10           33         1057 
TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61O 
         485          122          441          360          412          360 
TCGA-KU-A66S TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 
         224          392           56          111          112          254 
TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6T0 TCGA-P3-A6T2 
         910         1652          721         1120          578         1917 
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 
          64 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 4                  2 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              3837               2886 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             821.5              584.0 
[1] "4.0 - 3837.0 (821.5)" "2.0 - 2886.0 (584.0)"
[1] "hr=" "1.3"
D26V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  14Q GAIN MUTATED         9       20        22        54         3
  14Q GAIN WILD-TYPE      15       43        49       138         6
D26V3, multiclass
           clus
vv          14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  STAGE I                  9                 15
  STAGE II                20                 43
  STAGE III               22                 49
  STAGE IVA               54                138
  STAGE IVB                3                  6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  14Q GAIN MUTATED   10 33 25 40
  14Q GAIN WILD-TYPE 30 75 60 91
D26V4, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  T1               10                 30
  T2               33                 75
  T3               25                 60
  T4               40                 91
[1] 4 2
[1] 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   41 16 38  2
  14Q GAIN WILD-TYPE 95 40 91  5
D26V5, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  N0               41                 95
  N1               16                 40
  N2               38                 91
  N3                2                  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"
D26V6, binary
                    cls
clus                  0  1
  14Q GAIN MUTATED   31 12
  14Q GAIN WILD-TYPE 77 36
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     31   12
  14Q GAIN WILD-TYPE   77   36
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  M0               31                 77
  MX               12                 36
[1] 2 2
[1] FALSE
D26V7, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    40  83
  14Q GAIN WILD-TYPE  81 213
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     40   83
  14Q GAIN WILD-TYPE   81  213
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE               40                 81
  MALE                 83                213
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  14Q GAIN MUTATED                                     123
  14Q GAIN WILD-TYPE                                   287
                    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                                                   6
D26V8, multiclass
                                                             clus
vv                                                            14Q GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    123
  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                                      287
  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"
D26V9, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    21 102
  14Q GAIN WILD-TYPE  58 236
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     21  102
  14Q GAIN WILD-TYPE   58  236
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  NO                21                 58
  YES              102                236
[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                                0     7
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  14Q GAIN MUTATED                          14   100
  14Q GAIN WILD-TYPE                        19   261
D26V12, multiclass
                                  clus
vv                                 14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           3                  7
  BLACK OR AFRICAN AMERICAN                      14                 19
  WHITE                                         100                261
[1] 4 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     6 111
  14Q GAIN WILD-TYPE  12 270
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      6  111
  14Q GAIN WILD-TYPE   12  270
                        clus
vv                       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    6                 12
  NOT HISPANIC OR LATINO              111                270
[1] 2 2
[1] FALSE

Clustering(27) Variable = 15Q GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                  0   1
  15Q GAIN MUTATED    38  15
  15Q GAIN WILD-TYPE 219  83
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                53                302 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                15                 83 
$`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 
         240         1330          811          512         1980         1966 
TCGA-CN-6010 TCGA-CN-A63U TCGA-CQ-6228 TCGA-CQ-7069 TCGA-CQ-A4C9 TCGA-CR-6474 
         630          526         1959          901          613         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 
        1724         1976         1099         1955         1937         1984 
TCGA-CV-A6JD TCGA-D6-6516 TCGA-D6-8569 TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7589 
        1970          773          128          516         1965          575 
TCGA-F7-7848 TCGA-H7-8501 TCGA-HD-7753 TCGA-HD-7917 TCGA-HD-A633 TCGA-HD-A6HZ 
         564           58            5           37           49          111 
TCGA-HD-A6I0 TCGA-IQ-7632 TCGA-MT-A67A TCGA-MT-A67G TCGA-QK-A6IH 
          33          441          392          112          228 

$`15Q 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-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-6872 
        1636         1747          190          644          451          384 
TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE 
         236          895          513          351          216          182 
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-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-8601 TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 
         436          624            4          799          721          485 
TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
         142          452          613          462          993          642 
TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 
         369          395         1960         1268         1988          488 
TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5367 TCGA-CN-5370 
         173         1980         1081         1977         1966         1975 
TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 
         413          290          424          629          433          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-6994 
         424          224          318          611          394          119 
TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63T 
         432          429           46          443          447          225 
TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 TCGA-CQ-5323 TCGA-CQ-5324 
         484          348          175          367         1466         1207 
TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 
         654         1660         1422          896         1399          317 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 
         341          129          870         1000         1057          985 
TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 
        1959          815         1461         1378         1007          509 
TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CA TCGA-CQ-A4CB 
        1309          877          968         1960         1963          545 
TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 
         548          393          391          303          608         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-6478 TCGA-CR-6480 TCGA-CR-6481 
        1966         1050         1125         1969          362          311 
TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7367 
         345          234          379          479         1956         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-7382 TCGA-CR-7383 TCGA-CR-7385 
          30          972         1968          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-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-6433 TCGA-CV-6436 
        1478         1840          215         1315          641         1899 
TCGA-CV-6441 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 
        1970         1969         1952         1959         3835         1948 
TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7095 
        1969         1966         1957         1969         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-7245 TCGA-CV-7248 TCGA-CV-7250 
        1444         1095          954          797         1967         1960 
TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7428 TCGA-CV-7430 
        1974         1948         1957         1947         1973         1972 
TCGA-CV-7432 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q 
        1937         1958         1959         1981          851         1945 
TCGA-CV-A461 TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 
        1954          750          717          317          321          237 
TCGA-CX-7219 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 
         828          292          701           77          491          154 
TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-DQ-5624 TCGA-DQ-5625 
         568          106          112          104         1778         1081 
TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 
        1030          548          775          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-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-HD-7229 
           6          407          133          414          403            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-A634 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-A61E TCGA-IQ-A61G 
          10         1057          485          122          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          210 
TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67D TCGA-MT-A67F TCGA-MZ-A6I9 TCGA-P3-A5Q5 
          14           34           56          111          254          910 
TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 
        1652          721         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-A6II TCGA-QK-A6IJ 
         225           64 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 5                  2 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              3837               3835 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             630.0              626.5 
[1] "5.0 - 3837.0 (630.0)" "2.0 - 3835.0 (626.5)"
[1] "hr=" "1.1"
D27V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  15Q GAIN MUTATED         4       10        10        31         3
  15Q GAIN WILD-TYPE      20       53        61       161         6
D27V3, multiclass
           clus
vv          15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  STAGE I                  4                 20
  STAGE II                10                 53
  STAGE III               10                 61
  STAGE IVA               31                161
  STAGE IVB                3                  6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  15Q GAIN MUTATED     7  18   6  27
  15Q GAIN WILD-TYPE  33  90  79 104
D27V4, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  T1                7                 33
  T2               18                 90
  T3                6                 79
  T4               27                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
  15Q GAIN MUTATED    24   9  17   1
  15Q GAIN WILD-TYPE 112  47 112   6
D27V5, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  N0               24                112
  N1                9                 47
  N2               17                112
  N3                1                  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"
D27V6, binary
                    cls
clus                  0  1
  15Q GAIN MUTATED   16  8
  15Q GAIN WILD-TYPE 92 40
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     16    8
  15Q GAIN WILD-TYPE   92   40
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  M0               16                 92
  MX                8                 40
[1] 2 2
[1] FALSE
D27V7, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    21  43
  15Q GAIN WILD-TYPE 100 253
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     21   43
  15Q GAIN WILD-TYPE  100  253
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE               21                100
  MALE                 43                253
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  15Q GAIN MUTATED                                      64
  15Q GAIN WILD-TYPE                                   346
                    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                                                     0
  15Q GAIN WILD-TYPE                                                   6
D27V8, multiclass
                                                             clus
vv                                                            15Q GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     64
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        0
                                                             clus
vv                                                            15Q GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      346
  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"
D27V9, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    11  53
  15Q GAIN WILD-TYPE  68 285
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     11   53
  15Q GAIN WILD-TYPE   68  285
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  NO                11                 68
  YES               53                285
[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                                1     8
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  15Q GAIN MUTATED                           3    56
  15Q GAIN WILD-TYPE                        30   305
D27V12, multiclass
                                  clus
vv                                 15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           2                  8
  BLACK OR AFRICAN AMERICAN                       3                 30
  WHITE                                          56                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"
D27V13, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     1  59
  15Q GAIN WILD-TYPE  17 322
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      1   59
  15Q GAIN WILD-TYPE   17  322
                        clus
vv                       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                 17
  NOT HISPANIC OR LATINO               59                322
[1] 2 2
[1] FALSE

Clustering(28) Variable = 16P GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                  0   1
  16P GAIN MUTATED    47  23
  16P GAIN WILD-TYPE 210  75
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                70                285 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                23                 75 
$`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-C9-A47Z TCGA-CN-4728 TCGA-CN-4730 
          63          113          895            5          613          462 
TCGA-CN-4737 TCGA-CN-4739 TCGA-CN-5356 TCGA-CN-6013 TCGA-CN-6020 TCGA-CN-6022 
         240         1330          512          433           98          202 
TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-A63U TCGA-CQ-5329 TCGA-CQ-6223 TCGA-CQ-7067 
         119          432          526         1422         1057          509 
TCGA-CQ-A4CA TCGA-CR-5247 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6481 TCGA-CR-7365 
        1963          358          514         1969          311         1191 
TCGA-CR-7367 TCGA-CR-7370 TCGA-CR-7372 TCGA-CR-7379 TCGA-CR-7388 TCGA-CR-7390 
        1440          105          759         1036         1951          907 
TCGA-CV-5439 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-6003 TCGA-CV-6941 TCGA-CV-6945 
         546         1840          215         1665         1959         1969 
TCGA-CV-6954 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7099 TCGA-CV-7180 TCGA-CV-7242 
        1957         1959         1970         1936         1987         1095 
TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7433 TCGA-CV-7435 TCGA-CV-A461 
         954          797         1967         1984         1959         1954 
TCGA-CX-7086 TCGA-D6-6516 TCGA-D6-6823 TCGA-D6-8569 TCGA-DQ-5625 TCGA-DQ-5631 
         237          773          701          128         1081          548 
TCGA-DQ-7588 TCGA-F7-A50J TCGA-F7-A623 TCGA-HD-8634 TCGA-IQ-7631 TCGA-IQ-A61L 
        1965          585            6           24          122          351 
TCGA-MT-A51W TCGA-P3-A6T4 TCGA-QK-A6II TCGA-QK-A6IJ 
          14         1968          225           64 

$`16P 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-5557 TCGA-BA-5558 TCGA-BA-6872 
        1288         1762          725          623         1636          384 
TCGA-BA-7269 TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BB-4217 
         236          513          351          216          182          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 
         485          142          452          392          993          642 
TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 
         369          395         1960          811         1268         1988 
TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 
         488          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          413          290          630 
TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 
         424          629          594          629           45          432 
TCGA-CN-6021 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 
        1970          424          224          318          611          394 
TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63V 
         429           46          443          447          225          484 
TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
         348          175          367         1466         1207          654 
TCGA-CQ-5327 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 
        1660          896         1399          317          341          129 
TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 
         870         1000          985         1959         1959          815 
TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 
        1461         1378         1007         1309          901          877 
TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE 
         968         1960          613          545          548          393 
TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 
         391          303          608         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-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 
        1971          362          345          354          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-7371 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7382 
        1979          889           30          972         1968          796 
TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7389 TCGA-CR-7391 TCGA-CR-7392 
        1954          997         1430          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-5440 TCGA-CV-5441 TCGA-CV-5442 
        3295         1438          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-5979 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 
        1478         1315          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-7102 
        1959         3837         1970         1959         1939         1945 
TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 
        1979         1724         1444         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-7440 TCGA-CV-A45O 
        1973         1972         1937         1958         1981          851 
TCGA-CV-A45Q TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CX-7082 TCGA-CX-7085 
        1945         1970          750          717          317          321 
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-A4Z9 TCGA-D6-A4ZB TCGA-DQ-5624 TCGA-DQ-5629 TCGA-DQ-5630 
         106          112          104         1778          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          564          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-HD-7229 TCGA-HD-7753 
          58          133          414          403            2            5 
TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8635 TCGA-HD-A4C1 
          25           37           55           44           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-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-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F 
         224          210           34          392           56          111 
TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW 
         112          254          910         1652          721         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 
         245          218          228 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 5                  2 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              1987               3837 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             628.5              629.0 
[1] "5.0 - 1987.0 (628.5)" "2.0 - 3837.0 (629.0)"
[1] "hr=" "1.5"
D28V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  16P GAIN MUTATED         6       14        13        32         3
  16P GAIN WILD-TYPE      18       49        58       160         6
D28V3, multiclass
           clus
vv          16P GAIN MUTATED 16P GAIN WILD-TYPE
  STAGE I                  6                 18
  STAGE II                14                 49
  STAGE III               13                 58
  STAGE IVA               32                160
  STAGE IVB                3                  6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  16P GAIN MUTATED     7  21  15  25
  16P GAIN WILD-TYPE  33  87  70 106
D28V4, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  T1                7                 33
  T2               21                 87
  T3               15                 70
  T4               25                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
  16P GAIN MUTATED    29  11  20   2
  16P GAIN WILD-TYPE 107  45 109   5
D28V5, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  N0               29                107
  N1               11                 45
  N2               20                109
  N3                2                  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"
D28V6, binary
                    cls
clus                  0  1
  16P GAIN MUTATED   17  5
  16P GAIN WILD-TYPE 91 43
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     17    5
  16P GAIN WILD-TYPE   91   43
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  M0               17                 91
  MX                5                 43
[1] 2 2
[1] FALSE
D28V7, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    25  59
  16P GAIN WILD-TYPE  96 237
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     25   59
  16P GAIN WILD-TYPE   96  237
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE               25                 96
  MALE                 59                237
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  16P GAIN MUTATED                                      84
  16P GAIN WILD-TYPE                                   326
                    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                                                     0
  16P GAIN WILD-TYPE                                                   6
D28V8, multiclass
                                                             clus
vv                                                            16P GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     84
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        0
                                                             clus
vv                                                            16P GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      326
  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"
D28V9, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    17  67
  16P GAIN WILD-TYPE  62 271
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     17   67
  16P GAIN WILD-TYPE   62  271
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  NO                17                 62
  YES               67                271
[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                                1     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16P GAIN MUTATED                          12    68
  16P GAIN WILD-TYPE                        21   293
D28V12, multiclass
                                  clus
vv                                 16P GAIN MUTATED 16P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  9
  BLACK OR AFRICAN AMERICAN                      12                 21
  WHITE                                          68                293
[1] 4 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     4  74
  16P GAIN WILD-TYPE  14 307
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      4   74
  16P GAIN WILD-TYPE   14  307
                        clus
vv                       16P GAIN MUTATED 16P GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                 14
  NOT HISPANIC OR LATINO               74                307
[1] 2 2
[1] FALSE

Clustering(29) Variable = 16Q GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                  0   1
  16Q GAIN MUTATED    45  24
  16Q GAIN WILD-TYPE 212  74
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                69                286 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                24                 74 
$`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-A6DA TCGA-C9-A47Z TCGA-CN-4728 TCGA-CN-4730 TCGA-CN-4737 TCGA-CN-4739 
         351            5          613          462          240         1330 
TCGA-CN-6013 TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6996 
         433           98          202          611          119          432 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-6223 TCGA-CQ-7067 TCGA-CQ-A4CA TCGA-CR-5247 
        1422          896         1057          509         1963          358 
TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-7365 TCGA-CR-7372 TCGA-CR-7374 TCGA-CR-7379 
         514         1969         1191          759           30         1036 
TCGA-CR-7388 TCGA-CR-7390 TCGA-CV-5439 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 
        1951          907          546         1840          215         1315 
TCGA-CV-6003 TCGA-CV-6941 TCGA-CV-6945 TCGA-CV-6954 TCGA-CV-7091 TCGA-CV-7095 
        1665         1959         1969         1957         1959         1970 
TCGA-CV-7099 TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 
        1936         1945         1987         1095          954          797 
TCGA-CV-7248 TCGA-CV-7406 TCGA-CV-7433 TCGA-CV-7435 TCGA-D6-6516 TCGA-D6-6823 
        1967         1974         1984         1959          773          701 
TCGA-D6-8568 TCGA-D6-8569 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-F7-A50J TCGA-F7-A623 
         106          128          548         1965          585            6 
TCGA-HD-7753 TCGA-HD-8314 TCGA-HD-8634 TCGA-IQ-7631 TCGA-IQ-A61L TCGA-MT-A51W 
           5           44           24          122          351           14 
TCGA-MT-A51X TCGA-P3-A6T4 TCGA-QK-A6IJ 
          34         1968           64 

$`16Q 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-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 
        1288         1762          520          725          623         1636 
TCGA-BA-5559 TCGA-BA-6869 TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A6D8 TCGA-BA-A6DB 
        1747          644          384          236          513          216 
TCGA-BA-A6DE TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 
         182          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          485          142          452          392 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4740 
         993          642          369          395         1960          811 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 
        1268         1988          488          512          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 
         413          290          630          424          629          594 
TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6021 TCGA-CN-6023 TCGA-CN-6024 
         629           45          432         1970          424          224 
TCGA-CN-6988 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49B 
         318          394          429           46          443          447 
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-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-6224 TCGA-CQ-6227 
         341          129          870         1000          985         1959 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7068 
        1959          815         1461         1378         1007         1309 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB 
         901          877          968         1960          613          545 
TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 
         548          393          391          303          608         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-6480 TCGA-CR-6481 TCGA-CR-6482 
        1050         1125         1971          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-7373 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 
         889          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-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 
        1472         1955          522         1950         3295         1438 
TCGA-CV-5436 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 
         584         1978         2886         2327         1958         2437 
TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-6433 
         519          406          701         2641         1478          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-7100 TCGA-CV-7101 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7250 
        1959         1939         1979         1724         1444         1960 
TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 
        1976         1099         1948         1955         1957         1947 
TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7434 TCGA-CV-7440 
        1937         1973         1972         1937         1958         1981 
TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A461 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN 
         851         1945         1954         1970          750          717 
TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6517 TCGA-D6-6824 
         317          321          237          828          292           77 
TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-DQ-5624 
         491          154          568          112          104         1778 
TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 
        1081          516         1030          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          564 
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-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-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8635 
         403            2           25           37           55           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-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J 
         485          441          588          360          412          440 
TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F 
         360          224          210          392           56          111 
TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW 
         112          254          910         1652          721         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 
         245          218          228          225 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 5                  2 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              1987               3837 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
               613                629 
[1] "5.0 - 1987.0 (613.0)" "2.0 - 3837.0 (629.0)"
[1] "hr=" "1.5"
D29V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  16Q GAIN MUTATED         7       17        12        36         3
  16Q GAIN WILD-TYPE      17       46        59       156         6
D29V3, multiclass
           clus
vv          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  STAGE I                  7                 17
  STAGE II                17                 46
  STAGE III               12                 59
  STAGE IVA               36                156
  STAGE IVB                3                  6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  16Q GAIN MUTATED    10  25  15  25
  16Q GAIN WILD-TYPE  30  83  70 106
D29V4, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T1               10                 30
  T2               25                 83
  T3               15                 70
  T4               25                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
  16Q GAIN MUTATED    30  10  25   2
  16Q GAIN WILD-TYPE 106  46 104   5
D29V5, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  N0               30                106
  N1               10                 46
  N2               25                104
  N3                2                  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"
D29V6, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED   19  5
  16Q GAIN WILD-TYPE 89 43
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     19    5
  16Q GAIN WILD-TYPE   89   43
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  M0               19                 89
  MX                5                 43
[1] 2 2
[1] FALSE
D29V7, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    30  57
  16Q GAIN WILD-TYPE  91 239
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     30   57
  16Q GAIN WILD-TYPE   91  239
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE               30                 91
  MALE                 57                239
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  16Q GAIN MUTATED                                      86
  16Q GAIN WILD-TYPE                                   324
                    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                                                     1
  16Q GAIN WILD-TYPE                                                   5
D29V8, multiclass
                                                             clus
vv                                                            16Q GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     86
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        1
                                                             clus
vv                                                            16Q GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      324
  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"
D29V9, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    17  70
  16Q GAIN WILD-TYPE  62 268
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     17   70
  16Q GAIN WILD-TYPE   62  268
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  NO                17                 62
  YES               70                268
[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                                1     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16Q GAIN MUTATED                          11    72
  16Q GAIN WILD-TYPE                        22   289
D29V12, multiclass
                                  clus
vv                                 16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  9
  BLACK OR AFRICAN AMERICAN                      11                 22
  WHITE                                          72                289
[1] 4 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     4  77
  16Q GAIN WILD-TYPE  14 304
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      4   77
  16Q GAIN WILD-TYPE   14  304
                        clus
vv                       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                 14
  NOT HISPANIC OR LATINO               77                304
[1] 2 2
[1] FALSE

Clustering(30) Variable = 17P GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                  0   1
  17P GAIN MUTATED    33  13
  17P GAIN WILD-TYPE 224  85
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                46                309 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                13                 85 
$`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          613          512         1966         1975          424 
TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-A63U TCGA-CQ-5329 TCGA-CQ-6229 TCGA-CQ-A4CE 
         611          119          526         1422          815          393 
TCGA-CR-5247 TCGA-CR-6467 TCGA-CR-6478 TCGA-CR-6488 TCGA-CR-7365 TCGA-CR-7370 
         358         1777         1969          379         1191          105 
TCGA-CR-7383 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5440 
        1954         1472         1955         1950         3295         1978 
TCGA-CV-5977 TCGA-CV-6003 TCGA-CV-6941 TCGA-CV-6945 TCGA-CV-7095 TCGA-CV-7101 
        1840         1665         1959         1969         1970         1939 
TCGA-CV-7248 TCGA-CV-7254 TCGA-CV-7261 TCGA-F7-8298 TCGA-F7-A50I TCGA-HD-7917 
        1967         1976         1099          490           92           37 
TCGA-HD-A6HZ TCGA-IQ-A61L TCGA-IQ-A61O TCGA-QK-A6IG 
         111          351          360          218 

$`17P 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-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-6871 TCGA-BA-6873 
        1747          190          644          451           63          113 
TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BB-4217 TCGA-BB-4223 
         513          351          216          182          187         2878 
TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7863 
         278          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-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 
           4          799          721          485          142          452 
TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 
         392          462          993          642          369          395 
TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 
         240         1960         1330          811         1268         1988 
TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 
         488          173         1980         1081         1977         1980 
TCGA-CN-5367 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 
        1966          413          290          630          424          629 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 
         433          594          629           45          432           98 
TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6992 TCGA-CN-6996 
        1970          202          224          318          394          432 
TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63V 
         429           46          443          447          225          484 
TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
         348          175          367         1466         1207          654 
TCGA-CQ-5327 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 
        1660          896         1399          317          341          129 
TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 
         870         1000         1057          985         1959         1959 
TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 
        1461         1378         1007          509         1309          901 
TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB 
         877          968         1960          613         1963          545 
TCGA-CQ-A4CD TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5248 
         548          391          303          608         2562         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-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 
        1971          514          362          311          345          354 
TCGA-CR-6487 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7367 
         234          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-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-7398 TCGA-CR-7399 TCGA-CR-7401 
         898          930          216          156          181         1077 
TCGA-CR-7402 TCGA-CV-5431 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5441 
         911          522         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-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-6952 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 
        1966         1957         1969         1959         3837         1959 
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-7235 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7250 
        1724         1444         1095          954          797         1960 
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-A461 TCGA-CV-A6JD TCGA-CV-A6JE 
        1981          851         1945         1954         1970          750 
TCGA-CV-A6JN TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 
         717          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-DQ-5624 TCGA-DQ-5625 
         106          128          112          104         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-A50J TCGA-F7-A61S TCGA-F7-A61V 
         564          658           15          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-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-8224 
         414          403            2            5           25           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-KU-A66S TCGA-KU-A66T TCGA-MT-A51W 
         360          412          440          224          210           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-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 
         910         1652          721         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-A6IH TCGA-QK-A6II TCGA-QK-A6IJ 
         228          225           64 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 5                  2 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              3295               3837 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             719.5              629.0 
[1] "5.0 - 3295.0 (719.5)" "2.0 - 3837.0 (629.0)"
[1] "hr=" "1.2"
D30V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  17P GAIN MUTATED         2        9        14        21         0
  17P GAIN WILD-TYPE      22       54        57       171         9
D30V3, multiclass
           clus
vv          17P GAIN MUTATED 17P GAIN WILD-TYPE
  STAGE I                  2                 22
  STAGE II                 9                 54
  STAGE III               14                 57
  STAGE IVA               21                171
  STAGE IVB                0                  9
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  17P GAIN MUTATED     2  17  14  13
  17P GAIN WILD-TYPE  38  91  71 118
D30V4, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  T1                2                 38
  T2               17                 91
  T3               14                 71
  T4               13                118
[1] 4 2
[1] 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    16  10  16   0
  17P GAIN WILD-TYPE 120  46 113   7
D30V5, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  N0               16                120
  N1               10                 46
  N2               16                113
  N3                0                  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"
D30V6, binary
                    cls
clus                  0  1
  17P GAIN MUTATED   13  6
  17P GAIN WILD-TYPE 95 42
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     13    6
  17P GAIN WILD-TYPE   95   42
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  M0               13                 95
  MX                6                 42
[1] 2 2
[1] FALSE
D30V7, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    13  40
  17P GAIN WILD-TYPE 108 256
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     13   40
  17P GAIN WILD-TYPE  108  256
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE               13                108
  MALE                 40                256
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  17P GAIN MUTATED                                      52
  17P GAIN WILD-TYPE                                   358
                    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                                                     0
  17P GAIN WILD-TYPE                                                   6
D30V8, multiclass
                                                             clus
vv                                                            17P GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     52
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        0
                                                             clus
vv                                                            17P GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      358
  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"
D30V9, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    11  42
  17P GAIN WILD-TYPE  68 296
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     11   42
  17P GAIN WILD-TYPE   68  296
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  NO                11                 68
  YES               42                296
[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                                1     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17P GAIN MUTATED                           5    45
  17P GAIN WILD-TYPE                        28   316
D30V12, multiclass
                                  clus
vv                                 17P GAIN MUTATED 17P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  9
  BLACK OR AFRICAN AMERICAN                       5                 28
  WHITE                                          45                316
[1] 4 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     5  46
  17P GAIN WILD-TYPE  13 335
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      5   46
  17P GAIN WILD-TYPE   13  335
                        clus
vv                       17P GAIN MUTATED 17P GAIN WILD-TYPE
  HISPANIC OR LATINO                    5                 13
  NOT HISPANIC OR LATINO               46                335
[1] 2 2
[1] FALSE

Clustering(31) Variable = 17Q GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                  0   1
  17Q GAIN MUTATED    41  19
  17Q GAIN WILD-TYPE 216  79
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                60                295 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                19                 79 
$`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 
         613          240          512         1980         1966         1975 
TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-A63U 
         202          424          318          611          119          526 
TCGA-CN-A63W TCGA-CN-A641 TCGA-CQ-7069 TCGA-CQ-A4C9 TCGA-CQ-A4CE TCGA-CR-5247 
         348          367          901          613          393          358 
TCGA-CR-6467 TCGA-CR-6473 TCGA-CR-6478 TCGA-CR-7365 TCGA-CR-7370 TCGA-CR-7383 
        1777         1125         1969         1191          105         1954 
TCGA-CR-7390 TCGA-CR-7399 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5440 
         907          181         1472         1955         1950         1978 
TCGA-CV-5970 TCGA-CV-5977 TCGA-CV-6003 TCGA-CV-6941 TCGA-CV-6945 TCGA-CV-6952 
         406         1840         1665         1959         1969         1966 
TCGA-CV-7095 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7254 
        1970         1939         1945         1967         1960         1976 
TCGA-CV-7261 TCGA-CV-7424 TCGA-D6-8569 TCGA-DQ-7588 TCGA-H7-8502 TCGA-HD-7753 
        1099         1947          128         1965          133            5 
TCGA-HD-7917 TCGA-HD-A6HZ TCGA-IQ-A61L TCGA-IQ-A61O TCGA-MT-A67D TCGA-QK-A6IG 
          37          111          351          360           56          218 

$`17Q 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-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-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BB-4217 
         113          513          351          216          182          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-7870 TCGA-BB-7871 TCGA-BB-7872 
         423          687          638         1153          428          436 
TCGA-BB-8596 TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 
        1955            4          799          721          485          142 
TCGA-CN-4727 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 
         452          392          462          993          642          369 
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-5358 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5367 
         488          173         1081         1977         1980         1966 
TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 
         413          290          630          424          629          433 
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-6024 TCGA-CN-6992 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 
         224          394          432          429           46          443 
TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63Y TCGA-CQ-5323 TCGA-CQ-5324 
         447          225          484          175         1466         1207 
TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 
         654         1660         1422          896         1399          317 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 
         341          129          870         1000         1057          985 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 
        1959         1959          815         1461         1378         1007 
TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CA 
         509         1309          877          968         1960         1963 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 
         545          548          391          303          608         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-6474 TCGA-CR-6477 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 
        1971          514          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-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-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-7401 TCGA-CR-7402 
         898          930          216          156         1077          911 
TCGA-CV-5431 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5441 
         522         3295         1438          584          546         2886 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5971 TCGA-CV-5973 
        2327         1958         2437          519          701         2641 
TCGA-CV-5976 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 
        1478          215         1315          641         1899         1970 
TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6954 
        1948         1969         1952         3835         1948         1957 
TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7097 TCGA-CV-7099 
        1969         1959         3837         1959         1970         1936 
TCGA-CV-7100 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7242 
        1959         1987         1979         1724         1444         1095 
TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7422 
         954          797         1974         1948         1955         1957 
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-A461 TCGA-CV-A6JD 
        1959         1981          851         1945         1954         1970 
TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 
         750          717          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-DQ-5624 TCGA-DQ-5625 
         568          106          112          104         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          564 
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-A6C4 TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-8224 TCGA-HD-8314 
         414          403            2           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-KU-A66S TCGA-KU-A66T TCGA-MT-A51W TCGA-MT-A51X 
         412          440          224          210           14           34 
TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QA 
         392          111          112          254          910         1652 
TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T4 
         721         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 
          64 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 5                  2 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              1980               3837 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             618.5              629.0 
[1] "5.0 - 1980.0 (618.5)" "2.0 - 3837.0 (629.0)"
[1] "hr=" "1.1"
D31V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  17Q GAIN MUTATED         2        9        15        34         0
  17Q GAIN WILD-TYPE      22       54        56       158         9
D31V3, multiclass
           clus
vv          17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  STAGE I                  2                 22
  STAGE II                 9                 54
  STAGE III               15                 56
  STAGE IVA               34                158
  STAGE IVB                0                  9
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  17Q GAIN MUTATED     2  19  18  21
  17Q GAIN WILD-TYPE  38  89  67 110
D31V4, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T1                2                 38
  T2               19                 89
  T3               18                 67
  T4               21                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
  17Q GAIN MUTATED    18  12  26   0
  17Q GAIN WILD-TYPE 118  44 103   7
D31V5, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  N0               18                118
  N1               12                 44
  N2               26                103
  N3                0                  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"
D31V6, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED   18  9
  17Q GAIN WILD-TYPE 90 39
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     18    9
  17Q GAIN WILD-TYPE   90   39
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  M0               18                 90
  MX                9                 39
[1] 2 2
[1] FALSE
D31V7, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    16  53
  17Q GAIN WILD-TYPE 105 243
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     16   53
  17Q GAIN WILD-TYPE  105  243
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE               16                105
  MALE                 53                243
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  17Q GAIN MUTATED                                      68
  17Q GAIN WILD-TYPE                                   342
                    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                                                     0
  17Q GAIN WILD-TYPE                                                   6
D31V8, multiclass
                                                             clus
vv                                                            17Q GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     68
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        0
                                                             clus
vv                                                            17Q GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      342
  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"
D31V9, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    12  57
  17Q GAIN WILD-TYPE  67 281
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     12   57
  17Q GAIN WILD-TYPE   67  281
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  NO                12                 67
  YES               57                281
[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                                1     8
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17Q GAIN MUTATED                           4    60
  17Q GAIN WILD-TYPE                        29   301
D31V12, multiclass
                                  clus
vv                                 17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           2                  8
  BLACK OR AFRICAN AMERICAN                       4                 29
  WHITE                                          60                301
[1] 4 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     6  61
  17Q GAIN WILD-TYPE  12 320
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      6   61
  17Q GAIN WILD-TYPE   12  320
                        clus
vv                       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    6                 12
  NOT HISPANIC OR LATINO               61                320
[1] 2 2
[1] FALSE

Clustering(32) Variable = 18P GAIN MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                  0   1
  18P GAIN MUTATED    55  25
  18P GAIN WILD-TYPE 202  73
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                80                275 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                25                 73 
$`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-BB-4223 TCGA-BB-4224 TCGA-BB-4225 
          63          384          113         2878          278          140 
TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7870 TCGA-C9-A47Z TCGA-CN-4728 TCGA-CN-4730 
         310          536         1153            5          613          462 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-5363 TCGA-CN-5366 TCGA-CN-6012 TCGA-CN-6020 
         395          240         1977         1966          629           98 
TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63W 
         202          224          318          225          526          348 
TCGA-CN-A641 TCGA-CQ-5332 TCGA-CQ-6227 TCGA-CQ-7067 TCGA-CQ-A4C9 TCGA-CR-5247 
         367          317         1959          509          613          358 
TCGA-CR-6467 TCGA-CR-6482 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7370 
        1777          345         1956         1435         1191          105 
TCGA-CR-7372 TCGA-CR-7390 TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 
         759          907          181         1077          911         1472 
TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5973 TCGA-CV-5977 
        1950         3295         1978         2886         2641         1840 
TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6441 TCGA-CV-6935 TCGA-CV-6941 TCGA-CV-6945 
        1315          641         1970         1969         1959         1969 
TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7243 TCGA-CV-7406 TCGA-CV-7434 
        1939         1945         1987          954         1974         1958 
TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A461 TCGA-D6-8568 TCGA-D6-8569 TCGA-DQ-5631 
        1959         1981         1954          106          128          548 
TCGA-DQ-7590 TCGA-DQ-7595 TCGA-H7-8502 TCGA-H7-A6C5 TCGA-HD-A634 TCGA-HD-A6HZ 
         775          324          133          403           10          111 
TCGA-IQ-A61G TCGA-KU-A66T 
         360          210 

$`18P GAIN WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5152 
         462          283         1983          276          248         1288 
TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-7269 
        1762          725          623          190          451          236 
TCGA-BA-A4IF TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BB-4217 
         895          513          351          216          182          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 
         485          142          452          392          993          642 
TCGA-CN-4735 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 
         369         1960         1330          811         1268         1988 
TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5365 
         488          512          173         1980         1081         1980 
TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 
        1966         1975          413          290          630          424 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6021 
         433          594          629           45          432         1970 
TCGA-CN-6023 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 
         424          611          394          119          432          429 
TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63V TCGA-CN-A63Y TCGA-CQ-5323 
          46          443          447          484          175         1466 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 
        1207          654         1660         1422          896         1399 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 
         341          129          870         1000         1057          985 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7068 
        1959          815         1461         1378         1007         1309 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CA TCGA-CQ-A4CB 
         901          877          968         1960         1963          545 
TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 
         548          393          391          303          608         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         1724         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-A6JD TCGA-CV-A6JE 
        1937         1984          851         1945         1970          750 
TCGA-CV-A6JN TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 
         717          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-A4Z9 TCGA-D6-A4ZB TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 
         112          104         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          564          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-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-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX 
         254          910         1652          721         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 
         245          218          228          225           64 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 5                  2 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              3295               3837 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
               635                624 
[1] "5.0 - 3295.0 (635.0)" "2.0 - 3837.0 (624.0)"
[1] "hr=" "1.2"
D32V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  18P GAIN MUTATED         3        9        15        49         2
  18P GAIN WILD-TYPE      21       54        56       143         7
D32V3, multiclass
           clus
vv          18P GAIN MUTATED 18P GAIN WILD-TYPE
  STAGE I                  3                 21
  STAGE II                 9                 54
  STAGE III               15                 56
  STAGE IVA               49                143
  STAGE IVB                2                  7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  18P GAIN MUTATED     5  20  25  29
  18P GAIN WILD-TYPE  35  88  60 102
D32V4, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  T1                5                 35
  T2               20                 88
  T3               25                 60
  T4               29                102
[1] 4 2
[1] 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    23  11  37   2
  18P GAIN WILD-TYPE 113  45  92   5
D32V5, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  N0               23                113
  N1               11                 45
  N2               37                 92
  N3                2                  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"
D32V6, binary
                    cls
clus                  0  1
  18P GAIN MUTATED   16 12
  18P GAIN WILD-TYPE 92 36
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     16   12
  18P GAIN WILD-TYPE   92   36
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  M0               16                 92
  MX               12                 36
[1] 2 2
[1] FALSE
D32V7, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    13  82
  18P GAIN WILD-TYPE 108 214
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     13   82
  18P GAIN WILD-TYPE  108  214
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE               13                108
  MALE                 82                214
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  18P GAIN MUTATED                                      95
  18P GAIN WILD-TYPE                                   315
                    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                                                     0
  18P GAIN WILD-TYPE                                                   6
D32V8, multiclass
                                                             clus
vv                                                            18P GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     95
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        0
                                                             clus
vv                                                            18P GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      315
  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"
D32V9, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    16  79
  18P GAIN WILD-TYPE  63 259
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     16   79
  18P GAIN WILD-TYPE   63  259
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  NO                16                 63
  YES               79                259
[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                                1     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18P GAIN MUTATED                           9    82
  18P GAIN WILD-TYPE                        24   279
D32V12, multiclass
                                  clus
vv                                 18P GAIN MUTATED 18P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  9
  BLACK OR AFRICAN AMERICAN                       9                 24
  WHITE                                          82                279
[1] 4 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  88
  18P GAIN WILD-TYPE  14 293
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      4   88
  18P GAIN WILD-TYPE   14  293
                        clus
vv                       18P GAIN MUTATED 18P GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                 14
  NOT HISPANIC OR LATINO               88                293
[1] 2 2
[1] FALSE

Clustering(33) Variable = 18Q GAIN MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                  0   1
  18Q GAIN MUTATED    22   8
  18Q GAIN WILD-TYPE 235  90
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                30                325 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 8                 90 
$`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-4736 TCGA-CN-6012 TCGA-CN-6020 
         558          310         1153          395          629           98 
TCGA-CN-6024 TCGA-CN-6988 TCGA-CR-6467 TCGA-CR-6482 TCGA-CR-7367 TCGA-CR-7370 
         224          318         1777          345         1440          105 
TCGA-CR-7372 TCGA-CR-7401 TCGA-CR-7404 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-6433 
         759         1077         1472         1950         3295          641 
TCGA-CV-6441 TCGA-CV-7406 TCGA-CV-A461 TCGA-DQ-7590 TCGA-HD-A634 TCGA-QK-A6IG 
        1970         1974         1954          775           10          218 

$`18Q 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-5152 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6868 
        1288         1762          725          623         1636          190 
TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF 
         644          451          384          113          236          895 
TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BB-4217 TCGA-BB-4224 
         513          351          216          182          187          278 
TCGA-BB-4227 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7871 
         133          536          423          687          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-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 
         721          485          142          452          613          392 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4737 TCGA-CN-4738 
         462          993          642          369          240         1960 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 
        1330          811         1268         1988          488          512 
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          413          290          630          424 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6021 
         433          594          629           45          432         1970 
TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 
         202          424          611          394          119          432 
TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63U 
         429           46          443          447          225          526 
TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 TCGA-CQ-5323 TCGA-CQ-5324 
         484          348          175          367         1466         1207 
TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 
         654         1660         1422          896         1399          317 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 
         341          129          870         1000         1057          985 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 
        1959         1959          815         1461         1378         1007 
TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 
         509         1309          901          877          968         1960 
TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG 
         613         1963          545          548          393          391 
TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 
         303          608         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-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6484 TCGA-CR-6487 
         514         1969          362          311          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-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-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-7402 
         898          930          216          156          181          911 
TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 
        1955          522         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-6003 TCGA-CV-6436 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6941 
        1665         1899         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-7097 TCGA-CV-7099 
        1959         3837         1959         1970         1970         1936 
TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 
        1959         1939         1945         1987         1979         1724 
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-7410 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 
        1976         1099         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-A6JD TCGA-CV-A6JE 
        1959         1981          851         1945         1970          750 
TCGA-CV-A6JN TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 
         717          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-DQ-5624 TCGA-DQ-5625 
         106          128          112          104         1778         1081 
TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7591 
         516         1030          548         1965          575          622 
TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 
         299          369          368          324          340          564 
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-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-A6HZ TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 
          49          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-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A 
         360          224          210           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         1652 
TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T4 
         721         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 
          64 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                10                  2 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              3295               3837 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             681.5              623.0 
[1] "10.0 - 3295.0 (681.5)" "2.0 - 3837.0 (623.0)" 
[1] "hr=" "1.2"
D33V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  18Q GAIN MUTATED         2        2         7        17         0
  18Q GAIN WILD-TYPE      22       61        64       175         9
D33V3, multiclass
           clus
vv          18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  STAGE I                  2                 22
  STAGE II                 2                 61
  STAGE III                7                 64
  STAGE IVA               17                175
  STAGE IVB                0                  9
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  18Q GAIN MUTATED     4   7   7  11
  18Q GAIN WILD-TYPE  36 101  78 120
D33V4, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  T1                4                 36
  T2                7                101
  T3                7                 78
  T4               11                120
[1] 4 2
[1] 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     9   5  12   0
  18Q GAIN WILD-TYPE 127  51 117   7
D33V5, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  N0                9                127
  N1                5                 51
  N2               12                117
  N3                0                  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"
D33V6, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     6   2
  18Q GAIN WILD-TYPE 102  46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      6    2
  18Q GAIN WILD-TYPE  102   46
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  M0                6                102
  MX                2                 46
[1] 2 2
[1] FALSE
D33V7, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     2  35
  18Q GAIN WILD-TYPE 119 261
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      2   35
  18Q GAIN WILD-TYPE  119  261
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE                2                119
  MALE                 35                261
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  18Q GAIN MUTATED                                      37
  18Q GAIN WILD-TYPE                                   373
                    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                                                     0
  18Q GAIN WILD-TYPE                                                   6
D33V8, multiclass
                                                             clus
vv                                                            18Q GAIN 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                        0
                                                             clus
vv                                                            18Q GAIN 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                          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"
D33V9, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     7  30
  18Q GAIN WILD-TYPE  72 308
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      7   30
  18Q GAIN WILD-TYPE   72  308
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  NO                 7                 72
  YES               30                308
[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                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18Q GAIN MUTATED                           4    33
  18Q GAIN WILD-TYPE                        29   328
D33V12, multiclass
                                  clus
vv                                 18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 10
  BLACK OR AFRICAN AMERICAN                       4                 29
  WHITE                                          33                328
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V13, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     2  34
  18Q GAIN WILD-TYPE  16 347
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      2   34
  18Q GAIN WILD-TYPE   16  347
                        clus
vv                       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                 16
  NOT HISPANIC OR LATINO               34                347
[1] 2 2
[1] FALSE

Clustering(34) Variable = 19P GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                  0   1
  19P GAIN MUTATED    30   5
  19P GAIN WILD-TYPE 227  93
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                35                320 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 5                 93 
$`19P GAIN MUTATED`
TCGA-BA-5559 TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-7861 TCGA-BB-7871 TCGA-BB-8601 
        1747         2878          140          310          428          624 
TCGA-CN-6021 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6989 TCGA-CN-A63T TCGA-CN-A63V 
        1970          424          224          611          225          484 
TCGA-CN-A641 TCGA-CQ-5323 TCGA-CR-6467 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-7370 
         367         1466         1777          234          379          105 
TCGA-CR-7389 TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5977 
         392         1472          522         1978         2327         1840 
TCGA-CV-7101 TCGA-CV-7235 TCGA-CV-7245 TCGA-CV-7261 TCGA-CX-7219 TCGA-F7-8298 
        1939         1724          797         1099          828          490 
TCGA-F7-A50J TCGA-F7-A623 TCGA-HD-A6HZ TCGA-MT-A67G TCGA-P3-A6T4 
         585            6          111          112         1968 

$`19P 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-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-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB 
         113          236          895          513          351          216 
TCGA-BA-A6DE TCGA-BB-4217 TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7862 
         182          187          278          133          558          536 
TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7872 TCGA-BB-8596 
         423          687          638         1153          436         1955 
TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 
           5            4          799          721          485          142 
TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
         452          613          392          462          993          642 
TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 
         369          395          240         1960         1330          811 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 
        1268         1988          488          512          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-6013 
         413          290          630          424          629          433 
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-6988 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 
         318          394          119          432          429           46 
TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A63Y TCGA-CQ-5324 
         443          447          526          348          175         1207 
TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 
         654         1660         1422          896         1399          317 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 
         341          129          870         1000         1057          985 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 
        1959         1959          815         1461         1378         1007 
TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 
         509         1309          901          877          968         1960 
TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG 
         613         1963          545          548          393          391 
TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 
         303          608         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-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-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-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-CV-5430 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 
         911         1955         1950         3295         1438          584 
TCGA-CV-5439 TCGA-CV-5441 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 
         546         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-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-7102 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7238 
        1936         1959         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-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-A461 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN 
         851         1945         1954         1970          750          717 
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-D6-6825 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-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 
         112          104         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-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 
         369          368          324          340          564          658 
TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 
          15           92            3          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-A6I0 TCGA-HL-7533 
          25           11           49           10           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-MT-A51W 
         440          351          360          224          210           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-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 
        1652          721         1120         1954          578         1917 
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-A6IJ 
         225           64 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 6                  2 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              2878               3837 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
               585                634 
[1] "6.0 - 2878.0 (585.0)" "2.0 - 3837.0 (634.0)"
[1] "hr=" "2.2"
D34V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  19P GAIN MUTATED         3        3         6        21         0
  19P GAIN WILD-TYPE      21       60        65       171         9
D34V3, multiclass
           clus
vv          19P GAIN MUTATED 19P GAIN WILD-TYPE
  STAGE I                  3                 21
  STAGE II                 3                 60
  STAGE III                6                 65
  STAGE IVA               21                171
  STAGE IVB                0                  9
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  19P GAIN MUTATED     6   6   9  12
  19P GAIN WILD-TYPE  34 102  76 119
D34V4, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  T1                6                 34
  T2                6                102
  T3                9                 76
  T4               12                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
  19P GAIN MUTATED    10   5  17   0
  19P GAIN WILD-TYPE 126  51 112   7
D34V5, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  N0               10                126
  N1                5                 51
  N2               17                112
  N3                0                  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"
D34V6, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     8   8
  19P GAIN WILD-TYPE 100  40
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      8    8
  19P GAIN WILD-TYPE  100   40
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  M0                8                100
  MX                8                 40
[1] 2 2
[1] FALSE
D34V7, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     9  31
  19P GAIN WILD-TYPE 112 265
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      9   31
  19P GAIN WILD-TYPE  112  265
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE                9                112
  MALE                 31                265
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  19P GAIN MUTATED                                      40
  19P GAIN WILD-TYPE                                   370
                    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                                                     0
  19P GAIN WILD-TYPE                                                   6
D34V8, multiclass
                                                             clus
vv                                                            19P GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     40
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        0
                                                             clus
vv                                                            19P GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      370
  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"
D34V9, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     7  33
  19P GAIN WILD-TYPE  72 305
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      7   33
  19P GAIN WILD-TYPE   72  305
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  NO                 7                 72
  YES               33                305
[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                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19P GAIN MUTATED                           3    37
  19P GAIN WILD-TYPE                        30   324
D34V12, multiclass
                                  clus
vv                                 19P GAIN MUTATED 19P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 10
  BLACK OR AFRICAN AMERICAN                       3                 30
  WHITE                                          37                324
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V13, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     2  38
  19P GAIN WILD-TYPE  16 343
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      2   38
  19P GAIN WILD-TYPE   16  343
                        clus
vv                       19P GAIN MUTATED 19P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                 16
  NOT HISPANIC OR LATINO               38                343
[1] 2 2
[1] FALSE

Clustering(35) Variable = 19Q GAIN MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                  0   1
  19Q GAIN MUTATED    40   8
  19Q GAIN WILD-TYPE 217  90
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                48                307 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 8                 90 
$`19Q GAIN MUTATED`
TCGA-BA-5153 TCGA-BA-5559 TCGA-BA-7269 TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-7861 
        1762         1747          236         2878          140          310 
TCGA-CN-6012 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-A63T 
         629           98         1970          424          224          225 
TCGA-CN-A63V TCGA-CN-A641 TCGA-CQ-5324 TCGA-CQ-5330 TCGA-CQ-6223 TCGA-CR-6467 
         484          367         1207          896         1057         1777 
TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-7367 TCGA-CR-7370 TCGA-CR-7389 TCGA-CR-7404 
         234          379         1440          105          392         1472 
TCGA-CV-5431 TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5977 TCGA-CV-7101 TCGA-CV-7235 
         522         1978         2327         1840         1939         1724 
TCGA-CV-7243 TCGA-CV-7406 TCGA-CV-7435 TCGA-CX-7219 TCGA-D6-6825 TCGA-DQ-7592 
         954         1974         1959          828          491          299 
TCGA-F7-8298 TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A623 TCGA-HD-A6HZ TCGA-HL-7533 
         490           92          585            6          111         1057 
TCGA-IQ-7631 TCGA-IQ-A61G TCGA-KU-A66T TCGA-MT-A67G TCGA-P3-A5Q5 TCGA-P3-A6T4 
         122          360          210          112          910         1968 

$`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-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BB-4217 
         895          513          351          216          182          187 
TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7862 TCGA-BB-7863 TCGA-BB-7864 
         278          133          558          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          485          142 
TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
         452          613          392          462          993          642 
TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 
         369          395          240         1960         1330          811 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 
        1268         1988          488          512          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-6013 TCGA-CN-6016 
         413          290          630          424          433          594 
TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6022 TCGA-CN-6988 TCGA-CN-6989 
         629           45          432          202          318          611 
TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 
         394          119          432          429           46          443 
TCGA-CN-A49B TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A63Y TCGA-CQ-5323 TCGA-CQ-5325 
         447          526          348          175         1466          654 
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-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 
         870         1000          985         1959         1959          815 
TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 
        1461         1378         1007          509         1309          901 
TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB 
         877          968         1960          613         1963          545 
TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 
         548          393          391          303          608         2562 
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-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-6491 TCGA-CR-6492 TCGA-CR-6493 
         311          345          354          350          479         1956 
TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7372 
        1435         1191         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-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-7402 TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5434 
         181         1077          911         1955         1950         3295 
TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5441 TCGA-CV-5443 TCGA-CV-5444 
        1438          584          546         2886         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-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-7102 TCGA-CV-7180 
        1970         1970         1936         1959         1945         1987 
TCGA-CV-7183 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 
        1979         1444         1095          797         1967         1960 
TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 
        1976         1099         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-7440 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A461 TCGA-CV-A6JD TCGA-CV-A6JE 
        1981          851         1945         1954         1970          750 
TCGA-CV-A6JN TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-D6-6516 TCGA-D6-6517 
         717          317          321          237          773          292 
TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 
         701           77          154          568          106          128 
TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 
         112          104         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          564          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-MT-A51W 
         412          440          351          360          224           14 
TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MZ-A6I9 TCGA-P3-A5QA 
          34          392           56          111          254         1652 
TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T8 
         721         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 
          64 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 6                  2 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              2878               3837 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             553.5              630.0 
[1] "6.0 - 2878.0 (553.5)" "2.0 - 3837.0 (630.0)"
[1] "hr=" "1.7"
D35V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  19Q GAIN MUTATED         3        9        10        25         1
  19Q GAIN WILD-TYPE      21       54        61       167         8
D35V3, multiclass
           clus
vv          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  STAGE I                  3                 21
  STAGE II                 9                 54
  STAGE III               10                 61
  STAGE IVA               25                167
  STAGE IVB                1                  8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  19Q GAIN MUTATED     6  17  12  14
  19Q GAIN WILD-TYPE  34  91  73 117
D35V4, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  T1                6                 34
  T2               17                 91
  T3               12                 73
  T4               14                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
  19Q GAIN MUTATED    17   8  19   1
  19Q GAIN WILD-TYPE 119  48 110   6
D35V5, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  N0               17                119
  N1                8                 48
  N2               19                110
  N3                1                  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"
D35V6, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED   10  9
  19Q GAIN WILD-TYPE 98 39
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     10    9
  19Q GAIN WILD-TYPE   98   39
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  M0               10                 98
  MX                9                 39
[1] 2 2
[1] FALSE
D35V7, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    13  45
  19Q GAIN WILD-TYPE 108 251
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     13   45
  19Q GAIN WILD-TYPE  108  251
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE               13                108
  MALE                 45                251
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  19Q GAIN MUTATED                                      57
  19Q GAIN WILD-TYPE                                   353
                    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                                                     1
  19Q GAIN WILD-TYPE                                                   5
D35V8, multiclass
                                                             clus
vv                                                            19Q GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     57
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        1
                                                             clus
vv                                                            19Q GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      353
  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"
D35V9, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    12  46
  19Q GAIN WILD-TYPE  67 292
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     12   46
  19Q GAIN WILD-TYPE   67  292
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  NO                12                 67
  YES               46                292
[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                                0    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19Q GAIN MUTATED                           5    51
  19Q GAIN WILD-TYPE                        28   310
D35V12, multiclass
                                  clus
vv                                 19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           0                 10
  BLACK OR AFRICAN AMERICAN                       5                 28
  WHITE                                          51                310
[1] 4 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     2  54
  19Q GAIN WILD-TYPE  16 327
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      2   54
  19Q GAIN WILD-TYPE   16  327
                        clus
vv                       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                 16
  NOT HISPANIC OR LATINO               54                327
[1] 2 2
[1] FALSE

Clustering(36) Variable = 20P GAIN MUTATION ANALYSIS
D36V1, survival
                    sevent
clus2                  0   1
  20P GAIN MUTATED    98  28
  20P GAIN WILD-TYPE 159  70
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               126                229 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                28                 70 
$`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-BB-4224 TCGA-BB-4225 TCGA-BB-7861 
         384          236          216          278          140          310 
TCGA-BB-7862 TCGA-BB-7872 TCGA-C9-A47Z TCGA-CN-4728 TCGA-CN-4730 TCGA-CN-4731 
         536          436            5          613          462          993 
TCGA-CN-4733 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 
         642          395          240         1960         1330          811 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 
        1268         1988          512         1980         1081         1977 
TCGA-CN-5366 TCGA-CN-5374 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6020 TCGA-CN-6022 
        1966          290          629          433           98          202 
TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-A63T TCGA-CN-A63U 
         424          224          318          611          225          526 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6229 TCGA-CQ-7064 
        1422          896         1057          985          815         1378 
TCGA-CQ-7067 TCGA-CQ-7069 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CE 
         509          901          968         1960          613          393 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-6467 TCGA-CR-6484 TCGA-CR-6488 
         608         2562          358         1777          354          379 
TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7370 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7377 
        1191         1440          105          759          889         1968 
TCGA-CR-7389 TCGA-CR-7392 TCGA-CR-7399 TCGA-CR-7401 TCGA-CV-5430 TCGA-CV-5434 
         392          946          181         1077         1955         3295 
TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5442 TCGA-CV-5444 TCGA-CV-5970 TCGA-CV-5971 
        1438          584         2327         2437          406          701 
TCGA-CV-5973 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-6003 TCGA-CV-6945 TCGA-CV-6954 
        2641         1840          215         1665         1969         1957 
TCGA-CV-7090 TCGA-CV-7095 TCGA-CV-7180 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 
        3837         1970         1987         1095          954          797 
TCGA-CV-7248 TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CX-7082 TCGA-CX-7086 TCGA-D6-6516 
        1967          750          717          317          237          773 
TCGA-D6-6517 TCGA-D6-6825 TCGA-D6-8569 TCGA-D6-A4ZB TCGA-DQ-5624 TCGA-DQ-7588 
         292          491          128          104         1778         1965 
TCGA-DQ-7591 TCGA-DQ-7592 TCGA-F7-A50J TCGA-F7-A61S TCGA-H7-8501 TCGA-HD-7753 
         622          299          585            3           58            5 
TCGA-HD-8314 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-IQ-7630 TCGA-IQ-7632 TCGA-IQ-A61E 
          44           10          111          485          441          588 
TCGA-IQ-A61G TCGA-IQ-A61L TCGA-KU-A66T TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67G 
         360          351          210          392           56          112 
TCGA-P3-A5QA TCGA-P3-A6T0 TCGA-P3-A6T4 TCGA-QK-A652 TCGA-QK-A6IG TCGA-QK-A6IJ 
        1652          578         1968          357          218           64 

$`20P GAIN WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-5152 TCGA-BA-5153 
         462          283          415         1983         1288         1762 
TCGA-BA-5555 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 
         520          623         1636          644          451           63 
TCGA-BA-6873 TCGA-BA-A4IF TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DE TCGA-BB-4217 
         113          895          513          351          182          187 
TCGA-BB-4223 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 
        2878          133          558          423          687          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-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4729 TCGA-CN-4735 
         721          485          142          452          392          369 
TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5365 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 
         488          173         1980         1966         1975          413 
TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 
         630          424          594          629           45          432 
TCGA-CN-6021 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 
        1970          394          119          432          429           46 
TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 
         443          447          484          348          175          367 
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          870         1000         1959         1959 
TCGA-CQ-7063 TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-A4CA TCGA-CQ-A4CB 
        1461         1007         1309          877         1963          545 
TCGA-CQ-A4CD TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 
         548          391          303         1663         1152          799 
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-6491 
        1969          362          311          345          234          350 
TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7371 
         479         1956         1435         1245         1960         1979 
TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 
          30          972         1036          796         1954          997 
TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7393 TCGA-CR-7394 
        1430         1951          907          913          908          898 
TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5431 
         930          216          156          911         1472          522 
TCGA-CV-5432 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5443 TCGA-CV-5966 
        1950          546         1978         2886         1958          519 
TCGA-CV-5976 TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 
        1478         1315          641         1899         1970         1948 
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-6960 TCGA-CV-6961 TCGA-CV-7091 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 
        1969         1959         1959         1970         1936         1959 
TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7250 
        1939         1945         1979         1724         1444         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-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-A461 
        1958         1959         1981          851         1945         1954 
TCGA-CV-A6JD TCGA-CX-7085 TCGA-CX-7219 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6826 
        1970          321          828          701           77          154 
TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 
         568          106          112         1081          516         1030 
TCGA-DQ-5631 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 
         548          575          775          369          368          324 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I 
         340          564          490          658           15           92 
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-HD-7229 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 
         414          403            2           25           37           55 
TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A6I0 TCGA-HL-7533 
          24           25           11           49           33         1057 
TCGA-IQ-7631 TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61O TCGA-KU-A66S TCGA-MT-A51W 
         122          412          440          360          224           14 
TCGA-MT-A51X TCGA-MT-A67F TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A6SW 
          34          111          254          910          721         1120 
TCGA-P3-A6SX TCGA-P3-A6T2 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A6IF TCGA-QK-A6IH 
        1954         1917          400          553          245          228 
TCGA-QK-A6II 
         225 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 3                  2 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              3837               3835 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               598                654 
[1] "3.0 - 3837.0 (598.0)" "2.0 - 3835.0 (654.0)"
[1] "hr=" "1.5"
D36V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  20P GAIN MUTATED        11       21        31        71         4
  20P GAIN WILD-TYPE      13       42        40       121         5
D36V3, multiclass
           clus
vv          20P GAIN MUTATED 20P GAIN WILD-TYPE
  STAGE I                 11                 13
  STAGE II                21                 42
  STAGE III               31                 40
  STAGE IVA               71                121
  STAGE IVB                4                  5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  20P GAIN MUTATED   18 39 31 51
  20P GAIN WILD-TYPE 22 69 54 80
D36V4, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  T1               18                 22
  T2               39                 69
  T3               31                 54
  T4               51                 80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  20P GAIN MUTATED   47 29 47  3
  20P GAIN WILD-TYPE 89 27 82  4
D36V5, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  N0               47                 89
  N1               29                 27
  N2               47                 82
  N3                3                  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"
D36V6, binary
                    cls
clus                  0  1
  20P GAIN MUTATED   45 17
  20P GAIN WILD-TYPE 63 31
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     45   17
  20P GAIN WILD-TYPE   63   31
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  M0               45                 63
  MX               17                 31
[1] 2 2
[1] FALSE
D36V7, binary
                    cls
clus                   0   1
  20P GAIN MUTATED    46 108
  20P GAIN WILD-TYPE  75 188
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     46  108
  20P GAIN WILD-TYPE   75  188
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE               46                 75
  MALE                108                188
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  20P GAIN MUTATED                                     152
  20P GAIN WILD-TYPE                                   258
                    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                                                     2
  20P GAIN WILD-TYPE                                                   4
D36V8, multiclass
                                                             clus
vv                                                            20P GAIN 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                        2
                                                             clus
vv                                                            20P GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      258
  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"
D36V9, binary
                    cls
clus                   0   1
  20P GAIN MUTATED    34 120
  20P GAIN WILD-TYPE  45 218
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     34  120
  20P GAIN WILD-TYPE   45  218
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  NO                34                 45
  YES              120                218
[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                                0     6
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20P GAIN MUTATED                          14   128
  20P GAIN WILD-TYPE                        19   233
D36V12, multiclass
                                  clus
vv                                 20P GAIN MUTATED 20P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           4                  6
  BLACK OR AFRICAN AMERICAN                      14                 19
  WHITE                                         128                233
[1] 4 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    10 135
  20P GAIN WILD-TYPE   8 246
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     10  135
  20P GAIN WILD-TYPE    8  246
                        clus
vv                       20P GAIN MUTATED 20P GAIN WILD-TYPE
  HISPANIC OR LATINO                   10                  8
  NOT HISPANIC OR LATINO              135                246
[1] 2 2
[1] FALSE

Clustering(37) Variable = 20Q GAIN MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                  0   1
  20Q GAIN MUTATED    98  34
  20Q GAIN WILD-TYPE 159  64
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               132                223 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                34                 64 
$`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-BB-4225 TCGA-BB-7861 
         384          236          895          216          140          310 
TCGA-BB-7862 TCGA-BB-7864 TCGA-BB-7872 TCGA-C9-A47Z TCGA-CN-4725 TCGA-CN-4728 
         536          687          436            5          485          613 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 
         462          993          642          395          240         1960 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5359 
        1330          811         1268         1988          512         1980 
TCGA-CN-5363 TCGA-CN-5366 TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 
        1977         1966          290          424          629          433 
TCGA-CN-6018 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6994 
          45          202          424          224          318          119 
TCGA-CN-A63T TCGA-CN-A63U TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-6223 TCGA-CQ-6224 
         225          526         1422          896         1057          985 
TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7067 TCGA-CQ-7069 TCGA-CQ-A4C6 TCGA-CQ-A4C7 
         815         1378          509          901          968         1960 
TCGA-CQ-A4C9 TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CR-5247 TCGA-CR-6467 TCGA-CR-6474 
         613          393          391          358         1777         1971 
TCGA-CR-6477 TCGA-CR-6484 TCGA-CR-6488 TCGA-CR-6493 TCGA-CR-7365 TCGA-CR-7367 
         514          354          379         1956         1191         1440 
TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7389 TCGA-CR-7392 
         759          889         1968         1036          392          946 
TCGA-CR-7401 TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 
        1077         1955         1950         3295         1438          584 
TCGA-CV-5442 TCGA-CV-5444 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-6003 TCGA-CV-6936 
        2327         2437         1840          215         1665         1952 
TCGA-CV-6945 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-7090 TCGA-CV-7095 TCGA-CV-7097 
        1969         1957         1969         3837         1970         1970 
TCGA-CV-7180 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-A6JE 
        1987         1095          954          797         1967          750 
TCGA-CV-A6JN TCGA-CX-7086 TCGA-D6-6516 TCGA-D6-6823 TCGA-D6-6825 TCGA-D6-8569 
         717          237          773          701          491          128 
TCGA-DQ-5624 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7592 TCGA-F7-A50J 
        1778          548         1965          575          299          585 
TCGA-F7-A61S TCGA-F7-A623 TCGA-H7-8501 TCGA-HD-7753 TCGA-HD-8314 TCGA-HD-A634 
           3            6           58            5           44           10 
TCGA-HD-A6HZ TCGA-IQ-7630 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61L 
         111          485          441          588          360          351 
TCGA-KU-A66T TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67G 
         210           14           34          392           56          112 
TCGA-P3-A5QA TCGA-P3-A6T0 TCGA-P3-A6T4 TCGA-QK-A652 TCGA-QK-A6IG TCGA-QK-A6IJ 
        1652          578         1968          357          218           64 

$`20Q GAIN WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 
         462          415         1983         1288         1762          520 
TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 
         623         1636         1747          644          451           63 
TCGA-BA-6873 TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DE TCGA-BB-4217 TCGA-BB-4223 
         113          513          351          182          187         2878 
TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7863 TCGA-BB-7866 TCGA-BB-7870 
         278          133          558          423          638         1153 
TCGA-BB-7871 TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 
         428         1955          624            4          799          721 
TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4729 TCGA-CN-4735 TCGA-CN-5355 TCGA-CN-5358 
         142          452          392          369          488          173 
TCGA-CN-5360 TCGA-CN-5365 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6010 
        1081         1980         1966         1975          413          630 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6989 
         594          629          432           98         1970          611 
TCGA-CN-6992 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49B 
         394          432          429           46          443          447 
TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 TCGA-CQ-5323 TCGA-CQ-5324 
         484          348          175          367         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-6227 TCGA-CQ-6228 TCGA-CQ-7063 TCGA-CQ-7065 
         870         1000         1959         1959         1461         1007 
TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CH 
        1309          877         1963          545          548          303 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6470 
         608         2562         1663         1152          799         1521 
TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 
        1966         1050         1125         1969          362          311 
TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-7364 TCGA-CR-7368 
         345          234          350          479         1435         1245 
TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7382 
        1960          105         1979           30          972          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-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-CR-7404 TCGA-CV-5431 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 
         911         1472          522          546         1978         2886 
TCGA-CV-5443 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 
        1958          519          406          701         2641         1478 
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-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6952 TCGA-CV-6961 TCGA-CV-7091 
        1959         3835         1948         1966         1959         1959 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7183 TCGA-CV-7235 
        1936         1959         1939         1945         1979         1724 
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-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45O 
        1937         1984         1958         1959         1981          851 
TCGA-CV-A45Q TCGA-CV-A461 TCGA-CV-A6JD TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7219 
        1945         1954         1970          317          321          828 
TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-A4Z9 
         292           77          154          568          106          112 
TCGA-D6-A4ZB TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-7590 TCGA-DQ-7591 
         104         1081          516         1030          775          622 
TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 
         369          368          324          340          564          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-H7-7774 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-7754 
         407          133          414          403            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-7631 TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61O 
          33         1057          122          412          440          360 
TCGA-KU-A66S TCGA-MT-A67F TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A6SW 
         224          111          254          910          721         1120 
TCGA-P3-A6SX TCGA-P3-A6T2 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A6IF TCGA-QK-A6IH 
        1954         1917          400          553          245          228 
TCGA-QK-A6II 
         225 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 3                  2 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              3837               3835 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             586.5              641.0 
[1] "3.0 - 3837.0 (586.5)" "2.0 - 3835.0 (641.0)"
[1] "hr=" "1.1"
D37V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  20Q GAIN MUTATED        12       24        30        75         5
  20Q GAIN WILD-TYPE      12       39        41       117         4
D37V3, multiclass
           clus
vv          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  STAGE I                 12                 12
  STAGE II                24                 39
  STAGE III               30                 41
  STAGE IVA               75                117
  STAGE IVB                5                  4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  20Q GAIN MUTATED   21 40 31 55
  20Q GAIN WILD-TYPE 19 68 54 76
D37V4, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T1               21                 19
  T2               40                 68
  T3               31                 54
  T4               55                 76
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  20Q GAIN MUTATED   54 26 49  4
  20Q GAIN WILD-TYPE 82 30 80  3
D37V5, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  N0               54                 82
  N1               26                 30
  N2               49                 80
  N3                4                  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"
D37V6, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED   48 18
  20Q GAIN WILD-TYPE 60 30
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     48   18
  20Q GAIN WILD-TYPE   60   30
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  M0               48                 60
  MX               18                 30
[1] 2 2
[1] FALSE
D37V7, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED    48 114
  20Q GAIN WILD-TYPE  73 182
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     48  114
  20Q GAIN WILD-TYPE   73  182
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE               48                 73
  MALE                114                182
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  20Q GAIN MUTATED                                     161
  20Q GAIN WILD-TYPE                                   249
                    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                                                     1
  20Q GAIN WILD-TYPE                                                   5
D37V8, multiclass
                                                             clus
vv                                                            20Q GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    161
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        1
                                                             clus
vv                                                            20Q GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      249
  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"
D37V9, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED    35 127
  20Q GAIN WILD-TYPE  44 211
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     35  127
  20Q GAIN WILD-TYPE   44  211
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  NO                35                 44
  YES              127                211
[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                                0     6
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20Q GAIN MUTATED                          17   133
  20Q GAIN WILD-TYPE                        16   228
D37V12, multiclass
                                  clus
vv                                 20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           4                  6
  BLACK OR AFRICAN AMERICAN                      17                 16
  WHITE                                         133                228
[1] 4 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     9 144
  20Q GAIN WILD-TYPE   9 237
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      9  144
  20Q GAIN WILD-TYPE    9  237
                        clus
vv                       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    9                  9
  NOT HISPANIC OR LATINO              144                237
[1] 2 2
[1] FALSE

Clustering(38) Variable = 21Q GAIN MUTATION ANALYSIS
D38V1, survival
                    sevent
clus2                  0   1
  21Q GAIN MUTATED    16   7
  21Q GAIN WILD-TYPE 241  91
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                23                332 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 7                 91 
$`21Q GAIN MUTATED`
TCGA-BA-6873 TCGA-BB-4225 TCGA-CN-4727 TCGA-CN-4729 TCGA-CN-4740 TCGA-CN-5356 
         113          140          452          392          811          512 
TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-A63U TCGA-CR-6467 TCGA-CR-6478 TCGA-CR-7402 
         224          394          526         1777         1969          911 
TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5441 TCGA-CV-6945 TCGA-CV-7433 TCGA-CV-A461 
        1955         1950         2886         1969         1984         1954 
TCGA-DQ-7591 TCGA-HD-8224 TCGA-HD-8314 TCGA-IQ-A61O TCGA-P3-A6SW 
         622           55           44          360         1120 

$`21Q 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-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-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB 
         384          236          895          513          351          216 
TCGA-BA-A6DE TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-4228 
         182          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-4730 
         799          721          485          142          613          462 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 
         993          642          369          395          240         1960 
TCGA-CN-4739 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5359 
        1330         1268         1988          488          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-6013 
         413          290          630          424          629          433 
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-6023 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6996 
         202          424          318          611          119          432 
TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63V 
         429           46          443          447          225          484 
TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
         348          175          367         1466         1207          654 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 
        1660         1422          896         1399          317          341 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 
         129          870         1000         1057          985         1959 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 
        1959          815         1461         1378         1007          509 
TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
        1309          901          877          968         1960          613 
TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH 
        1963          545          548          393          391          303 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 
         608         2562          358         1663         1152          799 
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-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-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-7398 
         946          908          898          930          216          156 
TCGA-CR-7399 TCGA-CR-7401 TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5434 TCGA-CV-5435 
         181         1077         1472          522         3295         1438 
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-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-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-7242 TCGA-CV-7243 
        1987         1979         1724         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-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-7434 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45O 
        1972         1937         1958         1959         1981          851 
TCGA-CV-A45Q TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CX-7082 TCGA-CX-7085 
        1945         1970          750          717          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-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 
         491          154          568          106          128          112 
TCGA-D6-A4ZB TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 
         104         1778         1081          516         1030          548 
TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 
        1965          575          775          299          369          368 
TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G 
         324          340          564          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-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8634 TCGA-HD-8635 
           2            5           25           37           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-KU-A66S TCGA-KU-A66T TCGA-MT-A51W TCGA-MT-A51X 
         440          351          224          210           14           34 
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-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T4 
        1652          721         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-A6IJ 
         225           64 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                44                  2 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              2886               3837 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
               622                629 
[1] "44.0 - 2886.0 (622.0)" "2.0 - 3837.0 (629.0)" 
[1] "hr=" "1.2"
D38V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  21Q GAIN MUTATED         0        0         6        15         1
  21Q GAIN WILD-TYPE      24       63        65       177         8
D38V3, multiclass
           clus
vv          21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  STAGE I                  0                 24
  STAGE II                 0                 63
  STAGE III                6                 65
  STAGE IVA               15                177
  STAGE IVB                1                  8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  21Q GAIN MUTATED     1   4   6  11
  21Q GAIN WILD-TYPE  39 104  79 120
D38V4, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  T1                1                 39
  T2                4                104
  T3                6                 79
  T4               11                120
[1] 4 2
[1] 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     5   4  12   1
  21Q GAIN WILD-TYPE 131  52 117   6
D38V5, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  N0                5                131
  N1                4                 52
  N2               12                117
  N3                1                  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"
D38V6, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     4   3
  21Q GAIN WILD-TYPE 104  45
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      4    3
  21Q GAIN WILD-TYPE  104   45
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  M0                4                104
  MX                3                 45
[1] 2 2
[1] FALSE
D38V7, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     3  24
  21Q GAIN WILD-TYPE 118 272
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      3   24
  21Q GAIN WILD-TYPE  118  272
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE                3                118
  MALE                 24                272
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  21Q GAIN MUTATED                                      24
  21Q GAIN WILD-TYPE                                   386
                    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                                                   4
D38V8, multiclass
                                                             clus
vv                                                            21Q GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     24
  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                                      386
  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"
D38V9, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     7  20
  21Q GAIN WILD-TYPE  72 318
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      7   20
  21Q GAIN WILD-TYPE   72  318
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  NO                 7                 72
  YES               20                318
[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                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  21Q GAIN MUTATED                           0    26
  21Q GAIN WILD-TYPE                        33   335
D38V12, multiclass
                                  clus
vv                                 21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 10
  BLACK OR AFRICAN AMERICAN                       0                 33
  WHITE                                          26                335
[1] 4 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     3  23
  21Q GAIN WILD-TYPE  15 358
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      3   23
  21Q GAIN WILD-TYPE   15  358
                        clus
vv                       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                 15
  NOT HISPANIC OR LATINO               23                358
[1] 2 2
[1] FALSE

Clustering(39) Variable = 22Q GAIN MUTATION ANALYSIS
D39V1, survival
                    sevent
clus2                  0   1
  22Q GAIN MUTATED    47  27
  22Q GAIN WILD-TYPE 210  71
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                74                281 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                27                 71 
$`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-BB-7870 TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A480 TCGA-CN-4728 TCGA-CN-4737 
        1153         1955          624            4          613          240 
TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5367 TCGA-CN-6010 TCGA-CN-6012 TCGA-CN-6016 
        1988          512         1966          630          629          594 
TCGA-CN-6024 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-A498 TCGA-CQ-5332 TCGA-CQ-6221 
         224          611          119          443          317         1000 
TCGA-CQ-6224 TCGA-CQ-6229 TCGA-CQ-7067 TCGA-CQ-7069 TCGA-CR-6471 TCGA-CR-6474 
         985          815          509          901         1966         1971 
TCGA-CR-6482 TCGA-CR-7365 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7383 TCGA-CR-7389 
         345         1191          105         1979         1954          392 
TCGA-CR-7390 TCGA-CR-7397 TCGA-CR-7401 TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5434 
         907          216         1077         1955         1950         3295 
TCGA-CV-5970 TCGA-CV-5978 TCGA-CV-6941 TCGA-CV-7090 TCGA-CV-7101 TCGA-CV-7102 
         406          215         1959         3837         1939         1945 
TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7422 
         797         1967         1960         1976         1099         1957 
TCGA-CV-7424 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7440 TCGA-CV-A6JE TCGA-CX-7219 
        1947         1984         1958         1981          750          828 
TCGA-D6-A4ZB TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-7589 TCGA-HD-7753 TCGA-HD-7917 
         104         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          210           34 
TCGA-P3-A6SX TCGA-P3-A6T4 
        1954         1968 

$`22Q GAIN WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 
         283          415         1983          248          722         1288 
TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 
        1762          725         1636         1747          190          644 
TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-A4IF TCGA-BA-A6D8 
         451           63          384          113          895          513 
TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 
         216          182          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-C9-A47Z TCGA-CN-4722 TCGA-CN-4723 
         638          428          436            5          799          721 
TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 
         485          142          452          392          462          993 
TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 
         642          369          395         1960         1330          811 
TCGA-CN-4741 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 
        1268          488          173         1980         1081         1977 
TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6011 
        1980         1966         1975          413          290          424 
TCGA-CN-6013 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 
         433          629           45          432           98         1970 
TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6988 TCGA-CN-6992 TCGA-CN-6996 TCGA-CN-6997 
         202          424          318          394          432          429 
TCGA-CN-6998 TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W 
          46          447          225          526          484          348 
TCGA-CN-A63Y TCGA-CN-A641 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 
         175          367         1466         1207          654         1660 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 
        1422          896         1399          341          129          870 
TCGA-CQ-6223 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 
        1057         1959         1959         1461         1378         1007 
TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CA 
        1309          877          968         1960          613         1963 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI 
         545          548          393          391          303          608 
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-6472 TCGA-CR-6473 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 
        1521         1050         1125          514         1969          362 
TCGA-CR-6481 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 
         311          354          234          379          350          479 
TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7372 
        1956         1435         1440         1245         1960          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-7391 TCGA-CR-7392 TCGA-CR-7393 
         997         1430         1951          913          946          908 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7402 TCGA-CR-7404 
         898          930          156          181          911         1472 
TCGA-CV-5431 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 
         522         1438          584          546         1978         2886 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5971 TCGA-CV-5973 
        2327         1958         2437          519          701         2641 
TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 
        1478         1840         1315         1665          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-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-7100 TCGA-CV-7180 TCGA-CV-7183 
        1970         1970         1936         1959         1987         1979 
TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7406 TCGA-CV-7410 
        1724         1444         1095          954         1974         1948 
TCGA-CV-7418 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7435 
        1955         1937         1973         1972         1937         1959 
TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A461 TCGA-CV-A6JD TCGA-CV-A6JN TCGA-CX-7082 
         851         1945         1954         1970          717          317 
TCGA-CX-7085 TCGA-CX-7086 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 
         321          237          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          112 
TCGA-DQ-5624 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7590 TCGA-DQ-7591 
        1778         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          564 
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-HD-7229 TCGA-HD-7754 TCGA-HD-8224 
         133          414          403            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-MT-A51W TCGA-MT-A67A TCGA-MT-A67D 
         360          440          224           14          392           56 
TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE 
         111          112          254          910         1652          721 
TCGA-P3-A6SW TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 
        1120          578         1917          400          553          357 
TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ 
         245          218          228          225           64 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 4                  2 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              3837               3835 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
               690                613 
[1] "4.0 - 3837.0 (690.0)" "2.0 - 3835.0 (613.0)"
[1] "hr=" "1.1"
D39V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  22Q GAIN MUTATED         5       11        16        47         1
  22Q GAIN WILD-TYPE      19       52        55       145         8
D39V3, multiclass
           clus
vv          22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  STAGE I                  5                 19
  STAGE II                11                 52
  STAGE III               16                 55
  STAGE IVA               47                145
  STAGE IVB                1                  8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  22Q GAIN MUTATED    7 21 21 32
  22Q GAIN WILD-TYPE 33 87 64 99
D39V4, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  T1                7                 33
  T2               21                 87
  T3               21                 64
  T4               32                 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
  22Q GAIN MUTATED    28  12  32   1
  22Q GAIN WILD-TYPE 108  44  97   6
D39V5, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  N0               28                108
  N1               12                 44
  N2               32                 97
  N3                1                  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"
D39V6, binary
                    cls
clus                  0  1
  22Q GAIN MUTATED   18 13
  22Q GAIN WILD-TYPE 90 35
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     18   13
  22Q GAIN WILD-TYPE   90   35
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  M0               18                 90
  MX               13                 35
[1] 2 2
[1] FALSE
D39V7, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    24  66
  22Q GAIN WILD-TYPE  97 230
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     24   66
  22Q GAIN WILD-TYPE   97  230
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE               24                 97
  MALE                 66                230
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  22Q GAIN MUTATED                                      89
  22Q GAIN WILD-TYPE                                   321
                    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                                                     0
  22Q GAIN WILD-TYPE                                                   6
D39V8, multiclass
                                                             clus
vv                                                            22Q GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     89
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        0
                                                             clus
vv                                                            22Q GAIN WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      321
  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"
D39V9, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    20  70
  22Q GAIN WILD-TYPE  59 268
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     20   70
  22Q GAIN WILD-TYPE   59  268
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  NO                20                 59
  YES               70                268
[1] 2 2
[1] FALSE
D39V10, continuous
D39V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  22Q GAIN MUTATED                                  0     2
  22Q GAIN WILD-TYPE                                1     8
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  22Q GAIN MUTATED                           9    77
  22Q GAIN WILD-TYPE                        24   284
D39V12, multiclass
                                  clus
vv                                 22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           2                  8
  BLACK OR AFRICAN AMERICAN                       9                 24
  WHITE                                          77                284
[1] 4 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     7  82
  22Q GAIN WILD-TYPE  11 299
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      7   82
  22Q GAIN WILD-TYPE   11  299
                        clus
vv                       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    7                 11
  NOT HISPANIC OR LATINO               82                299
[1] 2 2
[1] FALSE

Clustering(40) Variable = XQ GAIN MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                 0   1
  XQ GAIN MUTATED    36  20
  XQ GAIN WILD-TYPE 221  78
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               56               299 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               20                78 
$`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          613          240          811         1988 
TCGA-CN-5359 TCGA-CN-5367 TCGA-CN-6012 TCGA-CN-6023 TCGA-CN-6988 TCGA-CN-6989 
        1980         1966          629          424          318          611 
TCGA-CN-A49B TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-6229 TCGA-CQ-A4C7 TCGA-CQ-A4CG 
         447         1660         1422          815         1960          391 
TCGA-CR-5247 TCGA-CR-6467 TCGA-CR-6477 TCGA-CR-6493 TCGA-CR-7370 TCGA-CV-5434 
         358         1777          514         1956          105         3295 
TCGA-CV-5435 TCGA-CV-5442 TCGA-CV-5444 TCGA-CV-5970 TCGA-CV-5977 TCGA-CV-6936 
        1438         2327         2437          406         1840         1952 
TCGA-CV-7102 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-A45Q 
        1945          954          797         1960         1976         1945 
TCGA-CX-7086 TCGA-D6-6516 TCGA-D6-6823 TCGA-D6-8568 TCGA-DQ-5625 TCGA-DQ-5629 
         237          773          701          106         1081          516 
TCGA-DQ-5631 TCGA-DQ-7592 TCGA-HD-7917 TCGA-HD-A6I0 TCGA-IQ-A61G TCGA-IQ-A61J 
         548          299           37           33          360          440 
TCGA-KU-A66T TCGA-MT-A51X 
         210           34 

$`XQ GAIN WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 
         462          415          276          722         1288         1762 
TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 
         520          725          623         1636         1747          190 
TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6873 TCGA-BA-A4IF TCGA-BA-A6D8 
         644          451           63          113          895          513 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BB-4217 TCGA-BB-4224 TCGA-BB-4228 
         351          216          182          187          278          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-4727 TCGA-CN-4729 
         799          721          485          142          452          392 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4738 
         462          993          642          369          395         1960 
TCGA-CN-4739 TCGA-CN-4741 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5360 
        1330         1268          488          512          173         1081 
TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 
        1977         1980         1966         1975          413          290 
TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 
         630          424          433          594          629           45 
TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6992 
         432           98         1970          202          224          394 
TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A63T 
         119          432          429           46          443          225 
TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 TCGA-CQ-5323 
         526          484          348          175          367         1466 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 
        1207          654          896         1399          317          341 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 
         129          870         1000         1057          985         1959 
TCGA-CQ-6228 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 
        1959         1461         1378         1007          509         1309 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB 
         901          877          968          613         1963          545 
TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5248 
         548          393          303          608         2562         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-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 
        1971         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-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-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-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-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5443 
        1950          584          546         1978         2886         1958 
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-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 
        1665          641         1899         1970         1948         1969 
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-7180 TCGA-CV-7183 TCGA-CV-7235 
        1936         1959         1939         1987         1979         1724 
TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7248 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 
        1444         1095         1967         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-7435 TCGA-CV-7440 TCGA-CV-A45O 
        1937         1984         1958         1959         1981          851 
TCGA-CV-A461 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CX-7082 TCGA-CX-7085 
        1954         1970          750          717          317          321 
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-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-DQ-5624 TCGA-DQ-5630 TCGA-DQ-7588 
         128          112          104         1778         1030         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          564          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-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-HL-7533 TCGA-IQ-7630 
          11           49           10          111         1057          485 
TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61H TCGA-IQ-A61L TCGA-IQ-A61O 
         122          441          588          412          351          360 
TCGA-KU-A66S TCGA-MT-A51W TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G 
         224           14          392           56          111          112 
TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX 
         254          910         1652          721         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 
         245          218          228          225           64 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               33                 2 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             3295              3837 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
              621               629 
[1] "33.0 - 3295.0 (621.0)" "2.0 - 3837.0 (629.0)" 
[1] "hr=" "1.1"
D40V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  XQ GAIN MUTATED         1        8        10        39         2
  XQ GAIN WILD-TYPE      23       55        61       153         7
D40V3, multiclass
           clus
vv          XQ GAIN MUTATED XQ GAIN WILD-TYPE
  STAGE I                 1                23
  STAGE II                8                55
  STAGE III              10                61
  STAGE IVA              39               153
  STAGE IVB               2                 7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  XQ GAIN MUTATED     2  14  16  28
  XQ GAIN WILD-TYPE  38  94  69 103
D40V4, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  T1               2                38
  T2              14                94
  T3              16                69
  T4              28               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
  XQ GAIN MUTATED    18   8  28   1
  XQ GAIN WILD-TYPE 118  48 101   6
D40V5, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  N0              18               118
  N1               8                48
  N2              28               101
  N3               1                 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"
D40V6, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED   13  7
  XQ GAIN WILD-TYPE 95 41
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     13    7
  XQ GAIN WILD-TYPE   95   41
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  M0              13                95
  MX               7                41
[1] 2 2
[1] FALSE
D40V7, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    18  52
  XQ GAIN WILD-TYPE 103 244
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     18   52
  XQ GAIN WILD-TYPE  103  244
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE              18               103
  MALE                52               244
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  XQ GAIN MUTATED                                      70
  XQ GAIN WILD-TYPE                                   340
                   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                                                     0
  XQ GAIN WILD-TYPE                                                   6
D40V8, multiclass
                                                             clus
vv                                                            XQ GAIN MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    70
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       0
                                                             clus
vv                                                            XQ 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                         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"
D40V9, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    22  48
  XQ GAIN WILD-TYPE  57 290
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     22   48
  XQ GAIN WILD-TYPE   57  290
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  NO               22                57
  YES              48               290
[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                                0     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XQ GAIN MUTATED                           7    60
  XQ GAIN WILD-TYPE                        26   301
D40V12, multiclass
                                  clus
vv                                 XQ GAIN MUTATED XQ GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      7                26
  WHITE                                         60               301
[1] 4 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     3  65
  XQ GAIN WILD-TYPE  15 316
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      3   65
  XQ GAIN WILD-TYPE   15  316
                        clus
vv                       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                15
  NOT HISPANIC OR LATINO              65               316
[1] 2 2
[1] FALSE

Clustering(41) Variable = 1P LOSS MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                 0   1
  1P LOSS MUTATED    26  13
  1P LOSS WILD-TYPE 231  85
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               39               316 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               13                85 
$`1P LOSS MUTATED`
TCGA-BA-4075 TCGA-BA-5152 TCGA-BA-6871 TCGA-BA-7269 TCGA-BA-A6D8 TCGA-CN-4736 
         283         1288           63          236          513          395 
TCGA-CN-5355 TCGA-CN-5360 TCGA-CN-6012 TCGA-CN-6018 TCGA-CN-6021 TCGA-CN-6024 
         488         1081          629           45         1970          224 
TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6997 TCGA-CN-A63T TCGA-CQ-5332 TCGA-CQ-A4CA 
         394          119          429          225          317         1963 
TCGA-CQ-A4CI TCGA-CR-7365 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CV-5432 
         608         1191          105         1979          759         1950 
TCGA-CV-5434 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-6003 TCGA-CV-6935 TCGA-CV-7254 
        3295          546         1978         1665         1969         1976 
TCGA-CV-7261 TCGA-CV-7424 TCGA-D6-6516 TCGA-DQ-7589 TCGA-F7-8489 TCGA-F7-A61W 
        1099         1947          773          575          658           14 
TCGA-HD-8634 TCGA-IQ-A61L TCGA-MZ-A6I9 
          24          351          254 

$`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-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 
         351          216          182          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-BB-8601 TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 
         624            5            4          799          721          485 
TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 
         142          452          613          392          462          993 
TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 
         642          369          240         1960         1330          811 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5363 
        1268         1988          512          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          413          290 
TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 
         630          424          433          594          629          432 
TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6996 
          98          202          424          318          611          432 
TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W 
          46          443          447          526          484          348 
TCGA-CN-A63Y TCGA-CN-A641 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 
         175          367         1466         1207          654         1660 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 
        1422          896         1399          341          129          870 
TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 
        1000         1057          985         1959         1959          815 
TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 
        1461         1378         1007          509         1309          901 
TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD 
         877          968         1960          613          545          548 
TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 
         393          391          303         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-6478 TCGA-CR-6480 TCGA-CR-6481 
        1125         1971          514         1969          362          311 
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-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7373 
        1956         1435         1440         1245         1960          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-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-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-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-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         1724         1444         1095          954          797 
TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7422 
        1967         1960         1974         1948         1955         1957 
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-A461 TCGA-CV-A6JD 
        1959         1981          851         1945         1954         1970 
TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 
         750          717          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-DQ-5624 TCGA-DQ-5625 
         106          128          112          104         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          564 
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-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-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-A61H TCGA-IQ-A61J TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T 
         360          412          440          360          224          210 
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-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 
         910         1652          721         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 
         218          228          225           64 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               14                 2 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             3295              3837 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
              575               634 
[1] "14.0 - 3295.0 (575.0)" "2.0 - 3837.0 (634.0)" 
[1] "hr=" "1.1"
D41V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  1P LOSS MUTATED         3        4         9        23         0
  1P LOSS WILD-TYPE      21       59        62       169         9
D41V3, multiclass
           clus
vv          1P LOSS MUTATED 1P LOSS WILD-TYPE
  STAGE I                 3                21
  STAGE II                4                59
  STAGE III               9                62
  STAGE IVA              23               169
  STAGE IVB               0                 9
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  1P LOSS MUTATED     4   9  13  14
  1P LOSS WILD-TYPE  36  99  72 117
D41V4, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  T1               4                36
  T2               9                99
  T3              13                72
  T4              14               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
  1P LOSS MUTATED    18   5  14   0
  1P LOSS WILD-TYPE 118  51 115   7
D41V5, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  N0              18               118
  N1               5                51
  N2              14               115
  N3               0                 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"
D41V6, binary
                   cls
clus                 0  1
  1P LOSS MUTATED   13  3
  1P LOSS WILD-TYPE 95 45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     13    3
  1P LOSS WILD-TYPE   95   45
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  M0              13                95
  MX               3                45
[1] 2 2
[1] FALSE
D41V7, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    10  35
  1P LOSS WILD-TYPE 111 261
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     10   35
  1P LOSS WILD-TYPE  111  261
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE              10               111
  MALE                35               261
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  1P LOSS MUTATED                                      44
  1P LOSS WILD-TYPE                                   366
                   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                                                   5
D41V8, multiclass
                                                             clus
vv                                                            1P LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    44
  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                                     366
  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"
D41V9, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    10  35
  1P LOSS WILD-TYPE  69 303
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     10   35
  1P LOSS WILD-TYPE   69  303
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  NO               10                69
  YES              35               303
[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                                1     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1P LOSS MUTATED                           4    38
  1P LOSS WILD-TYPE                        29   323
D41V12, multiclass
                                  clus
vv                                 1P LOSS MUTATED 1P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                 8
  BLACK OR AFRICAN AMERICAN                      4                29
  WHITE                                         38               323
[1] 4 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  40
  1P LOSS WILD-TYPE  16 341
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      2   40
  1P LOSS WILD-TYPE   16  341
                        clus
vv                       1P LOSS MUTATED 1P LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                16
  NOT HISPANIC OR LATINO              40               341
[1] 2 2
[1] FALSE

Clustering(42) Variable = 1Q LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                 0   1
  1Q LOSS MUTATED    18   8
  1Q LOSS WILD-TYPE 239  90
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               26               329 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                8                90 
$`1Q LOSS MUTATED`
TCGA-BA-5149 TCGA-BA-5152 TCGA-C9-A47Z TCGA-CN-4736 TCGA-CN-5355 TCGA-CN-6012 
         248         1288            5          395          488          629 
TCGA-CN-6018 TCGA-CN-6994 TCGA-CN-A63T TCGA-CN-A63W TCGA-CQ-6227 TCGA-CQ-A4C7 
          45          119          225          348         1959         1960 
TCGA-CQ-A4CA TCGA-CR-7365 TCGA-CR-7372 TCGA-CV-5432 TCGA-CV-5439 TCGA-CV-5441 
        1963         1191          759         1950          546         2886 
TCGA-CV-6003 TCGA-CV-7424 TCGA-DQ-7588 TCGA-F7-8489 TCGA-F7-A61W TCGA-HD-8634 
        1665         1947         1965          658           14           24 
TCGA-IQ-A61L TCGA-MZ-A6I9 
         351          254 

$`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-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE 
         236          895          513          351          216          182 
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-A480 TCGA-CN-4722 
         428          436         1955          624            4          799 
TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 
         721          485          142          452          613          392 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4737 TCGA-CN-4738 
         462          993          642          369          240         1960 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5358 
        1330          811         1268         1988          512          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-6013 
        1975          413          290          630          424          433 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 
         594          629          432           98         1970          202 
TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6996 
         424          224          318          611          394          432 
TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63U TCGA-CN-A63V 
         429           46          443          447          526          484 
TCGA-CN-A63Y TCGA-CN-A641 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 
         175          367         1466         1207          654         1660 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 
        1422          896         1399          317          341          129 
TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6228 TCGA-CQ-6229 
         870         1000         1057          985         1959          815 
TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 
        1461         1378         1007          509         1309          901 
TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE 
         877          968          613          545          548          393 
TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 
         391          303          608         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-6478 TCGA-CR-6480 TCGA-CR-6481 
        1125         1971          514         1969          362          311 
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-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 
        1956         1435         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-5440 
        1955          522         3295         1438          584         1978 
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-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-6954 TCGA-CV-6960 
        3835         1948         1969         1966         1957         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-7102 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 
        1959         1939         1945         1987         1979         1724 
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-7433 TCGA-CV-7434 
        1937         1973         1972         1937         1984         1958 
TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A461 TCGA-CV-A6JD 
        1959         1981          851         1945         1954         1970 
TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 
         750          717          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-DQ-5624 
         568          106          128          112          104         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-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S 
         564          490           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-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-8635 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 
          55           44           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-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F 
         210           14           34          392           56          111 
TCGA-MT-A67G TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX 
         112          910         1652          721         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 
         245          218          228          225           64 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                5                 2 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             2886              3837 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            587.5             629.0 
[1] "5.0 - 2886.0 (587.5)" "2.0 - 3837.0 (629.0)"
[1] "hr=" "1.3"
D42V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  1Q LOSS MUTATED         2        3         6        17         0
  1Q LOSS WILD-TYPE      22       60        65       175         9
D42V3, multiclass
           clus
vv          1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  STAGE I                 2                22
  STAGE II                3                60
  STAGE III               6                65
  STAGE IVA              17               175
  STAGE IVB               0                 9
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  1Q LOSS MUTATED     3   6  11   9
  1Q LOSS WILD-TYPE  37 102  74 122
D42V4, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  T1               3                37
  T2               6               102
  T3              11                74
  T4               9               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
  1Q LOSS MUTATED    13   3  11   0
  1Q LOSS WILD-TYPE 123  53 118   7
D42V5, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  N0              13               123
  N1               3                53
  N2              11               118
  N3               0                 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"
D42V6, binary
                   cls
clus                 0  1
  1Q LOSS MUTATED    9  3
  1Q LOSS WILD-TYPE 99 45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      9    3
  1Q LOSS WILD-TYPE   99   45
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  M0               9                99
  MX               3                45
[1] 2 2
[1] FALSE
D42V7, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     8  23
  1Q LOSS WILD-TYPE 113 273
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      8   23
  1Q LOSS WILD-TYPE  113  273
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE               8               113
  MALE                23               273
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  1Q LOSS MUTATED                                      31
  1Q LOSS WILD-TYPE                                   379
                   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                                                   6
D42V8, multiclass
                                                             clus
vv                                                            1Q 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                       0
                                                             clus
vv                                                            1Q LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     379
  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"
D42V9, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     6  25
  1Q LOSS WILD-TYPE  73 313
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      6   25
  1Q LOSS WILD-TYPE   73  313
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  NO                6                73
  YES              25               313
[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                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1Q LOSS MUTATED                           1    26
  1Q LOSS WILD-TYPE                        32   335
D42V12, multiclass
                                  clus
vv                                 1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          3                 7
  BLACK OR AFRICAN AMERICAN                      1                32
  WHITE                                         26               335
[1] 4 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  29
  1Q LOSS WILD-TYPE  17 352
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      1   29
  1Q LOSS WILD-TYPE   17  352
                        clus
vv                       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                17
  NOT HISPANIC OR LATINO              29               352
[1] 2 2
[1] FALSE

Clustering(43) Variable = 2P LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                 0   1
  2P LOSS MUTATED    18   5
  2P LOSS WILD-TYPE 239  93
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               23               332 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                5                93 
$`2P LOSS MUTATED`
TCGA-BA-5559 TCGA-BA-6873 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7864 TCGA-C9-A47Z 
        1747          113          310          536          687            5 
TCGA-CN-6011 TCGA-CN-A49B TCGA-CN-A63W TCGA-CQ-6218 TCGA-CQ-7064 TCGA-CV-5966 
         424          447          348          870         1378          519 
TCGA-CV-5973 TCGA-CV-6003 TCGA-CV-6961 TCGA-CV-7432 TCGA-D6-6826 TCGA-DQ-7588 
        2641         1665         1959         1937          154         1965 
TCGA-F7-A50J TCGA-F7-A623 TCGA-IQ-A61L TCGA-KU-A66T TCGA-MZ-A6I9 
         585            6          351          210          254 

$`2P LOSS 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-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-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE 
         236          895          513          351          216          182 
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-7863 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 
         423          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          485          142 
TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
         452          613          392          462          993          642 
TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 
         369          395          240         1960         1330          811 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 
        1268         1988          488          512          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-6012 TCGA-CN-6013 TCGA-CN-6016 
         413          290          630          629          433          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-6994 
         424          224          318          611          394          119 
TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A63T TCGA-CN-A63U 
         432          429           46          443          225          526 
TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A641 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
         484          175          367         1466         1207          654 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 
        1660         1422          896         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 
         815         1461         1007          509         1309          901 
TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB 
         877          968         1960          613         1963          545 
TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 
         548          393          391          303          608         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-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-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-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-5970 TCGA-CV-5971 
        2886         2327         1958         2437          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         1724         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-A461 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN 
         851         1945         1954         1970          750          717 
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-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 
         112          104         1778         1081          516         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-F7-7848 TCGA-F7-8298 TCGA-F7-8489 
         368          324          340          564          490          658 
TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 
          15           92            3          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-A61E TCGA-IQ-A61G 
        1057          485          122          441          588          360 
TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61O TCGA-KU-A66S TCGA-MT-A51W TCGA-MT-A51X 
         412          440          360          224           14           34 
TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-P3-A5Q5 TCGA-P3-A5QA 
         392           56          111          112          910         1652 
TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T4 
         721         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-A6IJ 
         225           64 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                5                 2 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             2641              3837 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
              519               634 
[1] "5.0 - 2641.0 (519.0)" "2.0 - 3837.0 (634.0)"
[1] "hr=" "1"  
D43V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  2P LOSS MUTATED         0        3         7        14         0
  2P LOSS WILD-TYPE      24       60        64       178         9
D43V3, multiclass
           clus
vv          2P LOSS MUTATED 2P LOSS WILD-TYPE
  STAGE I                 0                24
  STAGE II                3                60
  STAGE III               7                64
  STAGE IVA              14               178
  STAGE IVB               0                 9
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  2P LOSS MUTATED     2   6   6  10
  2P LOSS WILD-TYPE  38 102  79 121
D43V4, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  T1               2                38
  T2               6               102
  T3               6                79
  T4              10               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
  2P LOSS MUTATED     9   7   8   0
  2P LOSS WILD-TYPE 127  49 121   7
D43V5, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  N0               9               127
  N1               7                49
  N2               8               121
  N3               0                 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"
D43V6, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     5   5
  2P LOSS WILD-TYPE 103  43
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      5    5
  2P LOSS WILD-TYPE  103   43
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  M0               5               103
  MX               5                43
[1] 2 2
[1] FALSE
D43V7, binary
                   cls
clus                  0   1
  2P LOSS MUTATED    14  13
  2P LOSS WILD-TYPE 107 283
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     14   13
  2P LOSS WILD-TYPE  107  283
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE              14               107
  MALE                13               283
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  2P LOSS MUTATED                                      27
  2P LOSS WILD-TYPE                                   383
                   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                                                   6
D43V8, multiclass
                                                             clus
vv                                                            2P 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                       0
                                                             clus
vv                                                            2P LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     383
  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"
D43V9, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     2  25
  2P LOSS WILD-TYPE  77 313
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      2   25
  2P LOSS WILD-TYPE   77  313
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  NO                2                77
  YES              25               313
[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                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2P LOSS MUTATED                           1    24
  2P LOSS WILD-TYPE                        32   337
D43V12, multiclass
                                  clus
vv                                 2P LOSS MUTATED 2P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      1                32
  WHITE                                         24               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"
D43V13, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     2  25
  2P LOSS WILD-TYPE  16 356
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      2   25
  2P LOSS WILD-TYPE   16  356
                        clus
vv                       2P LOSS MUTATED 2P LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                16
  NOT HISPANIC OR LATINO              25               356
[1] 2 2
[1] FALSE

Clustering(44) Variable = 2Q LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                 0   1
  2Q LOSS MUTATED    23   6
  2Q LOSS WILD-TYPE 234  92
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               29               326 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                6                92 
$`2Q LOSS MUTATED`
TCGA-BA-5152 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-6873 TCGA-BB-7861 TCGA-BB-7862 
        1288         1747           63          113          310          536 
TCGA-BB-7864 TCGA-C9-A47Z TCGA-CN-4736 TCGA-CN-6018 TCGA-CN-A49B TCGA-CN-A63W 
         687            5          395           45          447          348 
TCGA-CQ-5327 TCGA-CQ-7064 TCGA-CR-6472 TCGA-CR-6484 TCGA-CR-7371 TCGA-CR-7399 
        1660         1378         1050          354         1979          181 
TCGA-CR-7402 TCGA-CV-5973 TCGA-CV-6003 TCGA-CV-6961 TCGA-D6-6826 TCGA-DQ-7593 
         911         2641         1665         1959          154          369 
TCGA-F7-A50J TCGA-F7-A620 TCGA-IQ-A61L TCGA-KU-A66T TCGA-MZ-A6I9 
         585           13          351          210          254 

$`2Q LOSS 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-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-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BB-4217 TCGA-BB-4223 
         513          351          216          182          187         2878 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7863 TCGA-BB-7866 
         278          140          133          558          423          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          485          142          452          613 
TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4737 
         392          462          993          642          369          240 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 
        1960         1330          811         1268         1988          488 
TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 
         512          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          413          290          630 
TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 
         424          629          433          594          629          432 
TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 
          98         1970          202          424          224          318 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 
         611          394          119          432          429           46 
TCGA-CN-A498 TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A641 
         443          225          526          484          175          367 
TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 
        1466         1207          654         1422          896         1399 
TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 
         317          341          129          870         1000         1057 
TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7065 
         985         1959         1959          815         1461         1007 
TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 
         509         1309          901          877          968         1960 
TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG 
         613         1963          545          548          393          391 
TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 
         303          608         2562          358         1663         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-6487 
         514         1969          362          311          345          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-7372 TCGA-CR-7373 
        1440         1245         1960          105          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-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-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-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 
        1840          215         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-6945 TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-7090 TCGA-CV-7091 
        1969         1966         1957         1969         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-7242 TCGA-CV-7243 
        1987         1979         1724         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-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-A461 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN 
         851         1945         1954         1970          750          717 
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-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 
         112          104         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          564          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-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-A61E TCGA-IQ-A61G 
        1057          485          122          441          588          360 
TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61O TCGA-KU-A66S TCGA-MT-A51W TCGA-MT-A51X 
         412          440          360          224           14           34 
TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-P3-A5Q5 TCGA-P3-A5QA 
         392           56          111          112          910         1652 
TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T4 
         721         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-A6IJ 
         225           64 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                5                 2 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             2641              3837 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            395.0             639.5 
[1] "5.0 - 2641.0 (395.0)" "2.0 - 3837.0 (639.5)"
[1] "hr=" "1"  
D44V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  2Q LOSS MUTATED         0        2        10        15         0
  2Q LOSS WILD-TYPE      24       61        61       177         9
D44V3, multiclass
           clus
vv          2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  STAGE I                 0                24
  STAGE II                2                61
  STAGE III              10                61
  STAGE IVA              15               177
  STAGE IVB               0                 9
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  2Q LOSS MUTATED     2   5  10  11
  2Q LOSS WILD-TYPE  38 103  75 120
D44V4, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  T1               2                38
  T2               5               103
  T3              10                75
  T4              11               120
[1] 4 2
[1] 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     8   9  10   0
  2Q LOSS WILD-TYPE 128  47 119   7
D44V5, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  N0               8               128
  N1               9                47
  N2              10               119
  N3               0                 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"
D44V6, binary
                   cls
clus                 0  1
  2Q LOSS MUTATED    9  4
  2Q LOSS WILD-TYPE 99 44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      9    4
  2Q LOSS WILD-TYPE   99   44
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  M0               9                99
  MX               4                44
[1] 2 2
[1] FALSE
D44V7, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    17  17
  2Q LOSS WILD-TYPE 104 279
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     17   17
  2Q LOSS WILD-TYPE  104  279
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE              17               104
  MALE                17               279
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  2Q LOSS MUTATED                                      34
  2Q LOSS WILD-TYPE                                   376
                   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                                                     0
  2Q LOSS WILD-TYPE                                                   6
D44V8, multiclass
                                                             clus
vv                                                            2Q LOSS 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                       0
                                                             clus
vv                                                            2Q LOSS 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                         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"
D44V9, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     2  32
  2Q LOSS WILD-TYPE  77 306
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      2   32
  2Q LOSS WILD-TYPE   77  306
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  NO                2                77
  YES              32               306
[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                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2Q LOSS MUTATED                           1    29
  2Q LOSS WILD-TYPE                        32   332
D44V12, multiclass
                                  clus
vv                                 2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          3                 7
  BLACK OR AFRICAN AMERICAN                      1                32
  WHITE                                         29               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"
D44V13, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     2  30
  2Q LOSS WILD-TYPE  16 351
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      2   30
  2Q LOSS WILD-TYPE   16  351
                        clus
vv                       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                16
  NOT HISPANIC OR LATINO              30               351
[1] 2 2
[1] FALSE

Clustering(45) Variable = 3P LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                 0   1
  3P LOSS MUTATED   134  74
  3P LOSS WILD-TYPE 123  24
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              208               147 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               74                24 
$`3P LOSS MUTATED`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-5149 TCGA-BA-5555 TCGA-BA-5558 
         462          283          415          248          520         1636 
TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A6D8 
         644          451           63          384          236          513 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-7862 
         351          216          182          278          133          536 
TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 
         687         1153          428          436         1955          624 
TCGA-C9-A47Z TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4735 
           5          485          142          613          392          369 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4742 
         395          240         1960         1330          811         1988 
TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 
         488          173         1980         1081         1977         1980 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5373 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 
        1966         1966          413          630          424          629 
TCGA-CN-6016 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6024 TCGA-CN-6989 TCGA-CN-6992 
         594           45          432          224          611          394 
TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63T 
         432          429           46          443          447          225 
TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A641 TCGA-CQ-5330 TCGA-CQ-5332 TCGA-CQ-6218 
         526          348          367          896          317          870 
TCGA-CQ-6221 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 
        1000          985         1959         1959          815         1378 
TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7069 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
        1007          509          901          968         1960          613 
TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CI TCGA-CR-5243 
        1963          545          548          393          608         2562 
TCGA-CR-5247 TCGA-CR-5250 TCGA-CR-6473 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 
         358          799         1125          514         1969          362 
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-7377 TCGA-CR-7379 
         105         1979          759          889         1968         1036 
TCGA-CR-7383 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7390 TCGA-CR-7398 TCGA-CR-7401 
        1954         1430         1951          907          156         1077 
TCGA-CR-7402 TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 
         911         1955         1950         3295         1438          584 
TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 
         546         1978         2886         2437          519          406 
TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6441 
        2641         1478          215         1315         1665         1970 
TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6945 TCGA-CV-6952 
        1948         1969         1952         1959         1969         1966 
TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7099 
        1957         1969         1959         1959         1970         1936 
TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7238 TCGA-CV-7242 
        1959         1939         1945         1987         1444         1095 
TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7254 TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7422 
         797         1967         1976         1948         1955         1957 
TCGA-CV-7424 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7434 TCGA-CV-7435 
        1947         1973         1972         1937         1958         1959 
TCGA-CV-A461 TCGA-CV-A6JE TCGA-CX-7082 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 
        1954          750          317          237          828          773 
TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-8568 TCGA-D6-8569 
         292          701          491          154          106          128 
TCGA-D6-A4ZB TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 
         104          516         1030          548         1965          575 
TCGA-DQ-7591 TCGA-DQ-7592 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-A50G TCGA-F7-A50I 
         622          299          564          490           15           92 
TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61W TCGA-F7-A620 TCGA-H7-8502 TCGA-H7-A6C4 
         585            3           14           13          133          414 
TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-8224 TCGA-HD-8635 TCGA-HD-A633 
         403            2            5           55           25           49 
TCGA-HD-A6HZ TCGA-IQ-7630 TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61L 
         111          485          360          412          440          351 
TCGA-IQ-A61O TCGA-KU-A66T TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67D TCGA-P3-A5QA 
         360          210           14           34           56         1652 
TCGA-P3-A6T4 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IH 
        1968          553          357          228 

$`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-BB-4217 
         623         1747          190          113          895          187 
TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7863 TCGA-BB-7866 
        2878          140          558          310          423          638 
TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4727 TCGA-CN-4730 TCGA-CN-4731 
           4          799          721          452          462          993 
TCGA-CN-4733 TCGA-CN-4741 TCGA-CN-5356 TCGA-CN-5370 TCGA-CN-5374 TCGA-CN-6013 
         642         1268          512         1975          290          433 
TCGA-CN-6017 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6988 
         629           98         1970          202          424          318 
TCGA-CN-6994 TCGA-CN-A63V TCGA-CN-A63Y TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
         119          484          175         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 
        1461         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-7243 TCGA-CV-7250 TCGA-CV-7261 
        1970         1979         1724          954         1960         1099 
TCGA-CV-7406 TCGA-CV-7427 TCGA-CV-7433 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q 
        1974         1937         1984         1981          851         1945 
TCGA-CV-A6JD TCGA-CV-A6JN TCGA-CX-7085 TCGA-D6-6824 TCGA-D6-6827 TCGA-D6-A4Z9 
        1970          717          321           77          568          112 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-7590 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 
        1778         1081          775          369          368          324 
TCGA-DQ-7596 TCGA-F7-8489 TCGA-F7-A61V TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8501 
         340          658          384            6          407           58 
TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-A4C1 TCGA-HD-A634 
          25           37           44           24           11           10 
TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-KU-A66S 
          33         1057          122          441          588          224 
TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QE 
         392          111          112          254          910          721 
TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T8 TCGA-QK-A6IF 
        1120         1954          578         1917          400          245 
TCGA-QK-A6IG TCGA-QK-A6II TCGA-QK-A6IJ 
         218          225           64 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                2                 4 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             3295              3837 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              612               654 
[1] "2.0 - 3295.0 (612.0)" "4.0 - 3837.0 (654.0)"
[1] "hr=" "1.9"
D45V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  3P LOSS MUTATED        14       32        40       121         6
  3P LOSS WILD-TYPE      10       31        31        71         3
D45V3, multiclass
           clus
vv          3P LOSS MUTATED 3P LOSS WILD-TYPE
  STAGE I                14                10
  STAGE II               32                31
  STAGE III              40                31
  STAGE IVA             121                71
  STAGE IVB               6                 3
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  3P LOSS MUTATED   21 56 58 80
  3P LOSS WILD-TYPE 19 52 27 51
D45V4, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  T1              21                19
  T2              56                52
  T3              58                27
  T4              80                51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2 N3
  3P LOSS MUTATED   75 32 87  4
  3P LOSS WILD-TYPE 61 24 42  3
D45V5, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  N0              75                61
  N1              32                24
  N2              87                42
  N3               4                 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"
D45V6, binary
                   cls
clus                 0  1
  3P LOSS MUTATED   61 24
  3P LOSS WILD-TYPE 47 24
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     61   24
  3P LOSS WILD-TYPE   47   24
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  M0              61                47
  MX              24                24
[1] 2 2
[1] FALSE
D45V7, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    62 178
  3P LOSS WILD-TYPE  59 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     62  178
  3P LOSS WILD-TYPE   59  118
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE              62                59
  MALE               178               118
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  3P LOSS MUTATED                                     238
  3P LOSS WILD-TYPE                                   172
                   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                                                     1
  3P LOSS WILD-TYPE                                                   5
D45V8, multiclass
                                                             clus
vv                                                            3P LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                   238
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       1
                                                             clus
vv                                                            3P LOSS WILD-TYPE
  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                         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"
D45V9, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    50 190
  3P LOSS WILD-TYPE  29 148
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     50  190
  3P LOSS WILD-TYPE   29  148
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  NO               50                29
  YES             190               148
[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                                0     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3P LOSS MUTATED                          25   200
  3P LOSS WILD-TYPE                         8   161
D45V12, multiclass
                                  clus
vv                                 3P LOSS MUTATED 3P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          6                 4
  BLACK OR AFRICAN AMERICAN                     25                 8
  WHITE                                        200               161
[1] 4 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    13 213
  3P LOSS WILD-TYPE   5 168
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     13  213
  3P LOSS WILD-TYPE    5  168
                        clus
vv                       3P LOSS MUTATED 3P LOSS WILD-TYPE
  HISPANIC OR LATINO                  13                 5
  NOT HISPANIC OR LATINO             213               168
[1] 2 2
[1] FALSE

Clustering(46) Variable = 3Q LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                 0   1
  3Q LOSS MUTATED    26  20
  3Q LOSS WILD-TYPE 231  78
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               46               309 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               20                78 
$`3Q LOSS MUTATED`
TCGA-BA-4076 TCGA-BA-5555 TCGA-BA-5558 TCGA-BA-6871 TCGA-BA-A6DB TCGA-BB-7870 
         415          520         1636           63          216         1153 
TCGA-CN-4735 TCGA-CN-4738 TCGA-CN-5366 TCGA-CN-6010 TCGA-CN-6018 TCGA-CN-6997 
         369         1960         1966          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          548 
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 
         750          154         1965           13          403            5 
TCGA-IQ-A61L TCGA-MT-A51W TCGA-MT-A51X TCGA-QK-A6IH 
         351           14           34          228 

$`3Q LOSS WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 
         462          283         1983          276          248          722 
TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6868 
        1288         1762          725          623         1747          190 
TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF 
         644          451          384          113          236          895 
TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DE TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 
         513          351          182          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          485          142 
TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
         452          613          392          462          993          642 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 
         395          240         1330          811         1268         1988 
TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 
         488          512          173         1980         1081         1977 
TCGA-CN-5365 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6011 
        1980         1966         1975          413          290          424 
TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6020 
         629          433          594          629          432           98 
TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 
        1970          202          424          224          318          611 
TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49B 
         394          119          432           46          443          447 
TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A641 TCGA-CQ-5323 TCGA-CQ-5324 
         225          484          175          367         1466         1207 
TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 
         654         1660         1422          896         1399          341 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6227 TCGA-CQ-6228 
         129          870         1000         1057         1959         1959 
TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 
         815         1461         1378          509         1309          901 
TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB 
         877          968         1960          613         1963          545 
TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 
         393          391          303          608         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-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 
        1050         1971          514         1969          362          311 
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-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-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 
        1979          759           30          972         1968         1036 
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-7397 TCGA-CR-7399 
         946          908          898          930          216          181 
TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5436 
         911         1472         1955          522         1950          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-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 
         406          701         2641         1840          215         1315 
TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 
        1665          641         1899         1948         1969         1952 
TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6954 TCGA-CV-6960 
        1959         3835         1948         1969         1957         1969 
TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7101 
        3837         1959         1970         1970         1936         1939 
TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7242 
        1945         1987         1979         1724         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-7422 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7432 
        1974         1948         1957         1947         1937         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-A461 TCGA-CV-A6JD TCGA-CV-A6JN TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 
        1954         1970          717          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-DQ-5624 
         568          106          128          112          104         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 
         564          490          658           15           92          585 
TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8501 
           3          384           14            6          407           58 
TCGA-H7-8502 TCGA-H7-A6C4 TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 
         133          414            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-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 
         210          392           56          111          112          254 
TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 
         910         1652          721         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 
         218          225           64 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                5                 2 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             3295              3837 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            819.5             623.0 
[1] "5.0 - 3295.0 (819.5)" "2.0 - 3837.0 (623.0)"
[1] "hr=" "1.6"
D46V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  3Q LOSS MUTATED         5        6         5        32         2
  3Q LOSS WILD-TYPE      19       57        66       160         7
D46V3, multiclass
           clus
vv          3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  STAGE I                 5                19
  STAGE II                6                57
  STAGE III               5                66
  STAGE IVA              32               160
  STAGE IVB               2                 7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  3Q LOSS MUTATED     7   8  11  24
  3Q LOSS WILD-TYPE  33 100  74 107
D46V4, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  T1               7                33
  T2               8               100
  T3              11                74
  T4              24               107
[1] 4 2
[1] 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    25   4  21   0
  3Q LOSS WILD-TYPE 111  52 108   7
D46V5, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  N0              25               111
  N1               4                52
  N2              21               108
  N3               0                 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"
D46V6, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED   14  3
  3Q LOSS WILD-TYPE 94 45
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     14    3
  3Q LOSS WILD-TYPE   94   45
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  M0              14                94
  MX               3                45
[1] 2 2
[1] FALSE
D46V7, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    13  43
  3Q LOSS WILD-TYPE 108 253
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     13   43
  3Q LOSS WILD-TYPE  108  253
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE              13               108
  MALE                43               253
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  3Q LOSS MUTATED                                      56
  3Q LOSS WILD-TYPE                                   354
                   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                                                   6
D46V8, multiclass
                                                             clus
vv                                                            3Q LOSS 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                       0
                                                             clus
vv                                                            3Q LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     354
  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"
D46V9, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     9  47
  3Q LOSS WILD-TYPE  70 291
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      9   47
  3Q LOSS WILD-TYPE   70  291
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  NO                9                70
  YES              47               291
[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                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3Q LOSS MUTATED                           8    47
  3Q LOSS WILD-TYPE                        25   314
D46V12, multiclass
                                  clus
vv                                 3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      8                25
  WHITE                                         47               314
[1] 4 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  52
  3Q LOSS WILD-TYPE  16 329
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      2   52
  3Q LOSS WILD-TYPE   16  329
                        clus
vv                       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                16
  NOT HISPANIC OR LATINO              52               329
[1] 2 2
[1] FALSE

Clustering(47) Variable = 4P LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                 0   1
  4P LOSS MUTATED    94  41
  4P LOSS WILD-TYPE 163  57
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              135               220 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               41                57 
$`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-A6D8 
         520          623          451           63          895          513 
TCGA-BA-A6DB TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-7861 TCGA-BB-7871 TCGA-BB-8596 
         216         2878          278          310          428         1955 
TCGA-BB-8601 TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 
         624            5            4          721          485          142 
TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4735 TCGA-CN-4739 TCGA-CN-4742 
         613          392          462          369         1330         1988 
TCGA-CN-5355 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 
         488         1081         1977          290          630          424 
TCGA-CN-6012 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6021 TCGA-CN-6989 TCGA-CN-6992 
         629           45          432         1970          611          394 
TCGA-CN-6994 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63T 
         119          429           46          443          447          225 
TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A641 TCGA-CQ-5323 TCGA-CQ-6223 TCGA-CQ-6228 
         526          348          367         1466         1057         1959 
TCGA-CQ-7064 TCGA-CQ-7067 TCGA-CQ-A4C9 TCGA-CQ-A4CD TCGA-CQ-A4CI TCGA-CR-5248 
        1378          509          613          548          608         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         1724         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-7424 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7435 TCGA-CV-7440 TCGA-CX-7082 
        1947         1972         1937         1959         1981          317 
TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6823 TCGA-D6-A4Z9 TCGA-DQ-5629 TCGA-DQ-7589 
         828          773          701          112          516          575 
TCGA-F7-8298 TCGA-F7-A50G TCGA-F7-A61S TCGA-F7-A61V TCGA-H7-8502 TCGA-H7-A6C5 
         490           15            3          384          133          403 
TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A633 TCGA-HD-A6HZ TCGA-IQ-A61E 
          37           55           44           49          111          588 
TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A5QA 
         360          412          440          112          254         1652 
TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T8 
        1120         1954          400 

$`4P LOSS WILD-TYPE`
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-5559 
         722         1288         1762          725         1636         1747 
TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A6DA 
         190          644          384          113          236          351 
TCGA-BA-A6DE TCGA-BB-4217 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7862 
         182          187          140          133          558          536 
TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7872 TCGA-CN-4722 
         423          687          638         1153          436          799 
TCGA-CN-4727 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 
         452          993          642          395          240         1960 
TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5365 
         811         1268          512          173         1980         1980 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6013 TCGA-CN-6016 
        1966         1966         1975          413          433          594 
TCGA-CN-6017 TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 
         629           98          202          424          224          318 
TCGA-CN-6996 TCGA-CN-A63V TCGA-CN-A63Y TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 
         432          484          175         1207          654         1660 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 
        1422          896         1399          317          341          129 
TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7063 
         870         1000          985         1959          815         1461 
TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 
        1007         1309          901          877          968         1960 
TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5243 
        1963          545          393          391          303         2562 
TCGA-CR-5247 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 
         358         1152          799         1777         1521         1966 
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-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7368 
         345          354          479         1956         1435         1245 
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-7401 TCGA-CR-7402 TCGA-CV-5430 TCGA-CV-5439 
         216          181         1077          911         1955          546 
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-5979 TCGA-CV-6003 TCGA-CV-6433 
        2641         1478         1840         1315         1665          641 
TCGA-CV-6436 TCGA-CV-6936 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-6954 
        1899         1952         1948         1969         1966         1957 
TCGA-CV-6960 TCGA-CV-7090 TCGA-CV-7095 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 
        1969         3837         1970         1936         1959         1945 
TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7243 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7406 
        1987         1979          954         1960         1976         1974 
TCGA-CV-7410 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-A45O 
        1948         1937         1973         1984         1958          851 
TCGA-CV-A45Q TCGA-CV-A461 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CX-7085 
        1945         1954         1970          750          717          321 
TCGA-CX-7086 TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 
         237          292           77          491          154          568 
TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4ZB TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 
         106          128          104         1778         1081         1030 
TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 TCGA-DQ-7593 
         548         1965          775          622          299          369 
TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50I 
         368          324          340          564          658           92 
TCGA-F7-A50J TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8501 
         585           14           13            6          407           58 
TCGA-H7-A6C4 TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-8634 TCGA-HD-8635 
         414            2            5           25           24           25 
TCGA-HD-A4C1 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 
          11           10           33         1057          485          122 
TCGA-IQ-7632 TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-MT-A51W 
         441          351          360          224          210           14 
TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-P3-A5Q5 TCGA-P3-A5QE 
          34          392           56          111          910          721 
TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF 
         578         1917         1968          553          357          245 
TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ 
         218          228          225           64 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                3                 2 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             3835              3837 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            588.0             672.5 
[1] "3.0 - 3835.0 (588.0)" "2.0 - 3837.0 (672.5)"
[1] "hr=" "1.1"
D47V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  4P LOSS MUTATED        11       21        29        76         4
  4P LOSS WILD-TYPE      13       42        42       116         5
D47V3, multiclass
           clus
vv          4P LOSS MUTATED 4P LOSS WILD-TYPE
  STAGE I                11                13
  STAGE II               21                42
  STAGE III              29                42
  STAGE IVA              76               116
  STAGE IVB               4                 5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  4P LOSS MUTATED   16 37 40 48
  4P LOSS WILD-TYPE 24 71 45 83
D47V4, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  T1              16                24
  T2              37                71
  T3              40                45
  T4              48                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
  4P LOSS MUTATED   51 22 54  4
  4P LOSS WILD-TYPE 85 34 75  3
D47V5, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  N0              51                85
  N1              22                34
  N2              54                75
  N3               4                 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"
D47V6, binary
                   cls
clus                 0  1
  4P LOSS MUTATED   33 22
  4P LOSS WILD-TYPE 75 26
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     33   22
  4P LOSS WILD-TYPE   75   26
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  M0              33                75
  MX              22                26
[1] 2 2
[1] FALSE
D47V7, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    41 115
  4P LOSS WILD-TYPE  80 181
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     41  115
  4P LOSS WILD-TYPE   80  181
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE              41                80
  MALE               115               181
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  4P LOSS MUTATED                                     153
  4P LOSS WILD-TYPE                                   257
                   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                                                     3
  4P LOSS WILD-TYPE                                                   3
D47V8, multiclass
                                                             clus
vv                                                            4P LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                   153
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       3
                                                             clus
vv                                                            4P LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     257
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                 1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                         3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V9, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    30 126
  4P LOSS WILD-TYPE  49 212
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     30  126
  4P LOSS WILD-TYPE   49  212
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  NO               30                49
  YES             126               212
[1] 2 2
[1] FALSE
D47V10, continuous
D47V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4P LOSS MUTATED                                  0     3
  4P LOSS WILD-TYPE                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4P LOSS MUTATED                          14   133
  4P LOSS WILD-TYPE                        19   228
D47V12, multiclass
                                  clus
vv                                 4P LOSS MUTATED 4P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          3                 7
  BLACK OR AFRICAN AMERICAN                     14                19
  WHITE                                        133               228
[1] 4 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    10 142
  4P LOSS WILD-TYPE   8 239
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     10  142
  4P LOSS WILD-TYPE    8  239
                        clus
vv                       4P LOSS MUTATED 4P LOSS WILD-TYPE
  HISPANIC OR LATINO                  10                 8
  NOT HISPANIC OR LATINO             142               239
[1] 2 2
[1] FALSE

Clustering(48) Variable = 4Q LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                 0   1
  4Q LOSS MUTATED    77  30
  4Q LOSS WILD-TYPE 180  68
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              107               248 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               30                68 
$`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-A6D8 TCGA-BA-A6DB TCGA-BB-4227 TCGA-BB-7870 TCGA-BB-7871 
         895          513          216          133         1153          428 
TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4725 TCGA-CN-4728 
        1955          624            5            4          485          613 
TCGA-CN-4729 TCGA-CN-4735 TCGA-CN-4737 TCGA-CN-4739 TCGA-CN-4742 TCGA-CN-5359 
         392          369          240         1330         1988         1980 
TCGA-CN-5360 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6018 TCGA-CN-6019 
        1081          630          424          629           45          432 
TCGA-CN-6021 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 
        1970          611          119          429           46          443 
TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63W TCGA-CQ-5323 TCGA-CQ-6224 
         447          225          526          348         1466          985 
TCGA-CQ-6228 TCGA-CQ-7064 TCGA-CQ-7067 TCGA-CQ-A4C9 TCGA-CQ-A4CI TCGA-CR-5248 
        1959         1378          509          613          608         1663 
TCGA-CR-6472 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-7365 TCGA-CR-7367 
        1050          354          234          379         1191         1440 
TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7383 
         105         1979          759          889           30         1954 
TCGA-CR-7392 TCGA-CR-7398 TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 
         946          156         1472          522         1950         3295 
TCGA-CV-5435 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5444 TCGA-CV-5976 TCGA-CV-6003 
        1438          546         1978         2437         1478         1665 
TCGA-CV-6441 TCGA-CV-6935 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6954 TCGA-CV-7091 
        1970         1969         1959         3835         1957         1959 
TCGA-CV-7097 TCGA-CV-7101 TCGA-CV-7180 TCGA-CV-7248 TCGA-CV-7261 TCGA-CV-7418 
        1970         1939         1987         1967         1099         1955 
TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7430 TCGA-CV-7435 TCGA-CV-7440 TCGA-CX-7086 
        1957         1947         1972         1959         1981          237 
TCGA-CX-7219 TCGA-D6-6823 TCGA-DQ-5629 TCGA-DQ-7589 TCGA-DQ-7592 TCGA-F7-A50G 
         828          701          516          575          299           15 
TCGA-F7-A61S TCGA-H7-A6C5 TCGA-HD-8634 TCGA-HD-A6HZ TCGA-IQ-A61H TCGA-IQ-A61J 
           3          403           24          111          412          440 
TCGA-MT-A67G TCGA-P3-A5QA TCGA-P3-A6SX TCGA-QK-A6IF TCGA-QK-A6IG 
         112         1652         1954          245          218 

$`4Q LOSS WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 
         462          415         1983          248          722         1288 
TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 
        1762          725         1636         1747          190          644 
TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A6DA TCGA-BA-A6DE TCGA-BB-4217 
          63          384          236          351          182          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          452          462          993          642          395 
TCGA-CN-4738 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 
        1960          811         1268          488          512          173 
TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 
        1977         1980         1966         1966         1975          413 
TCGA-CN-5374 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6020 TCGA-CN-6022 
         290          433          594          629           98          202 
TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6992 TCGA-CN-6996 TCGA-CN-A63V 
         424          224          318          394          432          484 
TCGA-CN-A63Y TCGA-CN-A641 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 
         175          367         1207          654         1660         1422 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 
         896         1399          317          341          129          870 
TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7065 
        1000         1057         1959          815         1461         1007 
TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CA 
        1309          901          877          968         1960         1963 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5243 
         545          548          393          391          303         2562 
TCGA-CR-5247 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 
         358         1152          799         1777         1521         1966 
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-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7368 
         345          350          479         1956         1435         1245 
TCGA-CR-7369 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7385 
        1960          972         1968         1036          796          997 
TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7393 
        1430         1951          392          907          913          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-5436 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5966 
        1955          584         2886         2327         1958          519 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 
         406          701         2641         1840          215         1315 
TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6934 TCGA-CV-6936 TCGA-CV-6943 TCGA-CV-6945 
         641         1899         1948         1952         1948         1969 
TCGA-CV-6952 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7095 TCGA-CV-7099 
        1966         1969         1959         3837         1970         1936 
TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7242 
        1959         1945         1979         1724         1444         1095 
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-7427 TCGA-CV-7428 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-A45O 
        1937         1973         1937         1984         1958          851 
TCGA-CV-A45Q TCGA-CV-A461 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CX-7082 
        1945         1954         1970          750          717          317 
TCGA-CX-7085 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 
         321          773          292           77          491          154 
TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-DQ-5624 
         568          106          128          112          104         1778 
TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7590 TCGA-DQ-7591 
        1081         1030          548         1965          775          622 
TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 
         369          368          324          340          564          490 
TCGA-F7-8489 TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 
         658           92          585          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-8224 TCGA-HD-8314 TCGA-HD-8635 
           5           25           37           55           44           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-A61L TCGA-IQ-A61O 
         122          441          588          360          351          360 
TCGA-KU-A66S TCGA-KU-A66T TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D 
         224          210           14           34          392           56 
TCGA-MT-A67F TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6T0 
         111          254          910          721         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 
         225           64 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                3                 2 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             3835              3837 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            623.0             639.5 
[1] "3.0 - 3835.0 (623.0)" "2.0 - 3837.0 (639.5)"
[1] "hr=" "1.3"
D48V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  4Q LOSS MUTATED         9       14        26        59         0
  4Q LOSS WILD-TYPE      15       49        45       133         9
D48V3, multiclass
           clus
vv          4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  STAGE I                 9                15
  STAGE II               14                49
  STAGE III              26                45
  STAGE IVA              59               133
  STAGE IVB               0                 9
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  4Q LOSS MUTATED   12 28 32 36
  4Q LOSS WILD-TYPE 28 80 53 95
D48V4, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  T1              12                28
  T2              28                80
  T3              32                53
  T4              36                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
  4Q LOSS MUTATED    35  20  42   0
  4Q LOSS WILD-TYPE 101  36  87   7
D48V5, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  N0              35               101
  N1              20                36
  N2              42                87
  N3               0                 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"
D48V6, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED   25 16
  4Q LOSS WILD-TYPE 83 32
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     25   16
  4Q LOSS WILD-TYPE   83   32
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  M0              25                83
  MX              16                32
[1] 2 2
[1] FALSE
D48V7, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    34  87
  4Q LOSS WILD-TYPE  87 209
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     34   87
  4Q LOSS WILD-TYPE   87  209
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE              34                87
  MALE                87               209
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  4Q LOSS MUTATED                                     120
  4Q LOSS WILD-TYPE                                   290
                   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                                                     1
  4Q LOSS WILD-TYPE                                                   5
D48V8, multiclass
                                                             clus
vv                                                            4Q LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                   120
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       1
                                                             clus
vv                                                            4Q LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     290
  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"
D48V9, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    29  92
  4Q LOSS WILD-TYPE  50 246
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     29   92
  4Q LOSS WILD-TYPE   50  246
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  NO               29                50
  YES              92               246
[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                                0     6
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4Q LOSS MUTATED                          12    98
  4Q LOSS WILD-TYPE                        21   263
D48V12, multiclass
                                  clus
vv                                 4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          4                 6
  BLACK OR AFRICAN AMERICAN                     12                21
  WHITE                                         98               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"
D48V13, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED     8 109
  4Q LOSS WILD-TYPE  10 272
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      8  109
  4Q LOSS WILD-TYPE   10  272
                        clus
vv                       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   8                10
  NOT HISPANIC OR LATINO             109               272
[1] 2 2
[1] FALSE

Clustering(49) Variable = 5P LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                 0   1
  5P LOSS MUTATED    24   4
  5P LOSS WILD-TYPE 233  94
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               28               327 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                4                94 
$`5P LOSS MUTATED`
TCGA-BA-6871 TCGA-BA-A6DA TCGA-BB-4224 TCGA-BB-7871 TCGA-CN-5355 TCGA-CN-5356 
          63          351          278          428          488          512 
TCGA-CN-6988 TCGA-CN-A63U TCGA-CQ-5332 TCGA-CQ-7069 TCGA-CQ-A4C9 TCGA-CQ-A4CE 
         318          526          317          901          613          393 
TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7372 TCGA-CR-7379 TCGA-CV-5432 TCGA-CV-5976 
        1956         1435          759         1036         1950         1478 
TCGA-CV-5977 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-7242 TCGA-CV-7248 TCGA-CV-7435 
        1840         1315         1665         1095         1967         1959 
TCGA-F7-A50G TCGA-IQ-A61G TCGA-IQ-A61H TCGA-QK-A6IH 
          15          360          412          228 

$`5P LOSS 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-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-6872 
        1636         1747          190          644          451          384 
TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A6D8 TCGA-BA-A6DB TCGA-BA-A6DE 
         113          236          895          513          216          182 
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-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-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 
         485          142          452          613          392          462 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 
         993          642          369          395          240         1960 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5358 TCGA-CN-5359 
        1330          811         1268         1988          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-6013 
         413          290          630          424          629          433 
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-6023 TCGA-CN-6024 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 
         202          424          224          611          394          119 
TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63T 
         432          429           46          443          447          225 
TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 TCGA-CQ-5323 TCGA-CQ-5324 
         484          348          175          367         1466         1207 
TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 
         654         1660         1422          896         1399          341 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 
         129          870         1000         1057          985         1959 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 
        1959          815         1461         1378         1007          509 
TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CA TCGA-CQ-A4CB 
        1309          877          968         1960         1963          545 
TCGA-CQ-A4CD TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 
         548          391          303          608         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-7382 
        1979          889           30          972         1968          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-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 
         522         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-5978 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 
         701         2641          215          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-7235 TCGA-CV-7238 TCGA-CV-7243 
        1945         1987         1979         1724         1444          954 
TCGA-CV-7245 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 
         797         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-A461 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CX-7082 TCGA-CX-7085 
        1954         1970          750          717          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-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 
         491          154          568          106          128          112 
TCGA-D6-A4ZB TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 
         104         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          564          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-F7-A623 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 
           6          407           58          133          414          403 
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-A61J TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-MT-A51W 
         440          351          360          224          210           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-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 
         910         1652          721         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 
         218          225           64 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               15                 2 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             1967              3837 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            569.5             629.0 
[1] "15.0 - 1967.0 (569.5)" "2.0 - 3837.0 (629.0)" 
[1] "hr=" "1.1"
D49V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  5P LOSS MUTATED         2        6         9        21         1
  5P LOSS WILD-TYPE      22       57        62       171         8
D49V3, multiclass
           clus
vv          5P LOSS MUTATED 5P LOSS WILD-TYPE
  STAGE I                 2                22
  STAGE II                6                57
  STAGE III               9                62
  STAGE IVA              21               171
  STAGE IVB               1                 8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  5P LOSS MUTATED     2  11  11  15
  5P LOSS WILD-TYPE  38  97  74 116
D49V4, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  T1               2                38
  T2              11                97
  T3              11                74
  T4              15               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
  5P LOSS MUTATED    11   5  19   0
  5P LOSS WILD-TYPE 125  51 110   7
D49V5, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  N0              11               125
  N1               5                51
  N2              19               110
  N3               0                 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"
D49V6, binary
                   cls
clus                 0  1
  5P LOSS MUTATED    9  5
  5P LOSS WILD-TYPE 99 43
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      9    5
  5P LOSS WILD-TYPE   99   43
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  M0               9                99
  MX               5                43
[1] 2 2
[1] FALSE
D49V7, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    14  26
  5P LOSS WILD-TYPE 107 270
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     14   26
  5P LOSS WILD-TYPE  107  270
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE              14               107
  MALE                26               270
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  5P LOSS MUTATED                                      40
  5P LOSS WILD-TYPE                                   370
                   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                                                     0
  5P LOSS WILD-TYPE                                                   6
D49V8, multiclass
                                                             clus
vv                                                            5P LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    40
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       0
                                                             clus
vv                                                            5P LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     370
  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"
D49V9, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     3  37
  5P LOSS WILD-TYPE  76 301
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      3   37
  5P LOSS WILD-TYPE   76  301
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  NO                3                76
  YES              37               301
[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                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5P LOSS MUTATED                           4    34
  5P LOSS WILD-TYPE                        29   327
D49V12, multiclass
                                  clus
vv                                 5P LOSS MUTATED 5P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      4                29
  WHITE                                         34               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"
D49V13, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     3  33
  5P LOSS WILD-TYPE  15 348
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      3   33
  5P LOSS WILD-TYPE   15  348
                        clus
vv                       5P LOSS MUTATED 5P LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                15
  NOT HISPANIC OR LATINO              33               348
[1] 2 2
[1] FALSE

Clustering(50) Variable = 5Q LOSS MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                 0   1
  5Q LOSS MUTATED    88  25
  5Q LOSS WILD-TYPE 169  73
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              113               242 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               25                73 
$`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-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BB-4217 
         236          513          351          216          182          187 
TCGA-BB-4224 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A47Z 
         278         1153          428         1955          624            5 
TCGA-CN-4725 TCGA-CN-4727 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4737 
         485          452          392          462          993          240 
TCGA-CN-4739 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5360 TCGA-CN-5366 
        1330         1988          488          512         1081         1966 
TCGA-CN-6010 TCGA-CN-6012 TCGA-CN-6019 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6992 
         630          629          432          224          318          394 
TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A641 TCGA-CQ-5332 TCGA-CQ-6227 TCGA-CQ-6229 
         526          348          367          317         1959          815 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-A4C9 TCGA-CQ-A4CE TCGA-CQ-A4CH 
        1378         1007          901          613          393          303 
TCGA-CQ-A4CI TCGA-CR-5247 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6488 TCGA-CR-6493 
         608          358         1971          514          379         1956 
TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 
        1435         1191         1245         1960          105         1979 
TCGA-CR-7372 TCGA-CR-7379 TCGA-CR-7390 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7404 
         759         1036          907          156          181         1472 
TCGA-CV-5432 TCGA-CV-5435 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5973 TCGA-CV-5976 
        1950         1438         1978         2886         2641         1478 
TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6960 TCGA-CV-7090 
        1840          215         1315         1665         1969         3837 
TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7101 TCGA-CV-7180 TCGA-CV-7242 TCGA-CV-7243 
        1959         1970         1939         1987         1095          954 
TCGA-CV-7248 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7424 TCGA-CV-7435 TCGA-CV-A6JE 
        1967         1976         1099         1947         1959          750 
TCGA-CX-7082 TCGA-CX-7086 TCGA-D6-6823 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 
         317          237          701          548         1965          575 
TCGA-DQ-7592 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-F7-7848 TCGA-F7-A50G TCGA-F7-A61W 
         299          368          324          564           15           14 
TCGA-H7-A6C4 TCGA-HD-7753 TCGA-HD-7917 TCGA-IQ-A61G TCGA-IQ-A61H TCGA-KU-A66T 
         414            5           37          360          412          210 
TCGA-MT-A67D TCGA-P3-A6SX TCGA-QK-A652 TCGA-QK-A6IH TCGA-QK-A6IJ 
          56         1954          357          228           64 

$`5Q LOSS WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 
         462          415         1983          248          722         1288 
TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 
        1762          725          623         1636         1747          190 
TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-A4IF TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-4227 
         644          451          895         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          613 
TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4740 TCGA-CN-4741 
         642          369          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 
         413          290          424          433          594          629 
TCGA-CN-6018 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6989 
          45           98         1970          202          424          611 
TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49B 
         119          432          429           46          443          447 
TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63Y TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
         225          484          175         1466         1207          654 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 
        1660         1422          896         1399          341          129 
TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6228 TCGA-CQ-7063 
         870         1000         1057          985         1959         1461 
TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CA 
         509         1309          877          968         1960         1963 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CG TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 
         545          548          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-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-7367 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7376 
         350          479         1440          889           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-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-7401 TCGA-CR-7402 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5434 
         216         1077          911         1955          522         3295 
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-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 
         406          701          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-7097 TCGA-CV-7099 TCGA-CV-7100 
        1966         1957         1959         1970         1936         1959 
TCGA-CV-7102 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7245 TCGA-CV-7250 
        1945         1979         1724         1444          797         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-7440 TCGA-CV-A45O 
        1972         1937         1984         1958         1981          851 
TCGA-CV-A45Q TCGA-CV-A461 TCGA-CV-A6JD TCGA-CV-A6JN TCGA-CX-7085 TCGA-CX-7219 
        1945         1954         1970          717          321          828 
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-DQ-5624 TCGA-DQ-5625 
         106          128          112          104         1778         1081 
TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7593 TCGA-DQ-7596 
         516         1030          775          622          369          340 
TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V 
         490          658           92          585            3          384 
TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C5 
          13            6          407           58          133          403 
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-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-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67F 
         360          224           14           34          392          111 
TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW 
         112          254          910         1652          721         1120 
TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A6IF 
         578         1917         1968          400          553          245 
TCGA-QK-A6IG TCGA-QK-A6II 
         218          225 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                5                 2 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             3837              3835 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              548               656 
[1] "5.0 - 3837.0 (548.0)" "2.0 - 3835.0 (656.0)"
[1] "hr=" "1.4"
D50V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  5Q LOSS MUTATED         5       22        27        63         2
  5Q LOSS WILD-TYPE      19       41        44       129         7
D50V3, multiclass
           clus
vv          5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  STAGE I                 5                19
  STAGE II               22                41
  STAGE III              27                44
  STAGE IVA              63               129
  STAGE IVB               2                 7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  5Q LOSS MUTATED    6 40 28 45
  5Q LOSS WILD-TYPE 34 68 57 86
D50V4, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  T1               6                34
  T2              40                68
  T3              28                57
  T4              45                86
[1] 4 2
[1] 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   38 21 47  1
  5Q LOSS WILD-TYPE 98 35 82  6
D50V5, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  N0              38                98
  N1              21                35
  N2              47                82
  N3               1                 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"
D50V6, binary
                   cls
clus                 0  1
  5Q LOSS MUTATED   34 14
  5Q LOSS WILD-TYPE 74 34
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     34   14
  5Q LOSS WILD-TYPE   74   34
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  M0              34                74
  MX              14                34
[1] 2 2
[1] FALSE
D50V7, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    34  99
  5Q LOSS WILD-TYPE  87 197
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     34   99
  5Q LOSS WILD-TYPE   87  197
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE              34                87
  MALE                99               197
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  5Q LOSS MUTATED                                     132
  5Q LOSS WILD-TYPE                                   278
                   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                                                     1
  5Q LOSS WILD-TYPE                                                   5
D50V8, multiclass
                                                             clus
vv                                                            5Q LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                   132
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       1
                                                             clus
vv                                                            5Q LOSS WILD-TYPE
  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                         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"
D50V9, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    25 108
  5Q LOSS WILD-TYPE  54 230
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     25  108
  5Q LOSS WILD-TYPE   54  230
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  NO               25                54
  YES             108               230
[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                                0     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5Q LOSS MUTATED                          14   109
  5Q LOSS WILD-TYPE                        19   252
D50V12, multiclass
                                  clus
vv                                 5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          5                 5
  BLACK OR AFRICAN AMERICAN                     14                19
  WHITE                                        109               252
[1] 4 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     5 122
  5Q LOSS WILD-TYPE  13 259
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      5  122
  5Q LOSS WILD-TYPE   13  259
                        clus
vv                       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   5                13
  NOT HISPANIC OR LATINO             122               259
[1] 2 2
[1] FALSE

Clustering(51) Variable = 6P LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                 0   1
  6P LOSS MUTATED    31  17
  6P LOSS WILD-TYPE 226  81
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               48               307 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               17                81 
$`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          485          613 
TCGA-CN-4729 TCGA-CN-4735 TCGA-CN-4740 TCGA-CN-5359 TCGA-CN-6010 TCGA-CN-6024 
         392          369          811         1980          630          224 
TCGA-CN-6994 TCGA-CN-6997 TCGA-CN-A63T TCGA-CQ-5332 TCGA-CQ-6223 TCGA-CQ-A4C9 
         119          429          225          317         1057          613 
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-D6-6823 TCGA-D6-6826 TCGA-DQ-5624 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7591 
         701          154         1778         1965          575          622 
TCGA-F7-A623 TCGA-HD-A6HZ TCGA-IQ-A61G TCGA-MT-A67G TCGA-P3-A5QA TCGA-P3-A6T0 
           6          111          360          112         1652          578 

$`6P LOSS 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-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-6871 TCGA-BA-6872 TCGA-BA-6873 
         190          644          451           63          384          113 
TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE 
         236          895          513          351          216          182 
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-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-4726 TCGA-CN-4727 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4736 
         142          452          462          993          642          395 
TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 
         240         1960         1330         1268         1988          488 
TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 
         512          173         1081         1977         1980         1966 
TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6012 
        1966         1975          413          290          424          629 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 
         433          594          629           45          432           98 
TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 
        1970          202          424          318          611          394 
TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63U TCGA-CN-A63V 
         432           46          443          447          526          484 
TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
         348          175          367         1466         1207          654 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 
        1660         1422          896         1399          341          129 
TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 
         870         1000          985         1959         1959          815 
TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 
        1461         1378         1007          509         1309          901 
TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD 
         877          968         1960         1963          545          548 
TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 
         393          391          303          608         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-6491 TCGA-CR-6492 
         311          345          354          234          350          479 
TCGA-CR-7364 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7372 
        1435         1440         1245         1960          105          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-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-7398 
         946          908          898          930          216          156 
TCGA-CR-7401 TCGA-CR-7402 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5435 
        1077          911         1955          522         1950         1438 
TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5966 TCGA-CV-5970 
         546         1978         2886         2327          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-6934 TCGA-CV-6935 TCGA-CV-6936 
        1665          641         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-6961 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 
        1959         3837         1959         1970         1936         1959 
TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7242 
        1945         1987         1979         1724         1444         1095 
TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7250 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 
         954          797         1960         1099         1974         1948 
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-A461 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CX-7082 TCGA-CX-7085 
        1954         1970          750          717          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-DQ-5625 
         568          106          128          112          104         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          564          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-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-A61H 
        1057          485          122          441          588          412 
TCGA-IQ-A61J TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-MT-A51W 
         440          351          360          224          210           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-A5QE TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-P3-A6T8 
         721         1120         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 
          64 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                6                 2 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             3295              3837 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            665.5             624.0 
[1] "6.0 - 3295.0 (665.5)" "2.0 - 3837.0 (624.0)"
[1] "hr=" "1.1"
D51V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  6P LOSS MUTATED         1        8        10        30         0
  6P LOSS WILD-TYPE      23       55        61       162         9
D51V3, multiclass
           clus
vv          6P LOSS MUTATED 6P LOSS WILD-TYPE
  STAGE I                 1                23
  STAGE II                8                55
  STAGE III              10                61
  STAGE IVA              30               162
  STAGE IVB               0                 9
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  6P LOSS MUTATED     4  12  14  19
  6P LOSS WILD-TYPE  36  96  71 112
D51V4, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  T1               4                36
  T2              12                96
  T3              14                71
  T4              19               112
[1] 4 2
[1] 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    15   7  20   0
  6P LOSS WILD-TYPE 121  49 109   7
D51V5, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  N0              15               121
  N1               7                49
  N2              20               109
  N3               0                 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"
D51V6, binary
                   cls
clus                 0  1
  6P LOSS MUTATED   11  7
  6P LOSS WILD-TYPE 97 41
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     11    7
  6P LOSS WILD-TYPE   97   41
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  M0              11                97
  MX               7                41
[1] 2 2
[1] FALSE
D51V7, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    13  43
  6P LOSS WILD-TYPE 108 253
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     13   43
  6P LOSS WILD-TYPE  108  253
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE              13               108
  MALE                43               253
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  6P LOSS MUTATED                                      56
  6P LOSS WILD-TYPE                                   354
                   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                                                     0
  6P LOSS WILD-TYPE                                                   6
D51V8, multiclass
                                                             clus
vv                                                            6P LOSS 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                       0
                                                             clus
vv                                                            6P LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     354
  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"
D51V9, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    12  44
  6P LOSS WILD-TYPE  67 294
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     12   44
  6P LOSS WILD-TYPE   67  294
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  NO               12                67
  YES              44               294
[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                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6P LOSS MUTATED                          10    42
  6P LOSS WILD-TYPE                        23   319
D51V12, multiclass
                                  clus
vv                                 6P LOSS MUTATED 6P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                     10                23
  WHITE                                         42               319
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V13, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     5  46
  6P LOSS WILD-TYPE  13 335
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      5   46
  6P LOSS WILD-TYPE   13  335
                        clus
vv                       6P LOSS MUTATED 6P LOSS WILD-TYPE
  HISPANIC OR LATINO                   5                13
  NOT HISPANIC OR LATINO              46               335
[1] 2 2
[1] FALSE

Clustering(52) Variable = 6Q LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                 0   1
  6Q LOSS MUTATED    37  13
  6Q LOSS WILD-TYPE 220  85
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               50               305 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               13                85 
$`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          485          613 
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 
         119          367         1057         1960          613         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         1724         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-P3-A6SW TCGA-P3-A6T0 
        1120          578 

$`6Q LOSS 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-5153 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6868 
         722         1762          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-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BB-4217 
         895          513          351          216          182          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-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-4726 TCGA-CN-4727 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 
         142          452          462          993          642          369 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4741 TCGA-CN-4742 
         395          240         1960         1330         1268         1988 
TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 
         488          512          173         1081         1977         1980 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6011 
        1966         1966         1975          413          290          424 
TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 
         629          433          594          629           45          432 
TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6989 TCGA-CN-6992 
          98         1970          202          424          611          394 
TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63T 
         432          429           46          443          447          225 
TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CQ-5323 TCGA-CQ-5324 
         526          484          348          175         1466         1207 
TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 
         654         1660         1422          896         1399          317 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6224 TCGA-CQ-6227 
         341          129          870         1000          985         1959 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 
        1959          815         1461         1378         1007          509 
TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4CA TCGA-CQ-A4CB 
        1309          901          877          968         1963          545 
TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 
         548          393          391          303          608         2562 
TCGA-CR-5247 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 
         358         1152          799         1777         1521         1966 
TCGA-CR-6472 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 
        1050         1971          514         1969          362          311 
TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6492 TCGA-CR-6493 
         345          354          234          379          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-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 
         759           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-7402 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 
         156         1077          911         1955          522         1950 
TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5966 
        1438          584          546         2886         2327          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-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-6960 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 
        1969         1959         3837         1970         1936         1959 
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-7261 TCGA-CV-7406 TCGA-CV-7410 
         797         1967         1960         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-7435 TCGA-CV-7440 TCGA-CV-A45O 
        1937         1984         1958         1959         1981          851 
TCGA-CV-A45Q TCGA-CV-A461 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CX-7082 
        1945         1954         1970          750          717          317 
TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6824 
         321          237          828          773          292           77 
TCGA-D6-6825 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB 
         491          568          106          128          112          104 
TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-7590 TCGA-DQ-7592 TCGA-DQ-7593 
        1081          516         1030          775          299          369 
TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 
         368          324          340          564          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-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-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-MT-A51W TCGA-MT-A51X TCGA-MT-A67A 
         360          224          210           14           34          392 
TCGA-MT-A67D TCGA-MT-A67F TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE 
          56          111          254          910         1652          721 
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 
         245          218          228          225           64 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                6                 2 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             3295              3837 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              756               623 
[1] "6.0 - 3295.0 (756.0)" "2.0 - 3837.0 (623.0)"
[1] "hr=" "1.4"
D52V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  6Q LOSS MUTATED         1        8        10        27         1
  6Q LOSS WILD-TYPE      23       55        61       165         8
D52V3, multiclass
           clus
vv          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  STAGE I                 1                23
  STAGE II                8                55
  STAGE III              10                61
  STAGE IVA              27               165
  STAGE IVB               1                 8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  6Q LOSS MUTATED     4  12  10  21
  6Q LOSS WILD-TYPE  36  96  75 110
D52V4, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T1               4                36
  T2              12                96
  T3              10                75
  T4              21               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
  6Q LOSS MUTATED    16   8  16   1
  6Q LOSS WILD-TYPE 120  48 113   6
D52V5, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  N0              16               120
  N1               8                48
  N2              16               113
  N3               1                 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"
D52V6, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED   12  7
  6Q LOSS WILD-TYPE 96 41
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     12    7
  6Q LOSS WILD-TYPE   96   41
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  M0              12                96
  MX               7                41
[1] 2 2
[1] FALSE
D52V7, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    11  46
  6Q LOSS WILD-TYPE 110 250
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     11   46
  6Q LOSS WILD-TYPE  110  250
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE              11               110
  MALE                46               250
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  6Q LOSS MUTATED                                      56
  6Q LOSS WILD-TYPE                                   354
                   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                                                   5
D52V8, multiclass
                                                             clus
vv                                                            6Q LOSS 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                       1
                                                             clus
vv                                                            6Q LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     354
  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"
D52V9, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    12  45
  6Q LOSS WILD-TYPE  67 293
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     12   45
  6Q LOSS WILD-TYPE   67  293
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  NO               12                67
  YES              45               293
[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                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6Q LOSS MUTATED                           9    46
  6Q LOSS WILD-TYPE                        24   315
D52V12, multiclass
                                  clus
vv                                 6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      9                24
  WHITE                                         46               315
[1] 4 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  50
  6Q LOSS WILD-TYPE  15 331
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      3   50
  6Q LOSS WILD-TYPE   15  331
                        clus
vv                       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                15
  NOT HISPANIC OR LATINO              50               331
[1] 2 2
[1] FALSE

Clustering(53) Variable = 7P LOSS MUTATION ANALYSIS
D53V1, survival
                   sevent
clus2                 0   1
  7P LOSS MUTATED    16   4
  7P LOSS WILD-TYPE 241  94
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               20               335 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                4                94 
$`7P LOSS MUTATED`
TCGA-BA-5559 TCGA-BA-A6DE TCGA-CN-5374 TCGA-CN-6992 TCGA-CN-6998 TCGA-CN-A49B 
        1747          182          290          394           46          447 
TCGA-CN-A63U TCGA-CN-A63W TCGA-CR-6473 TCGA-CV-5435 TCGA-CV-6003 TCGA-CV-7242 
         526          348         1125         1438         1665         1095 
TCGA-CV-7430 TCGA-CV-7433 TCGA-CX-7082 TCGA-F7-A50G TCGA-F7-A623 TCGA-HD-A6HZ 
        1972         1984          317           15            6          111 
TCGA-MZ-A6I9 TCGA-QK-A6IH 
         254          228 

$`7P LOSS 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-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-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB 
         113          236          895          513          351          216 
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-4727 TCGA-CN-4728 
         799          721          485          142          452          613 
TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 
         392          462          993          642          369          395 
TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 
         240         1960         1330          811         1268         1988 
TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 
         488          512          173         1980         1081         1977 
TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6010 
        1980         1966         1966         1975          413          630 
TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 
         424          629          433          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          424          224 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-A498 
         318          611          119          432          429          443 
TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A641 TCGA-CQ-5323 TCGA-CQ-5324 
         225          484          175          367         1466         1207 
TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 
         654         1660         1422          896         1399          317 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 
         341          129          870         1000         1057          985 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 
        1959         1959          815         1461         1378         1007 
TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 
         509         1309          901          877          968         1960 
TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG 
         613         1963          545          548          393          391 
TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 
         303          608         2562          358         1663         1152 
TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6474 
         799         1777         1521         1966         1050         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-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-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-5439 
        1955          522         1950         3295          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-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-7243 TCGA-CV-7245 TCGA-CV-7248 
        1979         1724         1444          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-7424 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7432 TCGA-CV-7434 
        1957         1947         1937         1973         1937         1958 
TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A461 TCGA-CV-A6JD 
        1959         1981          851         1945         1954         1970 
TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 
         750          717          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-DQ-5624 TCGA-DQ-5625 
         106          128          112          104         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 
         564          490          658           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-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-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-IQ-A61O 
         588          360          412          440          351          360 
TCGA-KU-A66S TCGA-KU-A66T TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D 
         224          210           14           34          392           56 
TCGA-MT-A67F TCGA-MT-A67G TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW 
         111          112          910         1652          721         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 
         357          245          218          225           64 

  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                6                 2 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
             1984              3837 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
              371               638 
[1] "6.0 - 1984.0 (371.0)" "2.0 - 3837.0 (638.0)"
[1] "hr=" "1.1"
D53V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  7P LOSS MUTATED         0        2         4        11         1
  7P LOSS WILD-TYPE      24       61        67       181         8
D53V3, multiclass
           clus
vv          7P LOSS MUTATED 7P LOSS WILD-TYPE
  STAGE I                 0                24
  STAGE II                2                61
  STAGE III               4                67
  STAGE IVA              11               181
  STAGE IVB               1                 8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  7P LOSS MUTATED     1   6   5   6
  7P LOSS WILD-TYPE  39 102  80 125
D53V4, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  T1               1                39
  T2               6               102
  T3               5                80
  T4               6               125
[1] 4 2
[1] 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     3   4  11   0
  7P LOSS WILD-TYPE 133  52 118   7
D53V5, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  N0               3               133
  N1               4                52
  N2              11               118
  N3               0                 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"
D53V6, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     5   4
  7P LOSS WILD-TYPE 103  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      5    4
  7P LOSS WILD-TYPE  103   44
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  M0               5               103
  MX               4                44
[1] 2 2
[1] FALSE
D53V7, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     7  14
  7P LOSS WILD-TYPE 114 282
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      7   14
  7P LOSS WILD-TYPE  114  282
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  FEMALE               7               114
  MALE                14               282
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  7P LOSS MUTATED                                      21
  7P LOSS WILD-TYPE                                   389
                   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                                                     0
  7P LOSS WILD-TYPE                                                   6
D53V8, multiclass
                                                             clus
vv                                                            7P LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    21
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       0
                                                             clus
vv                                                            7P LOSS 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                         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"
D53V9, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     3  18
  7P LOSS WILD-TYPE  76 320
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      3   18
  7P LOSS WILD-TYPE   76  320
     clus
vv    7P LOSS MUTATED 7P LOSS WILD-TYPE
  NO                3                76
  YES              18               320
[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                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7P LOSS MUTATED                           0    21
  7P LOSS WILD-TYPE                        33   340
D53V12, multiclass
                                  clus
vv                                 7P LOSS MUTATED 7P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      0                33
  WHITE                                         21               340
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V13, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     0  21
  7P LOSS WILD-TYPE  18 360
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      0   21
  7P LOSS WILD-TYPE   18  360
                        clus
vv                       7P LOSS MUTATED 7P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                18
  NOT HISPANIC OR LATINO              21               360
[1] 2 2
[1] FALSE

Clustering(54) Variable = 7Q LOSS MUTATION ANALYSIS
D54V1, survival
                   sevent
clus2                 0   1
  7Q LOSS MUTATED    26   8
  7Q LOSS WILD-TYPE 231  90
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               34               321 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                8                90 
$`7Q LOSS MUTATED`
TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-5152 TCGA-BA-5559 TCGA-BA-A6DE TCGA-BB-4224 
         462          415         1288         1747          182          278 
TCGA-BB-7863 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4737 TCGA-CN-5359 TCGA-CN-5374 
         423          462          993          240         1980          290 
TCGA-CN-6998 TCGA-CN-A49B TCGA-CN-A63U TCGA-CN-A63W TCGA-CR-6474 TCGA-CR-7365 
          46          447          526          348         1971         1191 
TCGA-CR-7374 TCGA-CR-7398 TCGA-CV-5444 TCGA-CV-6003 TCGA-CV-6954 TCGA-CV-7180 
          30          156         2437         1665         1957         1987 
TCGA-CV-7433 TCGA-CX-7082 TCGA-D6-6823 TCGA-F7-8489 TCGA-F7-A50G TCGA-HD-A6HZ 
        1984          317          701          658           15          111 
TCGA-IQ-7632 TCGA-KU-A66T TCGA-MZ-A6I9 TCGA-P3-A5QE 
         441          210          254          721 

$`7Q LOSS WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5153 
         283         1983          276          248          722         1762 
TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 
         520          725          623         1636          190          644 
TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF 
         451           63          384          113          236          895 
TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4225 
         513          351          216          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-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          485          142          452 
TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4738 
         613          392          642          369          395         1960 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 
        1330          811         1268         1988          488          512 
TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 
         173         1081         1977         1980         1966         1966 
TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 
        1975          413          630          424          629          433 
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-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 
         202          424          224          318          611          394 
TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-A498 TCGA-CN-A63T TCGA-CN-A63V 
         119          432          429          443          225          484 
TCGA-CN-A63Y TCGA-CN-A641 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 
         175          367         1466         1207          654         1660 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 
        1422          896         1399          317          341          129 
TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 
         870         1000         1057          985         1959         1959 
TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 
         815         1461         1378         1007          509         1309 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CA 
         901          877          968         1960          613         1963 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI 
         545          548          393          391          303          608 
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-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-7376 
        1960          105         1979          759          889          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-7399 TCGA-CR-7401 TCGA-CR-7402 
         898          930          216          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-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-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-7183 
        1970         1936         1959         1939         1945         1979 
TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 
        1724         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-7424 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 
        1957         1947         1937         1973         1972         1937 
TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A461 
        1958         1959         1981          851         1945         1954 
TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 
        1970          750          717          321          237          828 
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-DQ-5624 TCGA-DQ-5625 
         106          128          112          104         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 
         564          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-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-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-A61E 
          10           33         1057          485          122          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-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-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 
         910         1652         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 
         228          225           64 

  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               15                 2 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
             2437              3837 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            454.5             638.0 
[1] "15.0 - 2437.0 (454.5)" "2.0 - 3837.0 (638.0)" 
[1] "hr=" "1.5"
D54V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  7Q LOSS MUTATED         1        5         7        20         0
  7Q LOSS WILD-TYPE      23       58        64       172         9
D54V3, multiclass
           clus
vv          7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  STAGE I                 1                23
  STAGE II                5                58
  STAGE III               7                64
  STAGE IVA              20               172
  STAGE IVB               0                 9
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  7Q LOSS MUTATED     1  14   6  12
  7Q LOSS WILD-TYPE  39  94  79 119
D54V4, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  T1               1                39
  T2              14                94
  T3               6                79
  T4              12               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
  7Q LOSS MUTATED    10   7  13   0
  7Q LOSS WILD-TYPE 126  49 116   7
D54V5, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  N0              10               126
  N1               7                49
  N2              13               116
  N3               0                 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"
D54V6, binary
                   cls
clus                 0  1
  7Q LOSS MUTATED   10  6
  7Q LOSS WILD-TYPE 98 42
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED     10    6
  7Q LOSS WILD-TYPE   98   42
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  M0              10                98
  MX               6                42
[1] 2 2
[1] FALSE
D54V7, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED    12  25
  7Q LOSS WILD-TYPE 109 271
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED     12   25
  7Q LOSS WILD-TYPE  109  271
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  FEMALE              12               109
  MALE                25               271
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  7Q LOSS MUTATED                                      36
  7Q LOSS WILD-TYPE                                   374
                   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                                                     1
  7Q LOSS WILD-TYPE                                                   5
D54V8, multiclass
                                                             clus
vv                                                            7Q 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                       1
                                                             clus
vv                                                            7Q LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     374
  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"
D54V9, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     8  29
  7Q LOSS WILD-TYPE  71 309
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      8   29
  7Q LOSS WILD-TYPE   71  309
     clus
vv    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  NO                8                71
  YES              29               309
[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                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7Q LOSS MUTATED                           2    35
  7Q LOSS WILD-TYPE                        31   326
D54V12, multiclass
                                  clus
vv                                 7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      2                31
  WHITE                                         35               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"
D54V13, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     1  35
  7Q LOSS WILD-TYPE  17 346
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      1   35
  7Q LOSS WILD-TYPE   17  346
                        clus
vv                       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                17
  NOT HISPANIC OR LATINO              35               346
[1] 2 2
[1] FALSE

Clustering(55) Variable = 8P LOSS MUTATION ANALYSIS
D55V1, survival
                   sevent
clus2                 0   1
  8P LOSS MUTATED    86  41
  8P LOSS WILD-TYPE 171  57
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              127               228 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               41                57 
$`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          513          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          485 
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          413          290          424          433 
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-A49B TCGA-CN-A63U TCGA-CN-A641 TCGA-CQ-5332 TCGA-CQ-5334 TCGA-CQ-6227 
         447          526          367          317          129         1959 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 
        1959          815         1461         1378         1007          509 
TCGA-CQ-7069 TCGA-CQ-A4C6 TCGA-CQ-A4CB TCGA-CR-5247 TCGA-CR-6471 TCGA-CR-6474 
         901          968          545          358         1966         1971 
TCGA-CR-6484 TCGA-CR-6488 TCGA-CR-7364 TCGA-CR-7369 TCGA-CR-7372 TCGA-CR-7373 
         354          379         1435         1960          759          889 
TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7388 TCGA-CR-7399 TCGA-CR-7401 
          30          972         1968         1951          181         1077 
TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5441 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5973 
        1950         3295         2886         2437          519         2641 
TCGA-CV-6436 TCGA-CV-6935 TCGA-CV-6942 TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6960 
        1899         1969         3835         1966         1957         1969 
TCGA-CV-7090 TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7242 
        3837         1959         1945         1724         1444         1095 
TCGA-CV-7248 TCGA-CV-7261 TCGA-CV-7422 TCGA-CV-7427 TCGA-CV-7434 TCGA-CV-7440 
        1967         1099         1957         1937         1958         1981 
TCGA-CV-A6JD TCGA-CX-7219 TCGA-D6-6517 TCGA-D6-6825 TCGA-D6-A4Z9 TCGA-DQ-5624 
        1970          828          292          491          112         1778 
TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7592 TCGA-F7-8298 TCGA-F7-8489 
        1081         1030          548          299          490          658 
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          210           34 
TCGA-MZ-A6I9 TCGA-P3-A5QA TCGA-P3-A6SX TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 
         254         1652         1954          400          553          357 
TCGA-QK-A6IH 
         228 

$`8P LOSS WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 
         283         1983          276         1288         1762          520 
TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6871 
         725          623         1747          190          644           63 
TCGA-BA-A4IF TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 
         895          351          216          187         2878          278 
TCGA-BB-4225 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 
         140          558          310          687          638         1153 
TCGA-BB-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4727 
         436         1955          624          799          721          452 
TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 
         613          392          462          993          642          369 
TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-5355 
         240         1960         1330          811         1268          488 
TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5366 TCGA-CN-6010 TCGA-CN-6012 
         512          173         1980         1966          630          629 
TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 
         629           45          432         1970          202          424 
TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6998 TCGA-CN-A63T 
         224          318          611          119           46          225 
TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
         484          348          175         1466         1207          654 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-6218 
        1660         1422          896         1399          341          870 
TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-A4C7 
        1000         1057          985         1309          877         1960 
TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH 
         613         1963          548          393          391          303 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 
         608         2562         1663         1152          799         1777 
TCGA-CR-6470 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 
        1521         1050         1125          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-7365 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7379 
        1191         1440         1245          105         1979         1036 
TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7389 TCGA-CR-7390 
         796         1954          997         1430          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-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5435 
         156          911         1472         1955          522         1438 
TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5970 
         584          546         1978         2327         1958          406 
TCGA-CV-5971 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 
         701         1478         1840          215         1315         1665 
TCGA-CV-6433 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6943 
         641         1970         1948         1952         1959         1948 
TCGA-CV-6945 TCGA-CV-6961 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 
        1969         1959         1959         1970         1970         1936 
TCGA-CV-7101 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7250 
        1939         1987         1979          954          797         1960 
TCGA-CV-7254 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7424 TCGA-CV-7428 
        1976         1974         1948         1955         1947         1973 
TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7435 TCGA-CV-A45O TCGA-CV-A45Q 
        1972         1937         1984         1959          851         1945 
TCGA-CV-A461 TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 
        1954          750          717          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-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 
         128          104          516         1965          575          775 
TCGA-DQ-7591 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 
         622          369          368          324          340          564 
TCGA-F7-A50G TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-A6C4 
          15            3          384            6          407          414 
TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8314 TCGA-HD-8634 
         403            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-MT-A51W TCGA-MT-A67A TCGA-MT-A67D 
         441          360          224           14          392           56 
TCGA-MT-A67F TCGA-MT-A67G TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6T0 
         111          112          910          721         1120          578 
TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6II TCGA-QK-A6IJ 
        1917         1968          245          218          225           64 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                4                 2 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             3837              2878 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              536               649 
[1] "4.0 - 3837.0 (536.0)" "2.0 - 2878.0 (649.0)"
[1] "hr=" "1"  
D55V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  8P LOSS MUTATED        10       19        32        72         4
  8P LOSS WILD-TYPE      14       44        39       120         5
D55V3, multiclass
           clus
vv          8P LOSS MUTATED 8P LOSS WILD-TYPE
  STAGE I                10                14
  STAGE II               19                44
  STAGE III              32                39
  STAGE IVA              72               120
  STAGE IVB               4                 5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  8P LOSS MUTATED   17 34 38 49
  8P LOSS WILD-TYPE 23 74 47 82
D55V4, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  T1              17                23
  T2              34                74
  T3              38                47
  T4              49                82
[1] 4 2
[1] 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   45 25 52  2
  8P LOSS WILD-TYPE 91 31 77  5
D55V5, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  N0              45                91
  N1              25                31
  N2              52                77
  N3               2                 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"
D55V6, binary
                   cls
clus                 0  1
  8P LOSS MUTATED   44 19
  8P LOSS WILD-TYPE 64 29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     44   19
  8P LOSS WILD-TYPE   64   29
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  M0              44                64
  MX              19                29
[1] 2 2
[1] FALSE
D55V7, binary
                   cls
clus                  0   1
  8P LOSS MUTATED    51 101
  8P LOSS WILD-TYPE  70 195
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     51  101
  8P LOSS WILD-TYPE   70  195
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE              51                70
  MALE               101               195
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  8P LOSS MUTATED                                     152
  8P LOSS WILD-TYPE                                   258
                   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                                                     0
  8P LOSS WILD-TYPE                                                   6
D55V8, multiclass
                                                             clus
vv                                                            8P 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                       0
                                                             clus
vv                                                            8P LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     258
  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"
D55V9, binary
                   cls
clus                  0   1
  8P LOSS MUTATED    29 123
  8P LOSS WILD-TYPE  50 215
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     29  123
  8P LOSS WILD-TYPE   50  215
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  NO               29                50
  YES             123               215
[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                                0     4
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8P LOSS MUTATED                          13   127
  8P LOSS WILD-TYPE                        20   234
D55V12, multiclass
                                  clus
vv                                 8P LOSS MUTATED 8P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          6                 4
  BLACK OR AFRICAN AMERICAN                     13                20
  WHITE                                        127               234
[1] 4 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     9 135
  8P LOSS WILD-TYPE   9 246
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      9  135
  8P LOSS WILD-TYPE    9  246
                        clus
vv                       8P LOSS MUTATED 8P LOSS WILD-TYPE
  HISPANIC OR LATINO                   9                 9
  NOT HISPANIC OR LATINO             135               246
[1] 2 2
[1] FALSE

Clustering(56) Variable = 8Q LOSS MUTATION ANALYSIS
D56V1, survival
                   sevent
clus2                 0   1
  8Q LOSS MUTATED    14   6
  8Q LOSS WILD-TYPE 243  92
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               20               335 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                6                92 
$`8Q LOSS MUTATED`
TCGA-BA-4076 TCGA-BA-A6D8 TCGA-CN-4726 TCGA-CN-5360 TCGA-CN-5367 TCGA-CN-6011 
         415          513          142         1081         1966          424 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-A63U TCGA-CN-A641 TCGA-CQ-7063 TCGA-CQ-7064 
         433          594          526          367         1461         1378 
TCGA-CR-6471 TCGA-CV-7242 TCGA-CV-7261 TCGA-CV-7440 TCGA-CV-A6JD TCGA-H7-8502 
        1966         1095         1099         1981         1970          133 
TCGA-IQ-7630 TCGA-MZ-A6I9 
         485          254 

$`8Q LOSS WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 
         462          283         1983          276          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-6871 TCGA-BA-6872 
        1747          190          644          451           63          384 
TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE 
         113          236          895          351          216          182 
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-4727 TCGA-CN-4728 TCGA-CN-4729 
         799          721          485          452          613          392 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 
         462          993          642          369          395          240 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 
        1960         1330          811         1268         1988          488 
TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 
         512          173         1980         1977         1980         1966 
TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6012 TCGA-CN-6017 
        1975          413          290          630          629          629 
TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 
          45          432           98         1970          202          424 
TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 
         224          318          611          394          119          432 
TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63V 
         429           46          443          447          225          484 
TCGA-CN-A63W TCGA-CN-A63Y TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 
         348          175         1466         1207          654         1660 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 
        1422          896         1399          317          341          129 
TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 
         870         1000         1057          985         1959         1959 
TCGA-CQ-6229 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 
         815         1007          509         1309          901          877 
TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD 
         968         1960          613         1963          545          548 
TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 
         393          391          303          608         2562          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-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-6488 TCGA-CR-6491 TCGA-CR-6492 
         345          354          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-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-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-7097 TCGA-CV-7099 
        1959         3837         1959         1970         1970         1936 
TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 
        1959         1939         1945         1987         1979         1724 
TCGA-CV-7238 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7254 
        1444          954          797         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-A45O TCGA-CV-A45Q TCGA-CV-A461 TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CX-7082 
         851         1945         1954          750          717          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-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 
         112          104         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-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 
         369          368          324          340          564          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-A6C4 
          14           13            6          407           58          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-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-A61L TCGA-IQ-A61O TCGA-KU-A66S 
         360          412          440          351          360          224 
TCGA-KU-A66T TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F 
         210           14           34          392           56          111 
TCGA-MT-A67G TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX 
         112          910         1652          721         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 
         245          218          228          225           64 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
              133                 2 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             1981              3837 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
              560               629 
[1] "133.0 - 1981.0 (560.0)" "2.0 - 3837.0 (629.0)"  
[1] "hr=" "1.1"
D56V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  8Q LOSS MUTATED         1        3         4        14         0
  8Q LOSS WILD-TYPE      23       60        67       178         9
D56V3, multiclass
           clus
vv          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  STAGE I                 1                23
  STAGE II                3                60
  STAGE III               4                67
  STAGE IVA              14               178
  STAGE IVB               0                 9
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  8Q LOSS MUTATED     1   3   7  11
  8Q LOSS WILD-TYPE  39 105  78 120
D56V4, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  T1               1                39
  T2               3               105
  T3               7                78
  T4              11               120
[1] 4 2
[1] 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     6   4   9   0
  8Q LOSS WILD-TYPE 130  52 120   7
D56V5, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  N0               6               130
  N1               4                52
  N2               9               120
  N3               0                 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"
D56V6, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     8   4
  8Q LOSS WILD-TYPE 100  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      8    4
  8Q LOSS WILD-TYPE  100   44
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  M0               8               100
  MX               4                44
[1] 2 2
[1] FALSE
D56V7, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     5  20
  8Q LOSS WILD-TYPE 116 276
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      5   20
  8Q LOSS WILD-TYPE  116  276
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE               5               116
  MALE                20               276
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  8Q LOSS MUTATED                                      25
  8Q LOSS WILD-TYPE                                   385
                   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                                                     0
  8Q LOSS WILD-TYPE                                                   6
D56V8, multiclass
                                                             clus
vv                                                            8Q LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    25
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       0
                                                             clus
vv                                                            8Q LOSS 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                         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"
D56V9, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     6  19
  8Q LOSS WILD-TYPE  73 319
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      6   19
  8Q LOSS WILD-TYPE   73  319
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  NO                6                73
  YES              19               319
[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                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8Q LOSS MUTATED                           1    23
  8Q LOSS WILD-TYPE                        32   338
D56V12, multiclass
                                  clus
vv                                 8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      1                32
  WHITE                                         23               338
[1] 4 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  22
  8Q LOSS WILD-TYPE  16 359
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      2   22
  8Q LOSS WILD-TYPE   16  359
                        clus
vv                       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                16
  NOT HISPANIC OR LATINO              22               359
[1] 2 2
[1] FALSE

Clustering(57) Variable = 9P LOSS MUTATION ANALYSIS
D57V1, survival
                   sevent
clus2                 0   1
  9P LOSS MUTATED    82  41
  9P LOSS WILD-TYPE 175  57
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              123               232 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               41                57 
$`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          513 
TCGA-BA-A6DE TCGA-BB-4224 TCGA-BB-7862 TCGA-BB-7872 TCGA-BB-8601 TCGA-CN-4723 
         182          278          536          436          624          721 
TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4735 
         142          452          392          462          993          369 
TCGA-CN-4737 TCGA-CN-4740 TCGA-CN-5360 TCGA-CN-5373 TCGA-CN-6018 TCGA-CN-6020 
         240          811         1081          413           45           98 
TCGA-CN-6021 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6997 
        1970          224          318          611          394          429 
TCGA-CN-A63W TCGA-CN-A641 TCGA-CQ-5332 TCGA-CQ-6221 TCGA-CQ-6228 TCGA-CQ-7064 
         348          367          317         1000         1959         1378 
TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7069 TCGA-CQ-A4CB TCGA-CR-5247 TCGA-CR-6472 
        1007          509          901          545          358         1050 
TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-7364 TCGA-CR-7365 
        1971          514          379          350         1435         1191 
TCGA-CR-7368 TCGA-CR-7372 TCGA-CR-7374 TCGA-CR-7383 TCGA-CR-7388 TCGA-CR-7390 
        1245          759           30         1954         1951          907 
TCGA-CR-7398 TCGA-CR-7401 TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5435 TCGA-CV-5436 
         156         1077         1955         1950         1438          584 
TCGA-CV-5439 TCGA-CV-5444 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5979 TCGA-CV-6441 
         546         2437         2641         1478         1315         1970 
TCGA-CV-6934 TCGA-CV-6945 TCGA-CV-6960 TCGA-CV-7091 TCGA-CV-7097 TCGA-CV-7101 
        1948         1969         1969         1959         1970         1939 
TCGA-CV-7180 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7422 TCGA-CV-7430 
        1987         1095          954          797         1957         1972 
TCGA-CV-7432 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A461 TCGA-CX-7082 
        1937         1958         1959         1981         1954          317 
TCGA-CX-7086 TCGA-D6-6823 TCGA-D6-6826 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 
         237          701          154          106          128          112 
TCGA-D6-A4ZB TCGA-DQ-5629 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7595 TCGA-F7-7848 
         104          516          548         1965          324          564 
TCGA-F7-A50I TCGA-F7-A61W TCGA-F7-A623 TCGA-H7-A6C5 TCGA-HD-7753 TCGA-HD-7754 
          92           14            6          403            5           25 
TCGA-HD-8635 TCGA-HD-A633 TCGA-HD-A6HZ TCGA-IQ-7630 TCGA-IQ-A61G TCGA-IQ-A61J 
          25           49          111          485          360          440 
TCGA-KU-A66T TCGA-MT-A51X TCGA-MT-A67D TCGA-P3-A6SX TCGA-P3-A6T4 TCGA-P3-A6T8 
         210           34           56         1954         1968          400 
TCGA-QK-A64Z TCGA-QK-A6IH TCGA-QK-A6IJ 
         553          228           64 

$`9P LOSS WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 
         283         1983          248          722         1288         1762 
TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6873 TCGA-BA-A6DA 
         725          623         1636         1747          113          351 
TCGA-BA-A6DB TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 
         216          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          485          613 
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 
         488          512          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          424 
TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6022 
         629          433          594          629          432          202 
TCGA-CN-6023 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49B 
         424          119          432           46          443          447 
TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63Y TCGA-CQ-5323 TCGA-CQ-5324 
         225          526          484          175         1466         1207 
TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 
         654         1660         1422          896         1399          341 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6229 
         129          870         1057          985         1959          815 
TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
        1461         1309          877          968         1960          613 
TCGA-CQ-A4CA TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI 
        1963          548          393          391          303          608 
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-6473 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 
        1966         1125         1969          362          311          345 
TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7367 TCGA-CR-7369 
         354          234          479         1956         1440         1960 
TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7373 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 
         105         1979          889          972         1968         1036 
TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7389 TCGA-CR-7391 TCGA-CR-7392 
         796          997         1430          392          913          946 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7399 TCGA-CR-7402 
         908          898          930          216          181          911 
TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5434 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 
        1472          522         3295         1978         2886         2327 
TCGA-CV-5443 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5977 TCGA-CV-5978 
        1958          519          406          701         1840          215 
TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6941 
        1665          641         1899         1969         1952         1959 
TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6961 TCGA-CV-7090 
        3835         1948         1966         1957         1959         3837 
TCGA-CV-7095 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7183 TCGA-CV-7235 
        1970         1936         1959         1945         1979         1724 
TCGA-CV-7238 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7406 
        1444         1967         1960         1976         1099         1974 
TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7433 
        1948         1955         1947         1937         1973         1984 
TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CX-7085 
         851         1945         1970          750          717          321 
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-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 
        1778         1081         1030          575          775          622 
TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7596 TCGA-F7-8298 TCGA-F7-8489 
         299          369          368          340          490          658 
TCGA-F7-A50G TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A620 TCGA-H7-7774 
          15          585            3          384           13          407 
TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-HD-7229 TCGA-HD-7917 TCGA-HD-8224 
          58          133          414            2           37           55 
TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-A4C1 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 
          44           24           11           10           33         1057 
TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61H TCGA-IQ-A61L TCGA-IQ-A61O 
         122          441          588          412          351          360 
TCGA-KU-A66S TCGA-MT-A51W TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 
         224           14          392          111          112          254 
TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6T0 TCGA-P3-A6T2 
         910         1652          721         1120          578         1917 
TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6II 
         357          245          218          225 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                5                 2 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             2641              3837 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              516               719 
[1] "5.0 - 2641.0 (516.0)" "2.0 - 3837.0 (719.0)"
[1] "hr=" "1.7"
D57V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  9P LOSS MUTATED         8       22        24        67         2
  9P LOSS WILD-TYPE      16       41        47       125         7
D57V3, multiclass
           clus
vv          9P LOSS MUTATED 9P LOSS WILD-TYPE
  STAGE I                 8                16
  STAGE II               22                41
  STAGE III              24                47
  STAGE IVA              67               125
  STAGE IVB               2                 7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  9P LOSS MUTATED   13 43 26 42
  9P LOSS WILD-TYPE 27 65 59 89
D57V4, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  T1              13                27
  T2              43                65
  T3              26                59
  T4              42                89
[1] 4 2
[1] 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   45 22 47  1
  9P LOSS WILD-TYPE 91 34 82  6
D57V5, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  N0              45                91
  N1              22                34
  N2              47                82
  N3               1                 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"
D57V6, binary
                   cls
clus                 0  1
  9P LOSS MUTATED   31 16
  9P LOSS WILD-TYPE 77 32
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     31   16
  9P LOSS WILD-TYPE   77   32
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  M0              31                77
  MX              16                32
[1] 2 2
[1] FALSE
D57V7, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    37 105
  9P LOSS WILD-TYPE  84 191
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     37  105
  9P LOSS WILD-TYPE   84  191
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE              37                84
  MALE               105               191
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  9P LOSS MUTATED                                     142
  9P LOSS WILD-TYPE                                   268
                   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                                                     0
  9P LOSS WILD-TYPE                                                   6
D57V8, multiclass
                                                             clus
vv                                                            9P LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                   142
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT               0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                       0
                                                             clus
vv                                                            9P LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     268
  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"
D57V9, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    28 114
  9P LOSS WILD-TYPE  51 224
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     28  114
  9P LOSS WILD-TYPE   51  224
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  NO               28                51
  YES             114               224
[1] 2 2
[1] FALSE
D57V10, continuous
D57V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9P LOSS MUTATED                                  0     3
  9P LOSS WILD-TYPE                                1     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9P LOSS MUTATED                          14   123
  9P LOSS WILD-TYPE                        19   238
D57V12, multiclass
                                  clus
vv                                 9P LOSS MUTATED 9P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          3                 7
  BLACK OR AFRICAN AMERICAN                     14                19
  WHITE                                        123               238
[1] 4 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     6 129
  9P LOSS WILD-TYPE  12 252
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      6  129
  9P LOSS WILD-TYPE   12  252
                        clus
vv                       9P LOSS MUTATED 9P LOSS WILD-TYPE
  HISPANIC OR LATINO                   6                12
  NOT HISPANIC OR LATINO             129               252
[1] 2 2
[1] FALSE

Clustering(58) Variable = 9Q LOSS MUTATION ANALYSIS
D58V1, survival
                   sevent
clus2                 0   1
  9Q LOSS MUTATED    36  20
  9Q LOSS WILD-TYPE 221  78
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               56               299 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               20                78 
$`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          513 
TCGA-BB-8601 TCGA-CN-4740 TCGA-CN-6018 TCGA-CN-6020 TCGA-CN-6024 TCGA-CN-A63W 
         624          811           45           98          224          348 
TCGA-CQ-6221 TCGA-CQ-6228 TCGA-CQ-7067 TCGA-CQ-7069 TCGA-CR-5247 TCGA-CR-6472 
        1000         1959          509          901          358         1050 
TCGA-CR-6474 TCGA-CR-7364 TCGA-CR-7365 TCGA-CR-7372 TCGA-CR-7374 TCGA-CR-7390 
        1971         1435         1191          759           30          907 
TCGA-CV-5430 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5441 TCGA-CV-5973 TCGA-CV-5979 
        1955         1438          584         2886         2641         1315 
TCGA-CV-6441 TCGA-CV-6945 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7101 
        1970         1969         1959         1970         1970         1939 
TCGA-CV-7180 TCGA-CV-7243 TCGA-CV-7430 TCGA-CV-7435 TCGA-CV-7440 TCGA-CX-7082 
        1987          954         1972         1959         1981          317 
TCGA-D6-6823 TCGA-DQ-5631 TCGA-F7-7848 TCGA-F7-A50I TCGA-F7-A623 TCGA-H7-A6C5 
         701          548          564           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          210 
TCGA-MT-A67D TCGA-QK-A6IJ 
          56           64 

$`9Q LOSS WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 
         283          415         1983          276          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-6872 TCGA-BA-6873 TCGA-BA-A6DA 
        1747          190          644          384          113          351 
TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 
         216          182          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-C9-A47Z 
         638         1153          428          436         1955            5 
TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 
           4          799          721          485          142          452 
TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 
         613          392          462          993          642          369 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4741 TCGA-CN-4742 
         395          240         1960         1330         1268         1988 
TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 
         488          512          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          413          290 
TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 
         630          424          629          433          594          629 
TCGA-CN-6019 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6988 TCGA-CN-6989 
         432         1970          202          424          318          611 
TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 
         394          119          432          429           46          443 
TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A641 
         447          225          526          484          175          367 
TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 
        1466         1207          654         1660         1422          896 
TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6223 
        1399          317          341          129          870         1057 
TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 
         985         1959          815         1461         1378         1007 
TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CA 
        1309          877          968         1960          613         1963 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI 
         545          548          393          391          303          608 
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-6473 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 
        1966         1125          514         1969          362          311 
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-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 
        1956         1440         1245         1960          105         1979 
TCGA-CR-7373 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 
         889          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-5431 TCGA-CV-5432 TCGA-CV-5434 
        1077          911         1472          522         1950         3295 
TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 
         546         1978         2327         1958         2437          519 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-6003 
         406          701         1478         1840          215         1665 
TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6941 
         641         1899         1948         1969         1952         1959 
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-7090 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7183 TCGA-CV-7235 
        3837         1936         1959         1945         1979         1724 
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-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-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-A45O 
        1937         1973         1937         1984         1958          851 
TCGA-CV-A45Q TCGA-CV-A461 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CX-7085 
        1945         1954         1970          750          717          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-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB 
         154          568          106          128          112          104 
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-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50J TCGA-F7-A61S 
         340          490          658           15          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-HD-7229 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 
         414            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-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67F 
         360          224           14           34          392          111 
TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW 
         112          254          910         1652          721         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 
         357          245          218          228          225 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                5                 2 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             2886              3837 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            662.5             629.0 
[1] "5.0 - 2886.0 (662.5)" "2.0 - 3837.0 (629.0)"
[1] "hr=" "1"  
D58V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  9Q LOSS MUTATED         4       12        12        30         0
  9Q LOSS WILD-TYPE      20       51        59       162         9
D58V3, multiclass
           clus
vv          9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  STAGE I                 4                20
  STAGE II               12                51
  STAGE III              12                59
  STAGE IVA              30               162
  STAGE IVB               0                 9
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  9Q LOSS MUTATED     7  24   9  19
  9Q LOSS WILD-TYPE  33  84  76 112
D58V4, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T1               7                33
  T2              24                84
  T3               9                76
  T4              19               112
[1] 4 2
[1] 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    20  11  21   0
  9Q LOSS WILD-TYPE 116  45 108   7
D58V5, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  N0              20               116
  N1              11                45
  N2              21               108
  N3               0                 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"
D58V6, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED   16 10
  9Q LOSS WILD-TYPE 92 38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     16   10
  9Q LOSS WILD-TYPE   92   38
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  M0              16                92
  MX              10                38
[1] 2 2
[1] FALSE
D58V7, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    19  47
  9Q LOSS WILD-TYPE 102 249
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     19   47
  9Q LOSS WILD-TYPE  102  249
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE              19               102
  MALE                47               249
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  9Q LOSS MUTATED                                      66
  9Q LOSS WILD-TYPE                                   344
                   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                                                   6
D58V8, multiclass
                                                             clus
vv                                                            9Q LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    66
  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                                     344
  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"
D58V9, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    14  52
  9Q LOSS WILD-TYPE  65 286
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     14   52
  9Q LOSS WILD-TYPE   65  286
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  NO               14                65
  YES              52               286
[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                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9Q LOSS MUTATED                           7    57
  9Q LOSS WILD-TYPE                        26   304
D58V12, multiclass
                                  clus
vv                                 9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      7                26
  WHITE                                         57               304
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V13, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED     5  57
  9Q LOSS WILD-TYPE  13 324
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      5   57
  9Q LOSS WILD-TYPE   13  324
                        clus
vv                       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   5                13
  NOT HISPANIC OR LATINO              57               324
[1] 2 2
[1] FALSE

Clustering(59) Variable = 10P LOSS MUTATION ANALYSIS
D59V1, survival
                    sevent
clus2                  0   1
  10P LOSS MUTATED    68  42
  10P LOSS WILD-TYPE 189  56
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               110                245 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                42                 56 
$`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-BB-7870 TCGA-BB-7872 TCGA-BB-8601 
         113          895          513         1153          436          624 
TCGA-C9-A47Z TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4737 TCGA-CN-5355 TCGA-CN-5359 
           5          721          485          240          488         1980 
TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6018 
        1081         1977          290          424          629           45 
TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6996 TCGA-CN-6998 
         432           98          224          318          432           46 
TCGA-CN-A63U TCGA-CN-A63W TCGA-CQ-5323 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6228 
         526          348         1466         1057          985         1959 
TCGA-CQ-7064 TCGA-CQ-7069 TCGA-CQ-A4C7 TCGA-CR-6474 TCGA-CR-6484 TCGA-CR-7365 
        1378          901         1960         1971          354         1191 
TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7372 TCGA-CR-7373 
        1440         1245         1960          105          759          889 
TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7386 TCGA-CR-7389 TCGA-CR-7398 TCGA-CV-5435 
         796         1954         1430          392          156         1438 
TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5977 TCGA-CV-5979 TCGA-CV-6936 TCGA-CV-6941 
        2437          519         1840         1315         1952         1959 
TCGA-CV-6942 TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7097 
        3835         1966         1957         1959         3837         1970 
TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 
        1959         1939         1945         1095          954          797 
TCGA-CV-7248 TCGA-CV-7406 TCGA-CV-7418 TCGA-CV-7424 TCGA-CV-7428 TCGA-CV-7432 
        1967         1974         1955         1947         1973         1937 
TCGA-CV-7434 TCGA-CV-A6JD TCGA-CX-7219 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6826 
        1958         1970          828          292          701          154 
TCGA-D6-A4ZB TCGA-DQ-5629 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7590 TCGA-DQ-7593 
         104          516          548         1965          775          369 
TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A61V TCGA-F7-A620 TCGA-HD-8635 
         658           15           92          384           13           25 
TCGA-HD-A633 TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J TCGA-KU-A66T TCGA-MT-A51X 
          49          360          412          440          210           34 
TCGA-MZ-A6I9 TCGA-P3-A6SX TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A64Z 
         254         1954         1917         1968          400          553 
TCGA-QK-A6IF TCGA-QK-A6IH 
         245          228 

$`10P LOSS WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5153 
         462          415         1983          248          722         1762 
TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6869 TCGA-BA-6871 
         520          725          623         1636          644           63 
TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BB-4217 
         384          236          351          216          182          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-7871 TCGA-BB-8596 
         536          423          687          638          428         1955 
TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 
           4          799          142          452          613          392 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4738 
         462          993          642          369          395         1960 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5358 
        1330          811         1268         1988          512          173 
TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6010 
        1980         1966         1966         1975          413          630 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 
         433          594          629         1970          202          424 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6997 TCGA-CN-A498 TCGA-CN-A49B 
         611          394          119          429          443          447 
TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A641 TCGA-CQ-5324 TCGA-CQ-5325 
         225          484          175          367         1207          654 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 
        1660         1422          896         1399          317          341 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7063 
         129          870         1000         1959          815         1461 
TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C9 
        1007          509         1309          877          968          613 
TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH 
        1963          545          548          393          391          303 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 
         608         2562          358         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-6493 TCGA-CR-7364 TCGA-CR-7371 TCGA-CR-7374 
         350          479         1956         1435         1979           30 
TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7385 TCGA-CR-7388 TCGA-CR-7390 
         972         1968         1036          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-5431 
         181         1077          911         1472         1955          522 
TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 
        1950         3295          584          546         1978         2886 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 
        2327         1958          406          701         2641         1478 
TCGA-CV-5978 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 
         215         1665          641         1899         1970         1948 
TCGA-CV-6935 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6960 TCGA-CV-7091 TCGA-CV-7095 
        1969         1948         1969         1969         1959         1970 
TCGA-CV-7099 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7250 
        1936         1987         1979         1724         1444         1960 
TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7410 TCGA-CV-7422 TCGA-CV-7427 TCGA-CV-7430 
        1976         1099         1948         1957         1937         1972 
TCGA-CV-7433 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A461 
        1984         1959         1981          851         1945         1954 
TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-D6-6516 
         750          717          317          321          237          773 
TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 
          77          491          568          106          128          112 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-7589 TCGA-DQ-7591 TCGA-DQ-7592 
        1778         1081         1030          575          622          299 
TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-A50J 
         368          324          340          564          490          585 
TCGA-F7-A61S TCGA-F7-A61W TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 
           3           14            6          407           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-A4C1 TCGA-HD-A634 TCGA-HD-A6HZ 
          55           44           24           11           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-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-MT-A51W TCGA-MT-A67A TCGA-MT-A67D 
         351          360          224           14          392           56 
TCGA-MT-A67F TCGA-MT-A67G TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW 
         111          112          910         1652          721         1120 
TCGA-P3-A6T0 TCGA-QK-A652 TCGA-QK-A6IG TCGA-QK-A6II TCGA-QK-A6IJ 
         578          357          218          225           64 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 5                  2 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              3837               3295 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               767                611 
[1] "5.0 - 3837.0 (767.0)" "2.0 - 3295.0 (611.0)"
[1] "hr=" "1.6"
D59V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  10P LOSS MUTATED         5       18        18        68         3
  10P LOSS WILD-TYPE      19       45        53       124         6
D59V3, multiclass
           clus
vv          10P LOSS MUTATED 10P LOSS WILD-TYPE
  STAGE I                  5                 19
  STAGE II                18                 45
  STAGE III               18                 53
  STAGE IVA               68                124
  STAGE IVB                3                  6
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  10P LOSS MUTATED    8 32 23 49
  10P LOSS WILD-TYPE 32 76 62 82
D59V4, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  T1                8                 32
  T2               32                 76
  T3               23                 62
  T4               49                 82
[1] 4 2
[1] 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   37 19 45  1
  10P LOSS WILD-TYPE 99 37 84  6
D59V5, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  N0               37                 99
  N1               19                 37
  N2               45                 84
  N3                1                  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"
D59V6, binary
                    cls
clus                  0  1
  10P LOSS MUTATED   33 16
  10P LOSS WILD-TYPE 75 32
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     33   16
  10P LOSS WILD-TYPE   75   32
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  M0               33                 75
  MX               16                 32
[1] 2 2
[1] FALSE
D59V7, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    31  96
  10P LOSS WILD-TYPE  90 200
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     31   96
  10P LOSS WILD-TYPE   90  200
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE               31                 90
  MALE                 96                200
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  10P LOSS MUTATED                                     127
  10P LOSS WILD-TYPE                                   283
                    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                                                   6
D59V8, multiclass
                                                             clus
vv                                                            10P LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    127
  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                                      283
  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"
D59V9, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    28  99
  10P LOSS WILD-TYPE  51 239
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     28   99
  10P LOSS WILD-TYPE   51  239
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  NO                28                 51
  YES               99                239
[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                                1     6
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10P LOSS MUTATED                          16   105
  10P LOSS WILD-TYPE                        17   256
D59V12, multiclass
                                  clus
vv                                 10P LOSS MUTATED 10P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           4                  6
  BLACK OR AFRICAN AMERICAN                      16                 17
  WHITE                                         105                256
[1] 4 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     6 115
  10P LOSS WILD-TYPE  12 266
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      6  115
  10P LOSS WILD-TYPE   12  266
                        clus
vv                       10P LOSS MUTATED 10P LOSS WILD-TYPE
  HISPANIC OR LATINO                    6                 12
  NOT HISPANIC OR LATINO              115                266
[1] 2 2
[1] FALSE

Clustering(60) Variable = 10Q LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                  0   1
  10Q LOSS MUTATED    47  28
  10Q LOSS WILD-TYPE 210  70
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                75                280 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                28                 70 
$`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-BB-7870 TCGA-BB-8601 TCGA-C9-A47Z TCGA-CN-4725 TCGA-CN-5355 
         513         1153          624            5          485          488 
TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5374 TCGA-CN-6012 TCGA-CN-6018 TCGA-CN-6019 
        1980         1081          290          629           45          432 
TCGA-CN-6020 TCGA-CN-6024 TCGA-CN-6998 TCGA-CN-A63U TCGA-CQ-5332 TCGA-CQ-6224 
          98          224           46          526          317          985 
TCGA-CQ-6228 TCGA-CQ-7064 TCGA-CR-6470 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6484 
        1959         1378         1521         1971          514          354 
TCGA-CR-7365 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7372 TCGA-CR-7373 
        1191         1245         1960          105          759          889 
TCGA-CR-7383 TCGA-CR-7386 TCGA-CR-7389 TCGA-CR-7398 TCGA-CV-5431 TCGA-CV-5432 
        1954         1430          392          156          522         1950 
TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5977 TCGA-CV-5979 TCGA-CV-6936 TCGA-CV-6941 
        3295         1438         1840         1315         1952         1959 
TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7097 TCGA-CV-7101 TCGA-CV-7242 TCGA-CV-7245 
        1959         3837         1970         1939         1095          797 
TCGA-CV-7248 TCGA-CV-7406 TCGA-CV-7418 TCGA-CV-7424 TCGA-CV-7432 TCGA-D6-6823 
        1967         1974         1955         1947         1937          701 
TCGA-D6-A4ZB TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7593 
         104          548         1965          575          775          369 
TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J TCGA-KU-A66T TCGA-MT-A51X TCGA-MZ-A6I9 
         360          412          440          210           34          254 
TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-QK-A6IH 
         578         1917          228 

$`10Q LOSS WILD-TYPE`
TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5153 TCGA-BA-5556 
         415         1983          248          722         1762          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-A6DA TCGA-BA-A6DB 
         384          113          236          895          351          216 
TCGA-BA-A6DE TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 
         182          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-C9-A480 TCGA-CN-4722 TCGA-CN-4723 
         428          436         1955            4          799          721 
TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 
         142          452          613          392          462          993 
TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 
         642          369          395          240         1960         1330 
TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5363 
         811         1268         1988          512          173         1977 
TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6010 
        1980         1966         1966         1975          413          630 
TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6021 TCGA-CN-6022 
         424          433          594          629         1970          202 
TCGA-CN-6023 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 
         424          318          611          394          119          432 
TCGA-CN-6997 TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63W 
         429          443          447          225          484          348 
TCGA-CN-A63Y TCGA-CN-A641 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 
         175          367         1466         1207          654         1660 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 
        1422          896         1399          341          129          870 
TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7065 
        1000         1057         1959          815         1461         1007 
TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 
         509         1309          901          877          968         1960 
TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG 
         613         1963          545          548          393          391 
TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 
         303          608         2562          358         1663         1152 
TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6478 
         799         1777         1966         1050         1125         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-7367 TCGA-CR-7371 TCGA-CR-7374 
         479         1956         1435         1440         1979           30 
TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7388 
         972         1968         1036          796          997         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-7399 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 
         216          181         1077          911         1472         1955 
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-5978 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 
         215         1665          641         1899         1970         1948 
TCGA-CV-6935 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-6954 
        1969         3835         1948         1969         1966         1957 
TCGA-CV-6960 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 
        1969         1959         1970         1936         1959         1945 
TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7243 TCGA-CV-7250 
        1987         1979         1724         1444          954         1960 
TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7410 TCGA-CV-7422 TCGA-CV-7427 TCGA-CV-7428 
        1976         1099         1948         1957         1937         1973 
TCGA-CV-7430 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45O 
        1972         1984         1958         1959         1981          851 
TCGA-CV-A45Q TCGA-CV-A461 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CX-7082 
        1945         1954         1970          750          717          317 
TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6824 
         321          237          828          773          292           77 
TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 
         491          154          568          106          128          112 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-7591 TCGA-DQ-7592 
        1778         1081          516         1030          622          299 
TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 
         368          324          340          564          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-F7-A623 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 
          13            6          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-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-MT-A51W TCGA-MT-A67A 
         588          351          360          224           14          392 
TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE 
          56          111          112          910         1652          721 
TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 
        1120         1954         1968          400          553          357 
TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6II TCGA-QK-A6IJ 
         245          218          225           64 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 5                  2 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              3837               3835 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             759.0              617.5 
[1] "5.0 - 3837.0 (759.0)" "2.0 - 3835.0 (617.5)"
[1] "hr=" "1.5"
D60V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  10Q LOSS MUTATED         3       14        11        45         1
  10Q LOSS WILD-TYPE      21       49        60       147         8
D60V3, multiclass
           clus
vv          10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  STAGE I                  3                 21
  STAGE II                14                 49
  STAGE III               11                 60
  STAGE IVA               45                147
  STAGE IVB                1                  8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  10Q LOSS MUTATED     5  23  18  28
  10Q LOSS WILD-TYPE  35  85  67 103
D60V4, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T1                5                 35
  T2               23                 85
  T3               18                 67
  T4               28                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
  10Q LOSS MUTATED    27   7  33   0
  10Q LOSS WILD-TYPE 109  49  96   7
D60V5, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  N0               27                109
  N1                7                 49
  N2               33                 96
  N3                0                  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"
D60V6, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED   25  8
  10Q LOSS WILD-TYPE 83 40
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     25    8
  10Q LOSS WILD-TYPE   83   40
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  M0               25                 83
  MX                8                 40
[1] 2 2
[1] FALSE
D60V7, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    19  66
  10Q LOSS WILD-TYPE 102 230
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     19   66
  10Q LOSS WILD-TYPE  102  230
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE               19                102
  MALE                 66                230
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  10Q LOSS MUTATED                                      85
  10Q LOSS WILD-TYPE                                   325
                    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                                                   6
D60V8, multiclass
                                                             clus
vv                                                            10Q LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     85
  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                                      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"
D60V9, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    21  64
  10Q LOSS WILD-TYPE  58 274
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     21   64
  10Q LOSS WILD-TYPE   58  274
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  NO                21                 58
  YES               64                274
[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                                1     7
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10Q LOSS MUTATED                          11    71
  10Q LOSS WILD-TYPE                        22   290
D60V12, multiclass
                                  clus
vv                                 10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           3                  7
  BLACK OR AFRICAN AMERICAN                      11                 22
  WHITE                                          71                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"
D60V13, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     5  77
  10Q LOSS WILD-TYPE  13 304
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      5   77
  10Q LOSS WILD-TYPE   13  304
                        clus
vv                       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    5                 13
  NOT HISPANIC OR LATINO               77                304
[1] 2 2
[1] FALSE

Clustering(61) Variable = 11P LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                  0   1
  11P LOSS MUTATED    65  32
  11P LOSS WILD-TYPE 192  66
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                97                258 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                32                 66 
$`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-A6DE TCGA-BB-4227 TCGA-BB-7870 TCGA-BB-8596 TCGA-CN-4728 TCGA-CN-4729 
         182          133         1153         1955          613          392 
TCGA-CN-4735 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-5356 TCGA-CN-5359 TCGA-CN-5363 
         369         1330          811          512         1980         1977 
TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6020 
        1980         1966          290          424          629           98 
TCGA-CN-6021 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6998 TCGA-CN-A498 
        1970          318          611          394           46          443 
TCGA-CN-A63U TCGA-CN-A63Y TCGA-CQ-5332 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-A4CB 
         526          175          317         1959         1959          545 
TCGA-CQ-A4CI TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6481 
         608          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-5977 TCGA-CV-5978 
        1472          522         1950          546         1840          215 
TCGA-CV-6441 TCGA-CV-6936 TCGA-CV-6942 TCGA-CV-6945 TCGA-CV-7091 TCGA-CV-7095 
        1970         1952         3835         1969         1959         1970 
TCGA-CV-7097 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7235 TCGA-CV-7245 TCGA-CV-7430 
        1970         1939         1945         1724          797         1972 
TCGA-CV-7433 TCGA-CV-7435 TCGA-CX-7082 TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-D6-A4ZB 
        1984         1959          317          106          112          104 
TCGA-DQ-5624 TCGA-DQ-5629 TCGA-DQ-7589 TCGA-DQ-7594 TCGA-DQ-7596 TCGA-F7-7848 
        1778          516          575          368          340          564 
TCGA-F7-8298 TCGA-F7-A50I TCGA-F7-A623 TCGA-H7-A6C4 TCGA-HD-7753 TCGA-HD-7917 
         490           92            6          414            5           37 
TCGA-HD-8635 TCGA-HD-A6HZ TCGA-IQ-A61G TCGA-IQ-A61J TCGA-KU-A66T TCGA-MT-A51W 
          25          111          360          440          210           14 
TCGA-MT-A67D TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A6SW TCGA-P3-A6T4 TCGA-P3-A6T8 
          56          112          254         1120         1968          400 
TCGA-QK-A6IH 
         228 

$`11P LOSS WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 
         283          415         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-A4IF TCGA-BA-A6D8 TCGA-BA-A6DA 
         190          644          451          895          513          351 
TCGA-BA-A6DB TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4228 
         216          187         2878          278          140          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-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-4727 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
         485          142          452          462          993          642 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 
         395          240         1960         1268         1988          488 
TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6010 
         173         1081         1966         1975          413          630 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6022 
         433          594          629           45          432          202 
TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-A49B 
         424          224          119          432          429          447 
TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A641 TCGA-CQ-5323 TCGA-CQ-5324 
         225          484          348          367         1466         1207 
TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 
         654         1660         1422          896         1399          341 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6229 
         129          870         1000         1057          985          815 
TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 
        1461         1378         1007          509         1309          901 
TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CD 
         877          968         1960          613         1963          548 
TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5243 TCGA-CR-5249 TCGA-CR-5250 
         393          391          303         2562         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-6480 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 
         362          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-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7376 TCGA-CR-7377 
        1960         1979          759          889          972         1968 
TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7386 TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 
        1036          796         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-7401 TCGA-CR-7402 TCGA-CV-5430 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 
        1077          911         1955         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-6003 
         406          701         2641         1478         1315         1665 
TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6941 TCGA-CV-6943 
         641         1899         1948         1969         1959         1948 
TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7099 
        1966         1957         1969         1959         3837         1936 
TCGA-CV-7100 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 
        1959         1987         1979         1444         1095          954 
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-7440 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A461 TCGA-CV-A6JD 
        1958         1981          851         1945         1954         1970 
TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 
         750          717          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-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7590 
         128         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-HD-7229 TCGA-HD-7754 TCGA-HD-8224 
          58          133          403            2           25           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-A61H 
        1057          485          122          441          588          412 
TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67F 
         351          360          224           34          392          111 
TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 
         910         1652          721         1954          578         1917 
TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6II TCGA-QK-A6IJ 
         553          357          245          218          225           64 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 5                  2 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              3835               3837 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               512                719 
[1] "5.0 - 3835.0 (512.0)" "2.0 - 3837.0 (719.0)"
[1] "hr=" "1.3"
D61V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  11P LOSS MUTATED         5       12        16        50         6
  11P LOSS WILD-TYPE      19       51        55       142         3
D61V3, multiclass
           clus
vv          11P LOSS MUTATED 11P LOSS WILD-TYPE
  STAGE I                  5                 19
  STAGE II                12                 51
  STAGE III               16                 55
  STAGE IVA               50                142
  STAGE IVB                6                  3
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  11P LOSS MUTATED    11  26  22  31
  11P LOSS WILD-TYPE  29  82  63 100
D61V4, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  T1               11                 29
  T2               26                 82
  T3               22                 63
  T4               31                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
  11P LOSS MUTATED    28  11  38   5
  11P LOSS WILD-TYPE 108  45  91   2
D61V5, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  N0               28                108
  N1               11                 45
  N2               38                 91
  N3                5                  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"
D61V6, binary
                    cls
clus                  0  1
  11P LOSS MUTATED   25 14
  11P LOSS WILD-TYPE 83 34
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     25   14
  11P LOSS WILD-TYPE   83   34
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  M0               25                 83
  MX               14                 34
[1] 2 2
[1] FALSE
D61V7, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    29  80
  11P LOSS WILD-TYPE  92 216
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     29   80
  11P LOSS WILD-TYPE   92  216
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE               29                 92
  MALE                 80                216
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  11P LOSS MUTATED                                     107
  11P LOSS WILD-TYPE                                   303
                    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                                                     2
  11P LOSS WILD-TYPE                                                   4
D61V8, multiclass
                                                             clus
vv                                                            11P LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    107
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        2
                                                             clus
vv                                                            11P LOSS 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                          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    22  87
  11P LOSS WILD-TYPE  57 251
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     22   87
  11P LOSS WILD-TYPE   57  251
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  NO                22                 57
  YES               87                251
[1] 2 2
[1] FALSE
D61V10, continuous
D61V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11P LOSS MUTATED                                  0     0
  11P LOSS WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11P LOSS MUTATED                           8    97
  11P LOSS WILD-TYPE                        25   264
D61V12, multiclass
                                  clus
vv                                 11P LOSS MUTATED 11P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 10
  BLACK OR AFRICAN AMERICAN                       8                 25
  WHITE                                          97                264
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V13, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     7  97
  11P LOSS WILD-TYPE  11 284
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      7   97
  11P LOSS WILD-TYPE   11  284
                        clus
vv                       11P LOSS MUTATED 11P LOSS WILD-TYPE
  HISPANIC OR LATINO                    7                 11
  NOT HISPANIC OR LATINO               97                284
[1] 2 2
[1] FALSE

Clustering(62) Variable = 11Q LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                  0   1
  11Q LOSS MUTATED    83  38
  11Q LOSS WILD-TYPE 174  60
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               121                234 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                38                 60 
$`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-A6DA TCGA-BB-7866 TCGA-BB-7870 
         384          113          236          351          638         1153 
TCGA-BB-8596 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4735 TCGA-CN-4739 
        1955          452          613          392          369         1330 
TCGA-CN-4741 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 
        1268         1980         1081         1977         1980         1966 
TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6020 TCGA-CN-6021 
         290          424          629          433           98         1970 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63T 
         611          394           46          443          447          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          815          545         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-5441 TCGA-CV-5970 TCGA-CV-5977 
         522         1950          546         2886          406         1840 
TCGA-CV-6433 TCGA-CV-6441 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6942 TCGA-CV-6945 
         641         1970         1969         1952         3835         1969 
TCGA-CV-6961 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7101 TCGA-CV-7102 
        1959         1959         1970         1970         1939         1945 
TCGA-CV-7235 TCGA-CV-7406 TCGA-CV-7422 TCGA-CV-7433 TCGA-CV-7435 TCGA-CV-A6JE 
        1724         1974         1957         1984         1959          750 
TCGA-CX-7082 TCGA-D6-6825 TCGA-D6-A4Z9 TCGA-DQ-5624 TCGA-DQ-7588 TCGA-DQ-7589 
         317          491          112         1778         1965          575 
TCGA-DQ-7590 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 
         775          369          368          340          564          490 
TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A623 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 
          15           92            6          133          414          403 
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-IQ-A61L TCGA-KU-A66T TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67D 
         440          351          210           14           34           56 
TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T4 TCGA-P3-A6T8 
         112          254         1120         1954         1968          400 
TCGA-QK-A6IH 
         228 

$`11Q LOSS WILD-TYPE`
TCGA-BA-4075 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5556 
         283          722         1288         1762          520          725 
TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 
         623         1636         1747          644          451           63 
TCGA-BA-A4IF TCGA-BA-A6D8 TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BB-4217 TCGA-BB-4223 
         895          513          216          182          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-7871 TCGA-BB-7872 TCGA-BB-8601 TCGA-C9-A47Z 
         423          687          428          436          624            5 
TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4730 
           4          799          721          485          142          462 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4740 
         993          642          395          240         1960          811 
TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5367 TCGA-CN-5370 
        1988          488          512          173         1966         1975 
TCGA-CN-5373 TCGA-CN-6010 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 
         413          630          594          629           45          432 
TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6994 TCGA-CN-6996 
         202          424          224          318          119          432 
TCGA-CN-6997 TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CQ-5324 TCGA-CQ-5325 
         429          526          484          348         1207          654 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 
        1660         1422          896         1399          341          129 
TCGA-CQ-6218 TCGA-CQ-6223 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 
         870         1057         1461         1378         1007          509 
TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
        1309          901          877          968         1960          613 
TCGA-CQ-A4CA TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI 
        1963          548          393          391          303          608 
TCGA-CR-5247 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 
         358          799         1777         1966         1050         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-7364 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 
         479         1956         1435         1191         1440         1245 
TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7376 TCGA-CR-7379 
        1960         1979          759          889          972         1036 
TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7389 TCGA-CR-7390 
         796         1954          997         1430          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-7402 TCGA-CV-5430 TCGA-CV-5434 TCGA-CV-5435 
         156         1077          911         1955         3295         1438 
TCGA-CV-5436 TCGA-CV-5440 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5966 
         584         1978         2327         1958         2437          519 
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-6934 TCGA-CV-6941 TCGA-CV-6943 TCGA-CV-6952 TCGA-CV-6954 
        1899         1948         1959         1948         1966         1957 
TCGA-CV-6960 TCGA-CV-7090 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7180 TCGA-CV-7183 
        1969         3837         1936         1959         1987         1979 
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-7410 TCGA-CV-7418 TCGA-CV-7424 TCGA-CV-7427 
        1976         1099         1948         1955         1947         1937 
TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7434 TCGA-CV-7440 TCGA-CV-A45O 
        1973         1972         1937         1958         1981          851 
TCGA-CV-A45Q TCGA-CV-A461 TCGA-CV-A6JD TCGA-CV-A6JN TCGA-CX-7085 TCGA-CX-7086 
        1945         1954         1970          717          321          237 
TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6826 
         828          773          292          701           77          154 
TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4ZB TCGA-DQ-5625 TCGA-DQ-5629 
         568          106          128          104         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-A61O TCGA-KU-A66S TCGA-MT-A67A 
         122          441          588          360          224          392 
TCGA-MT-A67F TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6T0 TCGA-P3-A6T2 
         111          910         1652          721          578         1917 
TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6II TCGA-QK-A6IJ 
         553          357          245          218          225           64 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 5                  2 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              3835               3837 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             545.0              672.5 
[1] "5.0 - 3835.0 (545.0)" "2.0 - 3837.0 (672.5)"
[1] "hr=" "1"  
D62V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  11Q LOSS MUTATED         7       17        17        62         5
  11Q LOSS WILD-TYPE      17       46        54       130         4
D62V3, multiclass
           clus
vv          11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  STAGE I                  7                 17
  STAGE II                17                 46
  STAGE III               17                 54
  STAGE IVA               62                130
  STAGE IVB                5                  4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  11Q LOSS MUTATED   13 32 26 38
  11Q LOSS WILD-TYPE 27 76 59 93
D62V4, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T1               13                 27
  T2               32                 76
  T3               26                 59
  T4               38                 93
[1] 4 2
[1] 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    36  14  49   3
  11Q LOSS WILD-TYPE 100  42  80   4
D62V5, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  N0               36                100
  N1               14                 42
  N2               49                 80
  N3                3                  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"
D62V6, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED   29 20
  11Q LOSS WILD-TYPE 79 28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     29   20
  11Q LOSS WILD-TYPE   79   28
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  M0               29                 79
  MX               20                 28
[1] 2 2
[1] FALSE
D62V7, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    28 106
  11Q LOSS WILD-TYPE  93 190
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     28  106
  11Q LOSS WILD-TYPE   93  190
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE               28                 93
  MALE                106                190
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  11Q LOSS MUTATED                                     132
  11Q LOSS WILD-TYPE                                   278
                    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                                                     2
  11Q LOSS WILD-TYPE                                                   4
D62V8, multiclass
                                                             clus
vv                                                            11Q LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    132
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        2
                                                             clus
vv                                                            11Q LOSS WILD-TYPE
  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
[1] 3 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    31 103
  11Q LOSS WILD-TYPE  48 235
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     31  103
  11Q LOSS WILD-TYPE   48  235
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  NO                31                 48
  YES              103                235
[1] 2 2
[1] FALSE
D62V10, continuous
D62V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11Q LOSS MUTATED                                  0     0
  11Q LOSS WILD-TYPE                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11Q LOSS MUTATED                           6   124
  11Q LOSS WILD-TYPE                        27   237
D62V12, multiclass
                                  clus
vv                                 11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 10
  BLACK OR AFRICAN AMERICAN                       6                 27
  WHITE                                         124                237
[1] 4 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     9 120
  11Q LOSS WILD-TYPE   9 261
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      9  120
  11Q LOSS WILD-TYPE    9  261
                        clus
vv                       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    9                  9
  NOT HISPANIC OR LATINO              120                261
[1] 2 2
[1] FALSE

Clustering(63) Variable = 12P LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                  0   1
  12P LOSS MUTATED    12  12
  12P LOSS WILD-TYPE 245  86
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                24                331 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                12                 86 
$`12P LOSS MUTATED`
TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-6868 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 
        1983          248          190          384          113          236 
TCGA-BA-A6DA TCGA-BA-A6DE TCGA-BB-8596 TCGA-CN-5355 TCGA-CN-5365 TCGA-CN-5374 
         351          182         1955          488         1980          290 
TCGA-CR-6484 TCGA-CR-7377 TCGA-CR-7389 TCGA-CV-6441 TCGA-CV-7090 TCGA-CV-7100 
         354         1968          392         1970         3837         1959 
TCGA-CV-7432 TCGA-D6-6826 TCGA-DQ-5631 TCGA-HD-8224 TCGA-IQ-A61E TCGA-MZ-A6I9 
        1937          154          548           55          588          254 

$`12P LOSS WILD-TYPE`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5151 TCGA-BA-5152 
         462          283          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-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-A4IF TCGA-BA-A6D8 TCGA-BA-A6DB 
         644          451           63          895          513          216 
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-8601 TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 
         428          436          624            5            4          799 
TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 
         721          485          142          452          613          392 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 
         462          993          642          369          395          240 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5356 
        1960         1330          811         1268         1988          512 
TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5366 TCGA-CN-5367 
         173         1980         1081         1977         1966         1966 
TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 
        1975          413          630          424          629          433 
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-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 
         202          424          224          318          611          394 
TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49B 
         119          432          429           46          443          447 
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-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 
        1466         1207          654         1660         1422          896 
TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 
        1399          317          341          129          870         1000 
TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 
        1057          985         1959         1959          815         1461 
TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 
        1378         1007          509         1309          901          877 
TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD 
         968         1960          613         1963          545          548 
TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 
         393          391          303          608         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-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-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-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-6960 TCGA-CV-6961 TCGA-CV-7091 TCGA-CV-7095 
        1966         1957         1969         1959         1959         1970 
TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7183 
        1970         1936         1939         1945         1987         1979 
TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 
        1724         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-7424 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7433 
        1957         1947         1937         1973         1972         1984 
TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A461 
        1958         1959         1981          851         1945         1954 
TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 
        1970          750          717          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-DQ-5624 
         568          106          128          112          104         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-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J 
         564          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-HD-7229 TCGA-HD-7753 
          58          133          414          403            2            5 
TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 
          25           37           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-A61G TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61L 
         122          441          360          412          440          351 
TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A 
         360          224          210           14           34          392 
TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE 
          56          111          112          910         1652          721 
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 
          64 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                55                  2 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              3837               3835 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
               388                641 
[1] "55.0 - 3837.0 (388.0)" "2.0 - 3835.0 (641.0)" 
[1] "hr=" "1.3"
D63V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  12P LOSS MUTATED         0        4         4        13         1
  12P LOSS WILD-TYPE      24       59        67       179         8
D63V3, multiclass
           clus
vv          12P LOSS MUTATED 12P LOSS WILD-TYPE
  STAGE I                  0                 24
  STAGE II                 4                 59
  STAGE III                4                 67
  STAGE IVA               13                179
  STAGE IVB                1                  8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  12P LOSS MUTATED     0   8   4  10
  12P LOSS WILD-TYPE  40 100  81 121
D63V4, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  T1                0                 40
  T2                8                100
  T3                4                 81
  T4               10                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
  12P LOSS MUTATED     8   2   8   1
  12P LOSS WILD-TYPE 128  54 121   6
D63V5, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  N0                8                128
  N1                2                 54
  N2                8                121
  N3                1                  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"
D63V6, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     7   3
  12P LOSS WILD-TYPE 101  45
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      7    3
  12P LOSS WILD-TYPE  101   45
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  M0                7                101
  MX                3                 45
[1] 2 2
[1] FALSE
D63V7, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    10  17
  12P LOSS WILD-TYPE 111 279
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     10   17
  12P LOSS WILD-TYPE  111  279
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE               10                111
  MALE                 17                279
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  12P LOSS MUTATED                                      27
  12P LOSS WILD-TYPE                                   383
                    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                                                   6
D63V8, multiclass
                                                             clus
vv                                                            12P 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                        0
                                                             clus
vv                                                            12P LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      383
  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"
D63V9, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     6  21
  12P LOSS WILD-TYPE  73 317
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      6   21
  12P LOSS WILD-TYPE   73  317
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  NO                 6                 73
  YES               21                317
[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                                1     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12P LOSS MUTATED                           4    21
  12P LOSS WILD-TYPE                        29   340
D63V12, multiclass
                                  clus
vv                                 12P LOSS MUTATED 12P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  9
  BLACK OR AFRICAN AMERICAN                       4                 29
  WHITE                                          21                340
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V13, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     2  23
  12P LOSS WILD-TYPE  16 358
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      2   23
  12P LOSS WILD-TYPE   16  358
                        clus
vv                       12P LOSS MUTATED 12P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                 16
  NOT HISPANIC OR LATINO               23                358
[1] 2 2
[1] FALSE

Clustering(64) Variable = 12Q LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                  0   1
  12Q LOSS MUTATED    15   5
  12Q LOSS WILD-TYPE 242  93
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                20                335 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 5                 93 
$`12Q LOSS MUTATED`
TCGA-BA-6868 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A6DE TCGA-BB-8596 TCGA-CN-5355 
         190          113          236          182         1955          488 
TCGA-CN-5374 TCGA-CN-6024 TCGA-CN-6994 TCGA-CR-6493 TCGA-CR-7390 TCGA-CV-6003 
         290          224          119         1956          907         1665 
TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7254 TCGA-CV-7432 TCGA-CX-7219 TCGA-F7-7848 
        3837         1959         1976         1937          828          564 
TCGA-IQ-A61G TCGA-MZ-A6I9 
         360          254 

$`12Q LOSS 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-5555 TCGA-BA-5556 TCGA-BA-5557 
         722         1288         1762          520          725          623 
TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 
        1636         1747          644          451           63          384 
TCGA-BA-A4IF TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BB-4217 TCGA-BB-4223 
         895          513          351          216          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          485 
TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 
         142          452          613          392          462          993 
TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 
         642          369          395          240         1960         1330 
TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 
         811         1268         1988          512          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 
         413          630          424          629          433          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 
         424          318          611          394          432          429 
TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V 
          46          443          447          225          526          484 
TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
         348          175          367         1466         1207          654 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 
        1660         1422          896         1399          317          341 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 
         129          870         1000         1057          985         1959 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 
        1959          815         1461         1378         1007          509 
TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
        1309          901          877          968         1960          613 
TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH 
        1963          545          548          393          391          303 
TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 
         608         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         1724         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-A461 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN 
         851         1945         1954         1970          750          717 
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-D6-6825 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-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 
         112          104         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-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-8298 TCGA-F7-8489 
         369          368          324          340          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-F7-A623 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 
          13            6          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-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-A61H TCGA-IQ-A61J TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66S 
         588          412          440          351          360          224 
TCGA-KU-A66T TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F 
         210           14           34          392           56          111 
TCGA-MT-A67G TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX 
         112          910         1652          721         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 
         245          218          228          225           64 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
               113                  2 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
              3837               3835 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
               526                629 
[1] "113.0 - 3837.0 (526.0)" "2.0 - 3835.0 (629.0)"  
[1] "hr=" "1.3"
D64V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  12Q LOSS MUTATED         1        5         2        13         0
  12Q LOSS WILD-TYPE      23       58        69       179         9
D64V3, multiclass
           clus
vv          12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  STAGE I                  1                 23
  STAGE II                 5                 58
  STAGE III                2                 69
  STAGE IVA               13                179
  STAGE IVB                0                  9
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  12Q LOSS MUTATED     1   8   1  11
  12Q LOSS WILD-TYPE  39 100  84 120
D64V4, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  T1                1                 39
  T2                8                100
  T3                1                 84
  T4               11                120
[1] 4 2
[1] 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     8   3   6   0
  12Q LOSS WILD-TYPE 128  53 123   7
D64V5, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  N0                8                128
  N1                3                 53
  N2                6                123
  N3                0                  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"
D64V6, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     5   3
  12Q LOSS WILD-TYPE 103  45
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      5    3
  12Q LOSS WILD-TYPE  103   45
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  M0                5                103
  MX                3                 45
[1] 2 2
[1] FALSE
D64V7, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     6  17
  12Q LOSS WILD-TYPE 115 279
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      6   17
  12Q LOSS WILD-TYPE  115  279
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE                6                115
  MALE                 17                279
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  12Q LOSS MUTATED                                      23
  12Q LOSS WILD-TYPE                                   387
                    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                                                     0
  12Q LOSS WILD-TYPE                                                   6
D64V8, multiclass
                                                             clus
vv                                                            12Q LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     23
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        0
                                                             clus
vv                                                            12Q 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                          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"
D64V9, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     3  20
  12Q LOSS WILD-TYPE  76 318
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      3   20
  12Q LOSS WILD-TYPE   76  318
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  NO                 3                 76
  YES               20                318
[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                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12Q LOSS MUTATED                           5    17
  12Q LOSS WILD-TYPE                        28   344
D64V12, multiclass
                                  clus
vv                                 12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 10
  BLACK OR AFRICAN AMERICAN                       5                 28
  WHITE                                          17                344
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V13, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     2  20
  12Q LOSS WILD-TYPE  16 361
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      2   20
  12Q LOSS WILD-TYPE   16  361
                        clus
vv                       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                 16
  NOT HISPANIC OR LATINO               20                361
[1] 2 2
[1] FALSE

Clustering(65) Variable = 13Q LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                  0   1
  13Q LOSS MUTATED    85  28
  13Q LOSS WILD-TYPE 172  70
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               113                242 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                28                 70 
$`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-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB 
          63          113          236          513          351          216 
TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-7862 TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-7871 
         278          133          536          687         1153          428 
TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A47Z TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4730 
        1955          624            5          721          485          462 
TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5367 TCGA-CN-5373 
        1330          811         1081         1977         1966          413 
TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6018 TCGA-CN-6020 
         290          630          424          629           45           98 
TCGA-CN-6021 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6994 TCGA-CN-6998 TCGA-CN-A498 
        1970          224          318          119           46          443 
TCGA-CN-A63T TCGA-CQ-5323 TCGA-CQ-5330 TCGA-CQ-6224 TCGA-CQ-7064 TCGA-CQ-7067 
         225         1466          896          985         1378          509 
TCGA-CQ-A4CA TCGA-CQ-A4CE TCGA-CQ-A4CI TCGA-CR-5249 TCGA-CR-6472 TCGA-CR-6477 
        1963          393          608         1152         1050          514 
TCGA-CR-6478 TCGA-CR-6481 TCGA-CR-6487 TCGA-CR-7364 TCGA-CR-7372 TCGA-CR-7374 
        1969          311          234         1435          759           30 
TCGA-CR-7379 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7397 TCGA-CR-7402 TCGA-CR-7404 
        1036         1954          997          216          911         1472 
TCGA-CV-5434 TCGA-CV-5441 TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-6941 TCGA-CV-6942 
        3295         2886         1840          215         1959         3835 
TCGA-CV-6954 TCGA-CV-7091 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7235 TCGA-CV-7242 
        1957         1959         1936         1959         1724         1095 
TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7406 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7435 
         797         1967         1974         1955         1957         1959 
TCGA-CV-7440 TCGA-CV-A461 TCGA-CV-A6JE TCGA-CX-7082 TCGA-CX-7219 TCGA-D6-6825 
        1981         1954          750          317          828          491 
TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-DQ-5630 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7595 
         106          112         1030         1965          575          324 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A623 TCGA-HD-7753 
         340          564           15           92            6            5 
TCGA-HD-7917 TCGA-HD-8635 TCGA-HD-A6HZ TCGA-IQ-A61O TCGA-KU-A66T TCGA-MT-A67G 
          37           25          111          360          210          112 
TCGA-MZ-A6I9 TCGA-P3-A5QA TCGA-P3-A6SX TCGA-P3-A6T4 TCGA-QK-A6IG 
         254         1652         1954         1968          218 

$`13Q LOSS WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5153 
         283          415         1983          248          722         1762 
TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6872 
         725          623         1636          190          451          384 
TCGA-BA-A4IF TCGA-BA-A6DE TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-4228 
         895          182          187         2878          140          558 
TCGA-BB-7861 TCGA-BB-7863 TCGA-BB-7866 TCGA-BB-7872 TCGA-C9-A480 TCGA-CN-4722 
         310          423          638          436            4          799 
TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4731 TCGA-CN-4733 
         142          452          613          392          993          642 
TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4741 TCGA-CN-4742 
         369          395          240         1960         1268         1988 
TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5365 TCGA-CN-5366 
         488          512          173         1980         1980         1966 
TCGA-CN-5370 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6022 
        1975          433          594          629          432          202 
TCGA-CN-6023 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-A49B 
         424          611          394          432          429          447 
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-5329 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 
         654         1660         1422         1399          317          341 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6227 TCGA-CQ-6228 
         129          870         1000         1057         1959         1959 
TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 
         815         1461         1007         1309          901          877 
TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CG 
         968         1960          613          545          548          391 
TCGA-CQ-A4CH TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5250 TCGA-CR-6467 
         303         2562          358         1663          799         1777 
TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6480 TCGA-CR-6482 
        1521         1966         1125         1971          362          345 
TCGA-CR-6484 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7365 
         354          379          350          479         1956         1191 
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-7382 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 
         972         1968          796         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-7398 TCGA-CR-7399 TCGA-CR-7401 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 
         156          181         1077         1955          522         1950 
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-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-6943 TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-6960 
        1969         1952         1948         1969         1966         1969 
TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7101 TCGA-CV-7102 
        1959         3837         1970         1970         1939         1945 
TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7238 TCGA-CV-7243 TCGA-CV-7250 TCGA-CV-7254 
        1987         1979         1444          954         1960         1976 
TCGA-CV-7261 TCGA-CV-7410 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 
        1099         1948         1947         1937         1973         1972 
TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A6JD 
        1937         1984         1958          851         1945         1970 
TCGA-CV-A6JN TCGA-CX-7085 TCGA-CX-7086 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 
         717          321          237          773          292          701 
TCGA-D6-6824 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8569 TCGA-D6-A4ZB TCGA-DQ-5624 
          77          154          568          128          104         1778 
TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7592 
        1081          516          548          775          622          299 
TCGA-DQ-7593 TCGA-DQ-7594 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50J TCGA-F7-A61S 
         369          368          490          658          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-HD-7229 TCGA-HD-7754 TCGA-HD-8224 TCGA-HD-8314 
         414          403            2           25           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-A61G TCGA-IQ-A61H 
         485          122          441          588          360          412 
TCGA-IQ-A61J TCGA-IQ-A61L TCGA-KU-A66S TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A 
         440          351          224           14           34          392 
TCGA-MT-A67D TCGA-MT-A67F TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6T0 
          56          111          910          721         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 
         225           64 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 5                  2 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              3835               3837 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             624.0              633.5 
[1] "5.0 - 3835.0 (624.0)" "2.0 - 3837.0 (633.5)"
[1] "hr=" "1"  
D65V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  13Q LOSS MUTATED        11       14        20        63         2
  13Q LOSS WILD-TYPE      13       49        51       129         7
D65V3, multiclass
           clus
vv          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  STAGE I                 11                 13
  STAGE II                14                 49
  STAGE III               20                 51
  STAGE IVA               63                129
  STAGE IVB                2                  7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  13Q LOSS MUTATED   15 34 20 42
  13Q LOSS WILD-TYPE 25 74 65 89
D65V4, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T1               15                 25
  T2               34                 74
  T3               20                 65
  T4               42                 89
[1] 4 2
[1] 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   37 17 45  2
  13Q LOSS WILD-TYPE 99 39 84  5
D65V5, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  N0               37                 99
  N1               17                 39
  N2               45                 84
  N3                2                  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"
D65V6, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED   33 14
  13Q LOSS WILD-TYPE 75 34
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     33   14
  13Q LOSS WILD-TYPE   75   34
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  M0               33                 75
  MX               14                 34
[1] 2 2
[1] FALSE
D65V7, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    36  94
  13Q LOSS WILD-TYPE  85 202
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     36   94
  13Q LOSS WILD-TYPE   85  202
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE               36                 85
  MALE                 94                202
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  13Q LOSS MUTATED                                     128
  13Q LOSS WILD-TYPE                                   282
                    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                                                     1
  13Q LOSS WILD-TYPE                                                   5
D65V8, multiclass
                                                             clus
vv                                                            13Q LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    128
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        1
                                                             clus
vv                                                            13Q LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      282
  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"
D65V9, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    24 106
  13Q LOSS WILD-TYPE  55 232
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     24  106
  13Q LOSS WILD-TYPE   55  232
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO                24                 55
  YES              106                232
[1] 2 2
[1] FALSE
D65V10, continuous
D65V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  13Q LOSS MUTATED                                  0     1
  13Q LOSS WILD-TYPE                                1     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  13Q LOSS MUTATED                          14   110
  13Q LOSS WILD-TYPE                        19   251
D65V12, multiclass
                                  clus
vv                                 13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  9
  BLACK OR AFRICAN AMERICAN                      14                 19
  WHITE                                         110                251
[1] 4 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     5 114
  13Q LOSS WILD-TYPE  13 267
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      5  114
  13Q LOSS WILD-TYPE   13  267
                        clus
vv                       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    5                 13
  NOT HISPANIC OR LATINO              114                267
[1] 2 2
[1] FALSE

Clustering(66) Variable = 14Q LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                  0   1
  14Q LOSS MUTATED    19  12
  14Q LOSS WILD-TYPE 238  86
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                31                324 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                12                 86 
$`14Q LOSS MUTATED`
TCGA-BA-4078 TCGA-BA-5152 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-A6D8 
         276         1288          644          451           63          513 
TCGA-BB-7862 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6992 TCGA-CN-A63U TCGA-CQ-5332 
         536          432           98          394          526          317 
TCGA-CQ-6221 TCGA-CR-5247 TCGA-CR-6470 TCGA-CR-6472 TCGA-CR-7398 TCGA-CV-5966 
        1000          358         1521         1050          156          519 
TCGA-CV-6935 TCGA-CV-7406 TCGA-CV-7422 TCGA-CV-7435 TCGA-D6-6826 TCGA-D6-8569 
        1969         1974         1957         1959          154          128 
TCGA-DQ-5631 TCGA-DQ-7590 TCGA-F7-7848 TCGA-H7-A6C5 TCGA-HD-8224 TCGA-MZ-A6I9 
         548          775          564          403           55          254 
TCGA-P3-A6T0 
         578 

$`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-A6DA 
         190          384          113          236          895          351 
TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 
         216          182          187         2878          278          140 
TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 
         133          558          310          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          485          142          452 
TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 
         613          392          462          993          642          369 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 
         395          240         1960         1330          811         1268 
TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 
        1988          488          512          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          413 
TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 
         290          630          424          629          433          594 
TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
         629           45         1970          202          424          224 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 
         318          611          119          432          429           46 
TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y 
         443          447          225          484          348          175 
TCGA-CN-A641 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 
         367         1466         1207          654         1660         1422 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6223 
         896         1399          341          129          870         1057 
TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 
         985         1959         1959          815         1461         1378 
TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 
        1007          509         1309          901          877          968 
TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE 
        1960          613         1963          545          548          393 
TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 
         391          303          608         2562         1663         1152 
TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 
         799         1777         1966         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-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-5970 TCGA-CV-5971 
        2886         2327         1958         2437          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-6936 TCGA-CV-6941 
         641         1899         1970         1948         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-7097 TCGA-CV-7099 
        1959         3837         1959         1970         1970         1936 
TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 
        1959         1939         1945         1987         1979         1724 
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-7410 TCGA-CV-7418 TCGA-CV-7424 TCGA-CV-7427 
        1976         1099         1948         1955         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-A461 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN 
         851         1945         1954         1970          750          717 
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-A4Z9 
         701           77          491          568          106          112 
TCGA-D6-A4ZB TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-7588 
         104         1778         1081          516         1030         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-F7-8298 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-HD-7229 TCGA-HD-7753 TCGA-HD-7754 
          58          133          414            2            5           25 
TCGA-HD-7917 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A633 
          37           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-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A 
         360          224          210           14           34          392 
TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE 
          56          111          112          910         1652          721 
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           64 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                55                  2 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              1974               3837 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               519                648 
[1] "55.0 - 1974.0 (519.0)" "2.0 - 3837.0 (648.0)" 
[1] "hr=" "2.5"
D66V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  14Q LOSS MUTATED         0        7         4        17         0
  14Q LOSS WILD-TYPE      24       56        67       175         9
D66V3, multiclass
           clus
vv          14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  STAGE I                  0                 24
  STAGE II                 7                 56
  STAGE III                4                 67
  STAGE IVA               17                175
  STAGE IVB                0                  9
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  14Q LOSS MUTATED     0   9   9  11
  14Q LOSS WILD-TYPE  40  99  76 120
D66V4, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  T1                0                 40
  T2                9                 99
  T3                9                 76
  T4               11                120
[1] 4 2
[1] 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    11   5   9   0
  14Q LOSS WILD-TYPE 125  51 120   7
D66V5, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  N0               11                125
  N1                5                 51
  N2                9                120
  N3                0                  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"
D66V6, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED     6   3
  14Q LOSS WILD-TYPE 102  45
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      6    3
  14Q LOSS WILD-TYPE  102   45
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  M0                6                102
  MX                3                 45
[1] 2 2
[1] FALSE
D66V7, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED     7  30
  14Q LOSS WILD-TYPE 114 266
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      7   30
  14Q LOSS WILD-TYPE  114  266
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE                7                114
  MALE                 30                266
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  14Q LOSS MUTATED                                      37
  14Q LOSS WILD-TYPE                                   373
                    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                                                     0
  14Q LOSS WILD-TYPE                                                   6
D66V8, multiclass
                                                             clus
vv                                                            14Q 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                        0
                                                             clus
vv                                                            14Q 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                          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"
D66V9, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED     9  28
  14Q LOSS WILD-TYPE  70 310
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      9   28
  14Q LOSS WILD-TYPE   70  310
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  NO                 9                 70
  YES               28                310
[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                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  14Q LOSS MUTATED                           5    32
  14Q LOSS WILD-TYPE                        28   329
D66V12, multiclass
                                  clus
vv                                 14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 10
  BLACK OR AFRICAN AMERICAN                       5                 28
  WHITE                                          32                329
[1] 4 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     1  32
  14Q LOSS WILD-TYPE  17 349
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      1   32
  14Q LOSS WILD-TYPE   17  349
                        clus
vv                       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 17
  NOT HISPANIC OR LATINO               32                349
[1] 2 2
[1] FALSE

Clustering(67) Variable = 15Q LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                  0   1
  15Q LOSS MUTATED    39  24
  15Q LOSS WILD-TYPE 218  74
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                63                292 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                24                 74 
$`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-A6DE TCGA-BB-4225 TCGA-BB-7870 TCGA-CN-4725 TCGA-CN-4728 
         895          182          140         1153          485          613 
TCGA-CN-4730 TCGA-CN-5359 TCGA-CN-5363 TCGA-CN-5370 TCGA-CN-6012 TCGA-CN-6021 
         462         1980         1977         1975          629         1970 
TCGA-CN-6024 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A63W TCGA-CQ-5330 
         224          432          429           46          348          896 
TCGA-CQ-5332 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7067 TCGA-CQ-A4C6 
         317          985         1959          815          509          968 
TCGA-CQ-A4C7 TCGA-CQ-A4CE TCGA-CR-6478 TCGA-CR-7402 TCGA-CV-5435 TCGA-CV-5441 
        1960          393         1969          911         1438         2886 
TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-6441 TCGA-CV-6954 
         519          406         1478         1840         1970         1957 
TCGA-CV-7095 TCGA-CV-7242 TCGA-CV-7424 TCGA-CV-7432 TCGA-CV-7435 TCGA-CX-7219 
        1970         1095         1947         1937         1959          828 
TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6826 TCGA-DQ-5624 TCGA-DQ-5631 TCGA-DQ-7592 
         292          701          154         1778          548          299 
TCGA-F7-A50I TCGA-F7-A61S TCGA-F7-A623 TCGA-IQ-A61E TCGA-IQ-A61O TCGA-KU-A66T 
          92            3            6          588          360          210 
TCGA-P3-A5QA TCGA-P3-A6T4 TCGA-QK-A6IG 
        1652         1968          218 

$`15Q LOSS 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-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6869 TCGA-BA-6870 
         722          725          623         1636          644          451 
TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB 
          63          384          113          513          351          216 
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-7871 TCGA-BB-7872 
         536          423          687          638          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-4726 TCGA-CN-4727 TCGA-CN-4729 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 
         142          452          392          993          642          369 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 
         395          240         1960         1330          811         1268 
TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5365 
        1988          488          512          173         1081         1980 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 
        1966         1966          413          290          630          424 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 
         433          594          629           45          432           98 
TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 
         202          424          318          611          394          119 
TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63Y 
         443          447          225          526          484          175 
TCGA-CN-A641 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 
         367         1466         1207          654         1660         1422 
TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 
        1399          341          129          870         1000         1057 
TCGA-CQ-6228 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7069 
        1959         1461         1378         1007         1309          901 
TCGA-CQ-7071 TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CG 
         877          613         1963          545          548          391 
TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 
         303          608         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-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 
        1971          514          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-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-5436 TCGA-CV-5439 TCGA-CV-5440 
         522         1950         3295          584          546         1978 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5978 
        2327         1958         2437          701         2641          215 
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-6960 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7097 TCGA-CV-7099 
        1969         1959         3837         1959         1970         1936 
TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 
        1959         1939         1945         1987         1979         1724 
TCGA-CV-7238 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7254 
        1444          954          797         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-7433 TCGA-CV-7434 TCGA-CV-7440 TCGA-CV-A45O 
        1973         1972         1984         1958         1981          851 
TCGA-CV-A45Q TCGA-CV-A461 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CX-7082 
        1945         1954         1970          750          717          317 
TCGA-CX-7085 TCGA-CX-7086 TCGA-D6-6516 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6827 
         321          237          773           77          491          568 
TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-DQ-5625 TCGA-DQ-5629 
         106          128          112          104         1081          516 
TCGA-DQ-5630 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7593 
        1030         1965          575          775          622          369 
TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 
         368          324          340          564          490          658 
TCGA-F7-A50G TCGA-F7-A50J TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-H7-7774 
          15          585          384           14           13          407 
TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-7753 
          58          133          414          403            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-A61G TCGA-IQ-A61H TCGA-IQ-A61J 
         485          122          441          360          412          440 
TCGA-IQ-A61L TCGA-KU-A66S TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D 
         351          224           14           34          392           56 
TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A6SW 
         111          112          254          910          721         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 
         245          228          225           64 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 3                  2 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              2886               3837 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             815.0              622.5 
[1] "3.0 - 2886.0 (815.0)" "2.0 - 3837.0 (622.5)"
[1] "hr=" "1.4"
D67V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  15Q LOSS MUTATED         3       12        11        36         2
  15Q LOSS WILD-TYPE      21       51        60       156         7
D67V3, multiclass
           clus
vv          15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  STAGE I                  3                 21
  STAGE II                12                 51
  STAGE III               11                 60
  STAGE IVA               36                156
  STAGE IVB                2                  7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  15Q LOSS MUTATED     4  19  20  22
  15Q LOSS WILD-TYPE  36  89  65 109
D67V4, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T1                4                 36
  T2               19                 89
  T3               20                 65
  T4               22                109
[1] 4 2
[1] 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    21   8  26   2
  15Q LOSS WILD-TYPE 115  48 103   5
D67V5, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  N0               21                115
  N1                8                 48
  N2               26                103
  N3                2                  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"
D67V6, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED   14  9
  15Q LOSS WILD-TYPE 94 39
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     14    9
  15Q LOSS WILD-TYPE   94   39
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  M0               14                 94
  MX                9                 39
[1] 2 2
[1] FALSE
D67V7, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED    22  54
  15Q LOSS WILD-TYPE  99 242
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     22   54
  15Q LOSS WILD-TYPE   99  242
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE               22                 99
  MALE                 54                242
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  15Q LOSS MUTATED                                      75
  15Q LOSS WILD-TYPE                                   335
                    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                                                   6
D67V8, multiclass
                                                             clus
vv                                                            15Q LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     75
  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                                      335
  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"
D67V9, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED    18  58
  15Q LOSS WILD-TYPE  61 280
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     18   58
  15Q LOSS WILD-TYPE   61  280
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  NO                18                 61
  YES               58                280
[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                                0     8
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  15Q LOSS MUTATED                           5    65
  15Q LOSS WILD-TYPE                        28   296
D67V12, multiclass
                                  clus
vv                                 15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           2                  8
  BLACK OR AFRICAN AMERICAN                       5                 28
  WHITE                                          65                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"
D67V13, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     5  67
  15Q LOSS WILD-TYPE  13 314
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      5   67
  15Q LOSS WILD-TYPE   13  314
                        clus
vv                       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    5                 13
  NOT HISPANIC OR LATINO               67                314
[1] 2 2
[1] FALSE

Clustering(68) Variable = 16P LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                  0   1
  16P LOSS MUTATED    28  10
  16P LOSS WILD-TYPE 229  88
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                38                317 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                10                 88 
$`16P LOSS MUTATED`
TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-7269 TCGA-BA-A6DE TCGA-BB-7870 TCGA-BB-8596 
         415          276          236          182         1153         1955 
TCGA-BB-8601 TCGA-CN-4729 TCGA-CN-5363 TCGA-CN-5374 TCGA-CN-A63T TCGA-CQ-5330 
         624          392         1977          290          225          896 
TCGA-CQ-6224 TCGA-CQ-A4C7 TCGA-CR-6473 TCGA-CR-7368 TCGA-CR-7374 TCGA-CR-7383 
         985         1960         1125         1245           30         1954 
TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7402 TCGA-CV-5436 TCGA-CV-7235 TCGA-CV-7418 
         156          181          911          584         1724         1955 
TCGA-CV-7424 TCGA-CV-7432 TCGA-CX-7082 TCGA-D6-A4Z9 TCGA-F7-A50G TCGA-F7-A50I 
        1947         1937          317          112           15           92 
TCGA-HD-7753 TCGA-HD-8224 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-MZ-A6I9 
           5           55          588          360          412          254 
TCGA-P3-A6SW TCGA-QK-A6IG 
        1120          218 

$`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-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BB-4217 TCGA-BB-4223 
         895          513          351          216          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          485          142          452 
TCGA-CN-4728 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 
         613          462          993          642          369          395 
TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 
         240         1960         1330          811         1268         1988 
TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5365 
         488          512          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          413          630          424 
TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 
         629          433          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          424          224          318 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 
         611          394          119          432          429           46 
TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y 
         443          447          526          484          348          175 
TCGA-CN-A641 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 
         367         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          870         1000 
TCGA-CQ-6223 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 
        1057         1959         1959          815         1461         1378 
TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 
        1007          509         1309          901          877          968 
TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG 
         613         1963          545          548          393          391 
TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 
         303          608         2562          358         1663         1152 
TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6474 
         799         1777         1521         1966         1050         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-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-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7385 
         889          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-7401 TCGA-CR-7404 
         908          898          930          216         1077         1472 
TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5439 
        1955          522         1950         3295         1438          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-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 
        1987         1979         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-7422 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7433 TCGA-CV-7434 
        1957         1937         1973         1972         1984         1958 
TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A461 TCGA-CV-A6JD 
        1959         1981          851         1945         1954         1970 
TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 
         750          717          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-A4ZB TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 
         106          128          104         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-F7-7848 
         299          369          368          324          340          564 
TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W 
         490          658          585            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-HD-7229 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8314 TCGA-HD-8634 
         403            2           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-A61J TCGA-IQ-A61L 
        1057          485          122          441          440          351 
TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A 
         360          224          210           14           34          392 
TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE 
          56          111          112          910         1652          721 
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-A6IH TCGA-QK-A6II TCGA-QK-A6IJ 
         357          245          228          225           64 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 5                  2 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              1977               3837 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             413.5              641.0 
[1] "5.0 - 1977.0 (413.5)" "2.0 - 3837.0 (641.0)"
[1] "hr=" "1.8"
D68V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  16P LOSS MUTATED         3        6         9        22         2
  16P LOSS WILD-TYPE      21       57        62       170         7
D68V3, multiclass
           clus
vv          16P LOSS MUTATED 16P LOSS WILD-TYPE
  STAGE I                  3                 21
  STAGE II                 6                 57
  STAGE III                9                 62
  STAGE IVA               22                170
  STAGE IVB                2                  7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  16P LOSS MUTATED     3  14  14  11
  16P LOSS WILD-TYPE  37  94  71 120
D68V4, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  T1                3                 37
  T2               14                 94
  T3               14                 71
  T4               11                120
[1] 4 2
[1] 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    10   8  17   2
  16P LOSS WILD-TYPE 126  48 112   5
D68V5, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  N0               10                126
  N1                8                 48
  N2               17                112
  N3                2                  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"
D68V6, binary
                    cls
clus                  0  1
  16P LOSS MUTATED   13  8
  16P LOSS WILD-TYPE 95 40
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     13    8
  16P LOSS WILD-TYPE   95   40
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  M0               13                 95
  MX                8                 40
[1] 2 2
[1] FALSE
D68V7, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    15  33
  16P LOSS WILD-TYPE 106 263
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     15   33
  16P LOSS WILD-TYPE  106  263
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE               15                106
  MALE                 33                263
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  16P LOSS MUTATED                                      47
  16P LOSS WILD-TYPE                                   363
                    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                                                     1
  16P LOSS WILD-TYPE                                                   5
D68V8, multiclass
                                                             clus
vv                                                            16P LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     47
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        1
                                                             clus
vv                                                            16P LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      363
  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"
D68V9, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     5  43
  16P LOSS WILD-TYPE  74 295
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      5   43
  16P LOSS WILD-TYPE   74  295
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  NO                 5                 74
  YES               43                295
[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                                1     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16P LOSS MUTATED                           4    42
  16P LOSS WILD-TYPE                        29   319
D68V12, multiclass
                                  clus
vv                                 16P LOSS MUTATED 16P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  9
  BLACK OR AFRICAN AMERICAN                       4                 29
  WHITE                                          42                319
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V13, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     4  43
  16P LOSS WILD-TYPE  14 338
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      4   43
  16P LOSS WILD-TYPE   14  338
                        clus
vv                       16P LOSS MUTATED 16P LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                 14
  NOT HISPANIC OR LATINO               43                338
[1] 2 2
[1] FALSE

Clustering(69) Variable = 16Q LOSS MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                  0   1
  16Q LOSS MUTATED    41  11
  16Q LOSS WILD-TYPE 216  87
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                52                303 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                11                 87 
$`16Q LOSS MUTATED`
TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-5153 TCGA-BA-5559 TCGA-BB-4225 TCGA-BB-7861 
         415          276         1762         1747          140          310 
TCGA-BB-7862 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-8596 TCGA-BB-8601 TCGA-CN-4729 
         536          638         1153         1955          624          392 
TCGA-CN-5356 TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5374 TCGA-CN-6012 TCGA-CN-6021 
         512         1081         1977          290          629         1970 
TCGA-CN-A63T TCGA-CN-A63U TCGA-CQ-6224 TCGA-CQ-A4C7 TCGA-CR-5243 TCGA-CR-6467 
         225          526          985         1960         2562         1777 
TCGA-CR-6473 TCGA-CR-6481 TCGA-CR-6484 TCGA-CR-7368 TCGA-CR-7370 TCGA-CR-7398 
        1125          311          354         1245          105          156 
TCGA-CR-7402 TCGA-CV-5443 TCGA-CV-5444 TCGA-CV-7235 TCGA-CV-7418 TCGA-CV-7424 
         911         1958         2437         1724         1955         1947 
TCGA-CV-7428 TCGA-CV-7432 TCGA-CX-7082 TCGA-D6-6827 TCGA-D6-A4Z9 TCGA-DQ-7589 
        1973         1937          317          568          112          575 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-F7-A50I TCGA-HD-8224 TCGA-IQ-A61E TCGA-IQ-A61H 
         775          622           92           55          588          412 
TCGA-MZ-A6I9 TCGA-P3-A5QE TCGA-P3-A6SW TCGA-QK-A6IF 
         254          721         1120          245 

$`16Q 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-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 
         520          725          623         1636          190          644 
TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF 
         451           63          384          113          236          895 
TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BB-4217 TCGA-BB-4223 
         513          351          216          182          187         2878 
TCGA-BB-4224 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7871 
         278          133          558          423          687          428 
TCGA-BB-7872 TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 
         436            5            4          799          721          485 
TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
         142          452          613          462          993          642 
TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 
         369          395          240         1960         1330          811 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5365 
        1268         1988          488          173         1980         1980 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6010 TCGA-CN-6011 
        1966         1966         1975          413          630          424 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 
         433          594          629           45          432           98 
TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 
         202          424          224          318          611          394 
TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49B 
         119          432          429           46          443          447 
TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 TCGA-CQ-5323 TCGA-CQ-5324 
         484          348          175          367         1466         1207 
TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 
         654         1660         1422          896         1399          317 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6227 
         341          129          870         1000         1057         1959 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 
        1959          815         1461         1378         1007          509 
TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CA 
        1309          901          877          968          613         1963 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI 
         545          548          393          391          303          608 
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-A461 TCGA-CV-A6JD 
        1959         1981          851         1945         1954         1970 
TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 
         750          717          321          237          828          773 
TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-8568 
         292          701           77          491          154          106 
TCGA-D6-8569 TCGA-D6-A4ZB TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 
         128          104         1778         1081          516         1030 
TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 
         548         1965          299          369          368          324 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50J 
         340          564          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-HD-7229 TCGA-HD-7753 
          58          133          414          403            2            5 
TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A4C1 
          25           37           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-A61G TCGA-IQ-A61J TCGA-IQ-A61L TCGA-IQ-A61O 
         122          441          360          440          351          360 
TCGA-KU-A66S TCGA-KU-A66T TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D 
         224          210           14           34          392           56 
TCGA-MT-A67F TCGA-MT-A67G TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A6SX TCGA-P3-A6T0 
         111          112          910         1652         1954          578 
TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IG 
        1917         1968          400          553          357          218 
TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ 
         228          225           64 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                55                  2 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              2562               3837 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             626.5              629.0 
[1] "55.0 - 2562.0 (626.5)" "2.0 - 3837.0 (629.0)" 
[1] "hr=" "1.3"
D69V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  16Q LOSS MUTATED         2        5        11        23         2
  16Q LOSS WILD-TYPE      22       58        60       169         7
D69V3, multiclass
           clus
vv          16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  STAGE I                  2                 22
  STAGE II                 5                 58
  STAGE III               11                 60
  STAGE IVA               23                169
  STAGE IVB                2                  7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  16Q LOSS MUTATED     4  14  13  13
  16Q LOSS WILD-TYPE  36  94  72 118
D69V4, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  T1                4                 36
  T2               14                 94
  T3               13                 72
  T4               13                118
[1] 4 2
[1] 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    11   9  17   2
  16Q LOSS WILD-TYPE 125  47 112   5
D69V5, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  N0               11                125
  N1                9                 47
  N2               17                112
  N3                2                  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"
D69V6, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED   11  8
  16Q LOSS WILD-TYPE 97 40
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     11    8
  16Q LOSS WILD-TYPE   97   40
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  M0               11                 97
  MX                8                 40
[1] 2 2
[1] FALSE
D69V7, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    12  48
  16Q LOSS WILD-TYPE 109 248
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     12   48
  16Q LOSS WILD-TYPE  109  248
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE               12                109
  MALE                 48                248
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  16Q LOSS MUTATED                                      58
  16Q LOSS WILD-TYPE                                   352
                    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                                                     2
  16Q LOSS WILD-TYPE                                                   4
D69V8, multiclass
                                                             clus
vv                                                            16Q LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     58
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        2
                                                             clus
vv                                                            16Q LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      352
  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"
D69V9, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED     9  51
  16Q LOSS WILD-TYPE  70 287
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      9   51
  16Q LOSS WILD-TYPE   70  287
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  NO                 9                 70
  YES               51                287
[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                                1     8
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16Q LOSS MUTATED                           6    52
  16Q LOSS WILD-TYPE                        27   309
D69V12, multiclass
                                  clus
vv                                 16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           2                  8
  BLACK OR AFRICAN AMERICAN                       6                 27
  WHITE                                          52                309
[1] 4 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     2  57
  16Q LOSS WILD-TYPE  16 324
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      2   57
  16Q LOSS WILD-TYPE   16  324
                        clus
vv                       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                 16
  NOT HISPANIC OR LATINO               57                324
[1] 2 2
[1] FALSE

Clustering(70) Variable = 17P LOSS MUTATION ANALYSIS
D70V1, survival
                    sevent
clus2                  0   1
  17P LOSS MUTATED    53  26
  17P LOSS WILD-TYPE 204  72
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                79                276 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                26                 72 
$`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-A6D8 TCGA-BA-A6DE TCGA-BB-4223 TCGA-BB-7862 TCGA-BB-7866 
          63          513          182         2878          536          638 
TCGA-BB-7870 TCGA-BB-7871 TCGA-CN-4725 TCGA-CN-4730 TCGA-CN-4735 TCGA-CN-4739 
        1153          428          485          462          369         1330 
TCGA-CN-4742 TCGA-CN-5360 TCGA-CN-5374 TCGA-CN-6988 TCGA-CN-A63W TCGA-CQ-6221 
        1988         1081          290          318          348         1000 
TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6228 TCGA-CQ-7067 TCGA-CQ-7069 TCGA-CQ-A4C7 
        1057          985         1959          509          901         1960 
TCGA-CQ-A4C9 TCGA-CR-6472 TCGA-CR-6481 TCGA-CR-6484 TCGA-CR-7364 TCGA-CR-7371 
         613         1050          311          354         1435         1979 
TCGA-CR-7390 TCGA-CR-7398 TCGA-CV-5431 TCGA-CV-5439 TCGA-CV-5444 TCGA-CV-5966 
         907          156          522          546         2437          519 
TCGA-CV-5970 TCGA-CV-5978 TCGA-CV-6441 TCGA-CV-6961 TCGA-CV-7102 TCGA-CV-7180 
         406          215         1970         1959         1945         1987 
TCGA-CV-7245 TCGA-CV-7406 TCGA-CV-7424 TCGA-CV-7428 TCGA-CV-7435 TCGA-CV-7440 
         797         1974         1947         1973         1959         1981 
TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6823 TCGA-D6-6826 TCGA-D6-8569 TCGA-DQ-5629 
         237          828          701          154          128          516 
TCGA-DQ-7588 TCGA-DQ-7591 TCGA-DQ-7595 TCGA-F7-A50G TCGA-F7-A50J TCGA-F7-A620 
        1965          622          324           15          585           13 
TCGA-F7-A623 TCGA-H7-A6C5 TCGA-HD-8635 TCGA-IQ-7630 TCGA-IQ-A61G TCGA-IQ-A61H 
           6          403           25          485          360          412 
TCGA-MT-A67D TCGA-MT-A67G TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SX TCGA-P3-A6T8 
          56          112         1652          721         1954          400 
TCGA-QK-A64Z 
         553 

$`17P 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-5558 TCGA-BA-6869 TCGA-BA-6872 
        1762          520          725         1636          644          384 
TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BB-4217 
         113          236          895          351          216          187 
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-7872 TCGA-BB-8596 TCGA-BB-8601 TCGA-C9-A47Z TCGA-C9-A480 
         687          436         1955          624            5            4 
TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 
         799          721          142          452          613          392 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4740 
         993          642          395          240         1960          811 
TCGA-CN-4741 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5363 
        1268          488          512          173         1980         1977 
TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6010 
        1980         1966         1966         1975          413          630 
TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 
         424          629          433          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          424          224 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 
         611          394          119          432          429           46 
TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63Y 
         443          447          225          526          484          175 
TCGA-CN-A641 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 
         367         1466         1207          654         1660         1422 
TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 
         896         1399          317          341          129          870 
TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7068 
        1959          815         1461         1378         1007         1309 
TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE 
         877          968         1963          545          548          393 
TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 
         391          303          608         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-6482 TCGA-CR-6487 
        1971          514         1969          362          345          234 
TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7365 TCGA-CR-7367 
         379          350          479         1956         1191         1440 
TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7374 
        1245         1960          105          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-7391 TCGA-CR-7392 TCGA-CR-7393 
        1430         1951          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-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-5971 TCGA-CV-5973 
        1978         2886         2327         1958          701         2641 
TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 
        1478         1840         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-7090 TCGA-CV-7091 
        1969         1966         1957         1969         3837         1959 
TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7183 
        1970         1970         1936         1959         1939         1979 
TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7248 TCGA-CV-7250 
        1724         1444         1095          954         1967         1960 
TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7427 
        1976         1099         1948         1955         1957         1937 
TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-A45O TCGA-CV-A45Q 
        1972         1937         1984         1958          851         1945 
TCGA-CV-A461 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CX-7082 TCGA-CX-7085 
        1954         1970          750          717          317          321 
TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6827 TCGA-D6-8568 
         773          292           77          491          568          106 
TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 
         112          104         1778         1081         1030          548 
TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7596 
         575          775          299          369          368          340 
TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50I TCGA-F7-A61S TCGA-F7-A61V 
         564          490          658           92            3          384 
TCGA-F7-A61W TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-HD-7229 
          14          407           58          133          414            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-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67F 
         224          210           14           34          392          111 
TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A6SW TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T4 
         254          910         1120          578         1917         1968 
TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ 
         357          245          218          228          225           64 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 6                  2 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              2878               3837 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               553                643 
[1] "6.0 - 2878.0 (553.0)" "2.0 - 3837.0 (643.0)"
[1] "hr=" "1.1"
D70V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  17P LOSS MUTATED         2       17        17        42         1
  17P LOSS WILD-TYPE      22       46        54       150         8
D70V3, multiclass
           clus
vv          17P LOSS MUTATED 17P LOSS WILD-TYPE
  STAGE I                  2                 22
  STAGE II                17                 46
  STAGE III               17                 54
  STAGE IVA               42                150
  STAGE IVB                1                  8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  17P LOSS MUTATED     7  25  21  27
  17P LOSS WILD-TYPE  33  83  64 104
D70V4, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  T1                7                 33
  T2               25                 83
  T3               21                 64
  T4               27                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
  17P LOSS MUTATED    29  13  30   1
  17P LOSS WILD-TYPE 107  43  99   6
D70V5, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  N0               29                107
  N1               13                 43
  N2               30                 99
  N3                1                  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"
D70V6, binary
                    cls
clus                  0  1
  17P LOSS MUTATED   22 13
  17P LOSS WILD-TYPE 86 35
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     22   13
  17P LOSS WILD-TYPE   86   35
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  M0               22                 86
  MX               13                 35
[1] 2 2
[1] FALSE
D70V7, binary
                    cls
clus                   0   1
  17P LOSS MUTATED    23  68
  17P LOSS WILD-TYPE  98 228
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     23   68
  17P LOSS WILD-TYPE   98  228
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE               23                 98
  MALE                 68                228
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  17P LOSS MUTATED                                      90
  17P LOSS WILD-TYPE                                   320
                    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                                                     1
  17P LOSS WILD-TYPE                                                   5
D70V8, multiclass
                                                             clus
vv                                                            17P 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                        1
                                                             clus
vv                                                            17P LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      320
  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"
D70V9, binary
                    cls
clus                   0   1
  17P LOSS MUTATED    19  72
  17P LOSS WILD-TYPE  60 266
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     19   72
  17P LOSS WILD-TYPE   60  266
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  NO                19                 60
  YES               72                266
[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                                1     8
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17P LOSS MUTATED                           9    77
  17P LOSS WILD-TYPE                        24   284
D70V12, multiclass
                                  clus
vv                                 17P LOSS MUTATED 17P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           2                  8
  BLACK OR AFRICAN AMERICAN                       9                 24
  WHITE                                          77                284
[1] 4 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     8  78
  17P LOSS WILD-TYPE  10 303
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      8   78
  17P LOSS WILD-TYPE   10  303
                        clus
vv                       17P LOSS MUTATED 17P LOSS WILD-TYPE
  HISPANIC OR LATINO                    8                 10
  NOT HISPANIC OR LATINO               78                303
[1] 2 2
[1] FALSE

Clustering(71) Variable = 17Q LOSS MUTATION ANALYSIS
D71V1, survival
                    sevent
clus2                  0   1
  17Q LOSS MUTATED    19   8
  17Q LOSS WILD-TYPE 238  90
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                27                328 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 8                 90 
$`17Q LOSS MUTATED`
TCGA-BA-4075 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6871 TCGA-BB-4223 
         283         1747          190          451           63         2878 
TCGA-CN-4739 TCGA-CN-5374 TCGA-CN-6011 TCGA-CQ-6221 TCGA-CQ-6224 TCGA-CQ-7067 
        1330          290          424         1000          985          509 
TCGA-CQ-A4C7 TCGA-CR-6484 TCGA-CV-5966 TCGA-D6-6823 TCGA-D6-6826 TCGA-F7-A50G 
        1960          354          519          701          154           15 
TCGA-F7-A620 TCGA-HD-8635 TCGA-IQ-7630 TCGA-IQ-A61G TCGA-IQ-A61H TCGA-MT-A67G 
          13           25          485          360          412          112 
TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SX 
        1652          721         1954 

$`17Q 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-5558 
        1288         1762          520          725          623         1636 
TCGA-BA-6869 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A6D8 
         644          384          113          236          895          513 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BB-4217 TCGA-BB-4224 TCGA-BB-4225 
         351          216          182          187          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-4726 
           5            4          799          721          485          142 
TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
         452          613          392          462          993          642 
TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4740 TCGA-CN-4741 
         369          395          240         1960          811         1268 
TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 
        1988          488          512          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          413 
TCGA-CN-6010 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 
         630          629          433          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          424          224 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 
         318          611          394          119          432          429 
TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V 
          46          443          447          225          526          484 
TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 
         348          175          367         1466         1207          654 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 
        1660         1422          896         1399          317          341 
TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6223 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 
         129          870         1057         1959         1959          815 
TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 
        1461         1378         1007         1309          901          877 
TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE 
         968          613         1963          545          548          393 
TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 
         391          303          608         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-6478 TCGA-CR-6480 TCGA-CR-6481 
        1125         1971          514         1969          362          311 
TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 
         345          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-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-5970 TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 
        2437          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-7235 TCGA-CV-7238 TCGA-CV-7242 
        1945         1987         1979         1724         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-7433 TCGA-CV-7434 TCGA-CV-7435 
        1973         1972         1937         1984         1958         1959 
TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A461 TCGA-CV-A6JD TCGA-CV-A6JE 
        1981          851         1945         1954         1970          750 
TCGA-CV-A6JN TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 
         717          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-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 
         112          104         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-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8298 
         369          368          324          340          564          490 
TCGA-F7-8489 TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W 
         658           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-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-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 
          24           11           49           10          111           33 
TCGA-HL-7533 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61J TCGA-IQ-A61L 
        1057          122          441          588          440          351 
TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A 
         360          224          210           14           34          392 
TCGA-MT-A67D TCGA-MT-A67F TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A6SW TCGA-P3-A6T0 
          56          111          254          910         1120          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 
         218          228          225           64 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                13                  2 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              2878               3837 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             451.0              639.5 
[1] "13.0 - 2878.0 (451.0)" "2.0 - 3837.0 (639.5)" 
[1] "hr=" "1.7"
D71V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  17Q LOSS MUTATED         2        3         8        12         0
  17Q LOSS WILD-TYPE      22       60        63       180         9
D71V3, multiclass
           clus
vv          17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  STAGE I                  2                 22
  STAGE II                 3                 60
  STAGE III                8                 63
  STAGE IVA               12                180
  STAGE IVB                0                  9
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  17Q LOSS MUTATED     4  10   5   7
  17Q LOSS WILD-TYPE  36  98  80 124
D71V4, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  T1                4                 36
  T2               10                 98
  T3                5                 80
  T4                7                124
[1] 4 2
[1] 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     8   7   9   0
  17Q LOSS WILD-TYPE 128  49 120   7
D71V5, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  N0                8                128
  N1                7                 49
  N2                9                120
  N3                0                  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"
D71V6, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     8   8
  17Q LOSS WILD-TYPE 100  40
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      8    8
  17Q LOSS WILD-TYPE  100   40
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  M0                8                100
  MX                8                 40
[1] 2 2
[1] FALSE
D71V7, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     8  22
  17Q LOSS WILD-TYPE 113 274
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      8   22
  17Q LOSS WILD-TYPE  113  274
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE                8                113
  MALE                 22                274
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  17Q LOSS MUTATED                                      29
  17Q LOSS WILD-TYPE                                   381
                    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                                                   5
D71V8, multiclass
                                                             clus
vv                                                            17Q LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     29
  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                                      381
  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"
D71V9, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     8  22
  17Q LOSS WILD-TYPE  71 316
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      8   22
  17Q LOSS WILD-TYPE   71  316
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  NO                 8                 71
  YES               22                316
[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                                1     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17Q LOSS MUTATED                           3    25
  17Q LOSS WILD-TYPE                        30   336
D71V12, multiclass
                                  clus
vv                                 17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                  9
  BLACK OR AFRICAN AMERICAN                       3                 30
  WHITE                                          25                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"
D71V13, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     3  25
  17Q LOSS WILD-TYPE  15 356
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      3   25
  17Q LOSS WILD-TYPE   15  356
                        clus
vv                       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                 15
  NOT HISPANIC OR LATINO               25                356
[1] 2 2
[1] FALSE

Clustering(72) Variable = 18P LOSS MUTATION ANALYSIS
D72V1, survival
                    sevent
clus2                  0   1
  18P LOSS MUTATED    46  20
  18P LOSS WILD-TYPE 211  78
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                66                289 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                20                 78 
$`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          513 
TCGA-BA-A6DB TCGA-BB-8601 TCGA-CN-4727 TCGA-CN-4735 TCGA-CN-4739 TCGA-CN-4740 
         216          624          452          369         1330          811 
TCGA-CN-5370 TCGA-CN-6010 TCGA-CN-6019 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6998 
        1975          630          432          119          432           46 
TCGA-CQ-5325 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-A4C7 TCGA-CQ-A4CG TCGA-CR-6484 
         654         1057          985         1960          391          354 
TCGA-CR-7367 TCGA-CR-7373 TCGA-CR-7374 TCGA-CV-5435 TCGA-CV-5439 TCGA-CV-5444 
        1440          889           30         1438          546         2437 
TCGA-CV-5966 TCGA-CV-6003 TCGA-CV-6942 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7091 
         519         1665         3835         1969         1959         1959 
TCGA-CV-7095 TCGA-CV-7235 TCGA-CV-7245 TCGA-CV-7261 TCGA-CV-7424 TCGA-CV-7432 
        1970         1724          797         1099         1947         1937 
TCGA-CV-7433 TCGA-CX-7219 TCGA-DQ-5624 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-7588 
        1984          828         1778          516         1030         1965 
TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50I TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-A6C4 
         564          658           92           13            6          414 
TCGA-HD-7229 TCGA-IQ-7630 TCGA-IQ-A61E TCGA-IQ-A61H TCGA-IQ-A61L TCGA-IQ-A61O 
           2          485          588          412          351          360 
TCGA-KU-A66S TCGA-MT-A51W TCGA-MT-A67D TCGA-P3-A6T0 TCGA-P3-A6T8 TCGA-QK-A6IH 
         224           14           56          578          400          228 

$`18P 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-5558 TCGA-BA-5559 
        1288         1762          520          725         1636         1747 
TCGA-BA-6869 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A6DA 
         644           63          384          113          236          351 
TCGA-BA-A6DE TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4227 
         182          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-C9-A47Z TCGA-C9-A480 
        1153          428          436         1955            5            4 
TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 
         799          721          485          142          613          392 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 
         462          993          642          395          240         1960 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 
        1268         1988          488          512          173         1980 
TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5373 
        1081         1977         1980         1966         1966          413 
TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 
         290          424          629          433          594          629 
TCGA-CN-6018 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 
          45           98         1970          202          424          224 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A498 TCGA-CN-A49B 
         318          611          394          429          443          447 
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-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 
        1466         1207         1660         1422          896         1399 
TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6227 
         317          341          129          870         1000         1959 
TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 
        1959          815         1461         1378         1007          509 
TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CA 
        1309          901          877          968          613         1963 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 
         545          548          393          303          608         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-A461 
        1958         1959         1981          851         1945         1954 
TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 
        1970          750          717          317          321          237 
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-DQ-5625 
         568          106          128          112          104         1081 
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-A50J 
         368          324          340          490           15          585 
TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 
           3          384           14          407           58          133 
TCGA-H7-A6C5 TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 
         403            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-A61G TCGA-IQ-A61J 
          33         1057          122          441          360          440 
TCGA-KU-A66T TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 
         210           34          392          111          112          254 
TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T2 
         910         1652          721         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 
          64 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 2                  3 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              3835               3837 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               583                641 
[1] "2.0 - 3835.0 (583.0)" "3.0 - 3837.0 (641.0)"
[1] "hr=" "1.2"
D72V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  18P LOSS MUTATED         5       15        16        39         2
  18P LOSS WILD-TYPE      19       48        55       153         7
D72V3, multiclass
           clus
vv          18P LOSS MUTATED 18P LOSS WILD-TYPE
  STAGE I                  5                 19
  STAGE II                15                 48
  STAGE III               16                 55
  STAGE IVA               39                153
  STAGE IVB                2                  7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  18P LOSS MUTATED     8  22  18  29
  18P LOSS WILD-TYPE  32  86  67 102
D72V4, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  T1                8                 32
  T2               22                 86
  T3               18                 67
  T4               29                102
[1] 4 2
[1] 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    33  14  22   1
  18P LOSS WILD-TYPE 103  42 107   6
D72V5, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  N0               33                103
  N1               14                 42
  N2               22                107
  N3                1                  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"
D72V6, binary
                    cls
clus                  0  1
  18P LOSS MUTATED   22 10
  18P LOSS WILD-TYPE 86 38
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     22   10
  18P LOSS WILD-TYPE   86   38
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  M0               22                 86
  MX               10                 38
[1] 2 2
[1] FALSE
D72V7, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    29  56
  18P LOSS WILD-TYPE  92 240
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     29   56
  18P LOSS WILD-TYPE   92  240
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE               29                 92
  MALE                 56                240
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  18P LOSS MUTATED                                      83
  18P LOSS WILD-TYPE                                   327
                    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                                                   5
D72V8, multiclass
                                                             clus
vv                                                            18P LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     83
  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                                      327
  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"
D72V9, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    17  68
  18P LOSS WILD-TYPE  62 270
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     17   68
  18P LOSS WILD-TYPE   62  270
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  NO                17                 62
  YES               68                270
[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                                1     8
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18P LOSS MUTATED                          10    70
  18P LOSS WILD-TYPE                        23   291
D72V12, multiclass
                                  clus
vv                                 18P LOSS MUTATED 18P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           2                  8
  BLACK OR AFRICAN AMERICAN                      10                 23
  WHITE                                          70                291
[1] 4 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     8  72
  18P LOSS WILD-TYPE  10 309
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      8   72
  18P LOSS WILD-TYPE   10  309
                        clus
vv                       18P LOSS MUTATED 18P LOSS WILD-TYPE
  HISPANIC OR LATINO                    8                 10
  NOT HISPANIC OR LATINO               72                309
[1] 2 2
[1] FALSE

Clustering(73) Variable = 18Q LOSS MUTATION ANALYSIS
D73V1, survival
                    sevent
clus2                  0   1
  18Q LOSS MUTATED   104  46
  18Q LOSS WILD-TYPE 153  52
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               150                205 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                46                 52 
$`18Q LOSS MUTATED`
TCGA-BA-4074 TCGA-BA-4075 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6870 
         462          283          623         1636          190          451 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A6D8 TCGA-BA-A6DB 
         384          113          236          895          513          216 
TCGA-BA-A6DE TCGA-BB-4224 TCGA-BB-7862 TCGA-BB-7872 TCGA-BB-8601 TCGA-C9-A47Z 
         182          278          536          436          624            5 
TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4730 
         721          485          142          452          613          462 
TCGA-CN-4735 TCGA-CN-4737 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-5355 TCGA-CN-5363 
         369          240         1330          811          488         1977 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6010 TCGA-CN-6011 
        1966         1966         1975          413          630          424 
TCGA-CN-6019 TCGA-CN-6022 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A63T 
         432          202          119          432           46          225 
TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A641 TCGA-CQ-5325 TCGA-CQ-5332 TCGA-CQ-6218 
         526          348          367          654          317          870 
TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7064 
        1057          985         1959         1959          815         1378 
TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CB TCGA-CQ-A4CG 
        1007          509          968         1960          545          391 
TCGA-CR-5247 TCGA-CR-6474 TCGA-CR-6484 TCGA-CR-6493 TCGA-CR-7365 TCGA-CR-7373 
         358         1971          354         1956         1191          889 
TCGA-CR-7374 TCGA-CR-7377 TCGA-CR-7386 TCGA-CR-7399 TCGA-CR-7402 TCGA-CV-5435 
          30         1968         1430          181          911         1438 
TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 
         546         1978         2886         2437          519          406 
TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6935 
        2641         1478         1840         1315         1665         1969 
TCGA-CV-6942 TCGA-CV-6945 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-7090 TCGA-CV-7091 
        3835         1969         1957         1969         3837         1959 
TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7101 TCGA-CV-7180 TCGA-CV-7235 TCGA-CV-7243 
        1970         1970         1939         1987         1724          954 
TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7424 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 
         797         1967         1947         1972         1937         1984 
TCGA-CV-7434 TCGA-CV-7440 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6823 
        1958         1981          237          828          773          701 
TCGA-D6-6825 TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-DQ-5624 TCGA-DQ-5629 TCGA-DQ-5630 
         491          106          112         1778          516         1030 
TCGA-DQ-7588 TCGA-DQ-7595 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I 
        1965          324          564          658           15           92 
TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 
          14           13            6           58          133          414 
TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8635 TCGA-HD-A6HZ 
         403            2           37           55           25          111 
TCGA-IQ-7630 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61L TCGA-IQ-A61O 
         485          588          360          412          351          360 
TCGA-KU-A66S TCGA-KU-A66T TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67D TCGA-P3-A5QA 
         224          210           14           34           56         1652 
TCGA-P3-A6T0 TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IH 
         578         1968          400          553          357          228 

$`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-A6DA TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 
         351          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-A480 TCGA-CN-4722 TCGA-CN-4729 TCGA-CN-4731 TCGA-CN-4733 
        1955            4          799          392          993          642 
TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5358 
         395         1960         1268         1988          512          173 
TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5365 TCGA-CN-5374 TCGA-CN-6012 TCGA-CN-6013 
        1980         1081         1980          290          629          433 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6023 
         594          629           45           98         1970          424 
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-A49B TCGA-CN-A63V TCGA-CN-A63Y TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5327 
         447          484          175         1466         1207         1660 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6221 
        1422          896         1399          341          129         1000 
TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C9 TCGA-CQ-A4CA 
        1461         1309          901          877          613         1963 
TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5248 
         548          393          303          608         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-6477 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 
        1125          514         1969          362          311          345 
TCGA-CR-6487 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-7364 TCGA-CR-7367 
         234          379          350          479         1435         1440 
TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7376 
        1245         1960          105         1979          759          972 
TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7385 TCGA-CR-7388 TCGA-CR-7389 
        1036          796         1954          997         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-7404 TCGA-CV-5430 TCGA-CV-5431 
         216          156         1077         1472         1955          522 
TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5436 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5971 
        1950         3295          584         2327         1958          701 
TCGA-CV-5978 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6936 
         215          641         1899         1970         1948         1952 
TCGA-CV-6941 TCGA-CV-6943 TCGA-CV-6952 TCGA-CV-6961 TCGA-CV-7099 TCGA-CV-7100 
        1959         1948         1966         1959         1936         1959 
TCGA-CV-7102 TCGA-CV-7183 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7250 TCGA-CV-7254 
        1945         1979         1444         1095         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-7435 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A461 TCGA-CV-A6JD 
        1973         1959          851         1945         1954         1970 
TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CX-7082 TCGA-CX-7085 TCGA-D6-6517 TCGA-D6-6824 
         750          717          317          321          292           77 
TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-8569 TCGA-D6-A4ZB TCGA-DQ-5625 TCGA-DQ-5631 
         154          568          128          104         1081          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-7596 TCGA-F7-8298 TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-H7-7774 
         340          490          585            3          384          407 
TCGA-HD-7753 TCGA-HD-7754 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-A4C1 TCGA-HD-A633 
           5           25           44           24           11           49 
TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61J 
          10           33         1057          122          441          440 
TCGA-MT-A67A TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QE 
         392          111          112          254          910          721 
TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T2 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6II 
        1120         1954         1917          245          218          225 
TCGA-QK-A6IJ 
          64 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 2                  3 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              3837               3295 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             545.5              717.0 
[1] "2.0 - 3837.0 (545.5)" "3.0 - 3295.0 (717.0)"
[1] "hr=" "1"  
D73V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  18Q LOSS MUTATED        11       28        30        90         4
  18Q LOSS WILD-TYPE      13       35        41       102         5
D73V3, multiclass
           clus
vv          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  STAGE I                 11                 13
  STAGE II                28                 35
  STAGE III               30                 41
  STAGE IVA               90                102
  STAGE IVB                4                  5
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  18Q LOSS MUTATED   19 46 36 62
  18Q LOSS WILD-TYPE 21 62 49 69
D73V4, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T1               19                 21
  T2               46                 62
  T3               36                 49
  T4               62                 69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  18Q LOSS MUTATED   55 29 61  3
  18Q LOSS WILD-TYPE 81 27 68  4
D73V5, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  N0               55                 81
  N1               29                 27
  N2               61                 68
  N3                3                  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"
D73V6, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED   43 25
  18Q LOSS WILD-TYPE 65 23
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     43   25
  18Q LOSS WILD-TYPE   65   23
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  M0               43                 65
  MX               25                 23
[1] 2 2
[1] FALSE
D73V7, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED    46 131
  18Q LOSS WILD-TYPE  75 165
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     46  131
  18Q LOSS WILD-TYPE   75  165
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE               46                 75
  MALE                131                165
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  18Q LOSS MUTATED                                     175
  18Q LOSS WILD-TYPE                                   235
                    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                                                   5
D73V8, multiclass
                                                             clus
vv                                                            18Q LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    175
  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                                      235
  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"
D73V9, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED    36 141
  18Q LOSS WILD-TYPE  43 197
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     36  141
  18Q LOSS WILD-TYPE   43  197
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  NO                36                 43
  YES              141                197
[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                                1     3
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18Q LOSS MUTATED                          19   145
  18Q LOSS WILD-TYPE                        14   216
D73V12, multiclass
                                  clus
vv                                 18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           7                  3
  BLACK OR AFRICAN AMERICAN                      19                 14
  WHITE                                         145                216
[1] 4 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    11 158
  18Q LOSS WILD-TYPE   7 223
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     11  158
  18Q LOSS WILD-TYPE    7  223
                        clus
vv                       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   11                  7
  NOT HISPANIC OR LATINO              158                223
[1] 2 2
[1] FALSE

Clustering(74) Variable = 19P LOSS MUTATION ANALYSIS
D74V1, survival
                    sevent
clus2                  0   1
  19P LOSS MUTATED    40  28
  19P LOSS WILD-TYPE 217  70
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                68                287 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                28                 70 
$`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          485          392          240 
TCGA-CN-4738 TCGA-CN-5356 TCGA-CN-5363 TCGA-CN-5370 TCGA-CN-5374 TCGA-CN-6012 
        1960          512         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          119          432 
TCGA-CQ-5330 TCGA-CQ-6223 TCGA-CQ-7064 TCGA-CQ-7069 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
         896         1057         1378          901         1960          613 
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-D6-6825 TCGA-D6-6826 TCGA-D6-8569 
        1972         1981          717          491          154          128 
TCGA-DQ-5624 TCGA-DQ-7588 TCGA-DQ-7592 TCGA-F7-7848 TCGA-F7-A50I TCGA-F7-A61W 
        1778         1965          299          564           92           14 
TCGA-HD-7753 TCGA-HL-7533 TCGA-IQ-A61G TCGA-IQ-A61L TCGA-MT-A51X TCGA-P3-A6SX 
           5         1057          360          351           34         1954 
TCGA-QK-A652 TCGA-QK-A6IJ 
         357           64 

$`19P 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-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6869 
         520          725          623         1636         1747          644 
TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A6D8 
         451           63          384          113          236          513 
TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 
         216          182          187         2878          278          140 
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-A480 TCGA-CN-4722 
        1153          428          436          624            4          799 
TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4730 TCGA-CN-4731 
         721          142          452          613          462          993 
TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 
         642          369          395         1330          811         1268 
TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5365 
        1988          488          173         1980         1081         1980 
TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5373 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6013 
        1966         1966          413          630          424          433 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6021 TCGA-CN-6023 TCGA-CN-6024 
         594          629          432         1970          424          224 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49B 
         318          611          429           46          443          447 
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-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-6221 TCGA-CQ-6224 
         317          341          129          870         1000          985 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7065 TCGA-CQ-7067 
        1959         1959          815         1461         1007          509 
TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD 
        1309          877          968         1963          545          548 
TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 
         393          391          303          608         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-6478 TCGA-CR-6480 TCGA-CR-6481 
        1050         1125         1971         1969          362          311 
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-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 
        1956         1440         1245         1960          105         1979 
TCGA-CR-7372 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 
         759           30          972         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-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 
        1077          911         1472         1955          522         1950 
TCGA-CV-5436 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5444 
         584         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-6433 TCGA-CV-6436 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 
         215          641         1899         1948         1969         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-7090 TCGA-CV-7091 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 
        3837         1959         1936         1959         1939         1945 
TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 
        1979         1724         1444         1095          954          797 
TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 
        1967         1960         1099         1974         1948         1955 
TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7432 TCGA-CV-7433 
        1957         1947         1937         1973         1937         1984 
TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A461 TCGA-CV-A6JD 
        1958         1959          851         1945         1954         1970 
TCGA-CV-A6JE TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 
         750          317          321          237          828          773 
TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-A4Z9 
         292          701           77          568          106          112 
TCGA-D6-A4ZB TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7589 
         104         1081          516         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-F7-8298 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V 
         490          658           15          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-HD-7229 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 
         403            2           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-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61H 
          33          485          122          441          588          412 
TCGA-IQ-A61J TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-MT-A51W TCGA-MT-A67A 
         440          360          224          210           14          392 
TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QA 
          56          111          112          254          910         1652 
TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T4 TCGA-P3-A6T8 
         721         1120          578         1917         1968          400 
TCGA-QK-A64Z TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II 
         553          245          218          228          225 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 5                  2 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              3295               3837 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
               621                629 
[1] "5.0 - 3295.0 (621.0)" "2.0 - 3837.0 (629.0)"
[1] "hr=" "1.3"
D74V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  19P LOSS MUTATED         2       12        21        35         1
  19P LOSS WILD-TYPE      22       51        50       157         8
D74V3, multiclass
           clus
vv          19P LOSS MUTATED 19P LOSS WILD-TYPE
  STAGE I                  2                 22
  STAGE II                12                 51
  STAGE III               21                 50
  STAGE IVA               35                157
  STAGE IVB                1                  8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  19P LOSS MUTATED     5  25  19  23
  19P LOSS WILD-TYPE  35  83  66 108
D74V4, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  T1                5                 35
  T2               25                 83
  T3               19                 66
  T4               23                108
[1] 4 2
[1] 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    22  17  24   1
  19P LOSS WILD-TYPE 114  39 105   6
D74V5, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  N0               22                114
  N1               17                 39
  N2               24                105
  N3                1                  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"
D74V6, binary
                    cls
clus                  0  1
  19P LOSS MUTATED   24  5
  19P LOSS WILD-TYPE 84 43
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     24    5
  19P LOSS WILD-TYPE   84   43
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  M0               24                 84
  MX                5                 43
[1] 2 2
[1] FALSE
D74V7, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    18  62
  19P LOSS WILD-TYPE 103 234
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     18   62
  19P LOSS WILD-TYPE  103  234
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE               18                103
  MALE                 62                234
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  19P LOSS MUTATED                                      80
  19P LOSS WILD-TYPE                                   330
                    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                                                   6
D74V8, multiclass
                                                             clus
vv                                                            19P LOSS 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                        0
                                                             clus
vv                                                            19P LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      330
  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"
D74V9, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    19  61
  19P LOSS WILD-TYPE  60 277
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     19   61
  19P LOSS WILD-TYPE   60  277
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  NO                19                 60
  YES               61                277
[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                                0     8
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19P LOSS MUTATED                           7    67
  19P LOSS WILD-TYPE                        26   294
D74V12, multiclass
                                  clus
vv                                 19P LOSS MUTATED 19P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           2                  8
  BLACK OR AFRICAN AMERICAN                       7                 26
  WHITE                                          67                294
[1] 4 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     5  73
  19P LOSS WILD-TYPE  13 308
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      5   73
  19P LOSS WILD-TYPE   13  308
                        clus
vv                       19P LOSS MUTATED 19P LOSS WILD-TYPE
  HISPANIC OR LATINO                    5                 13
  NOT HISPANIC OR LATINO               73                308
[1] 2 2
[1] FALSE

Clustering(75) Variable = 19Q LOSS MUTATION ANALYSIS
D75V1, survival
                    sevent
clus2                  0   1
  19Q LOSS MUTATED    38  22
  19Q LOSS WILD-TYPE 219  76
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                60                295 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                22                 76 
$`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          485          240          512         1977          290 
TCGA-CN-6018 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 
          45          611          394          119          432          429 
TCGA-CQ-7064 TCGA-CQ-7069 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CI TCGA-CR-6477 
        1378          901         1960          613          608          514 
TCGA-CR-7365 TCGA-CR-7373 TCGA-CR-7377 TCGA-CR-7398 TCGA-CV-5432 TCGA-CV-5434 
        1191          889         1968          156         1950         3295 
TCGA-CV-5435 TCGA-CV-5439 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6441 TCGA-CV-6941 
        1438          546         1315         1665         1970         1959 
TCGA-CV-6960 TCGA-CV-7097 TCGA-CV-7180 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7430 
        1969         1970         1987         1976         1099         1972 
TCGA-CV-A6JN TCGA-D6-6517 TCGA-D6-6826 TCGA-D6-8569 TCGA-DQ-7588 TCGA-F7-A61W 
         717          292          154          128         1965           14 
TCGA-HD-7753 TCGA-IQ-A61L TCGA-MT-A51X TCGA-P3-A6T2 TCGA-QK-A652 TCGA-QK-A6IJ 
           5          351           34         1917          357           64 

$`19Q 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-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6869 
        1762          725          623         1636         1747          644 
TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A6D8 TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BB-4217 
         384          236          513          216          182          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-7870 TCGA-BB-7871 TCGA-BB-7872 
         423          687          638         1153          428          436 
TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 
           4          799          721          142          452          613 
TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4736 
         392          462          993          642          369          395 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 
        1960         1330          811         1268         1988          488 
TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 
         173         1980         1081         1980         1966         1966 
TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 
        1975          413          630          424          629          433 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6022 
         594          629          432           98         1970          202 
TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49B 
         424          224          318           46          443          447 
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-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 
        1466         1207          654         1660         1422          896 
TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 
        1399          317          341          129          870         1000 
TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 
        1057          985         1959         1959          815         1461 
TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4CA 
        1007          509         1309          877          968         1963 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5243 
         545          548          393          391          303         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-6478 TCGA-CR-6480 
        1966         1050         1125         1971         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-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-5436 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 
         522          584         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-6433 TCGA-CV-6436 TCGA-CV-6934 TCGA-CV-6935 
        1840          215          641         1899         1948         1969 
TCGA-CV-6936 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-6954 
        1952         3835         1948         1969         1966         1957 
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-7183 TCGA-CV-7235 TCGA-CV-7238 TCGA-CV-7242 
        1939         1945         1979         1724         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-7432 
        1955         1957         1947         1937         1973         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-A461 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 
        1954         1970          750          317          321          237 
TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6827 
         828          773          701           77          491          568 
TCGA-D6-8568 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 
         106          112          104         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          564          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-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-HD-7229 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 
         403            2           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-A66T 
         360          412          440          360          224          210 
TCGA-MT-A51W TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A6I9 
          14          392           56          111          112          254 
TCGA-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 
         910         1652          721         1120         1954          578 
TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH 
        1968          400          553          245          218          228 
TCGA-QK-A6II 
         225 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 5                  2 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              3295               3837 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
               533                642 
[1] "5.0 - 3295.0 (533.0)" "2.0 - 3837.0 (642.0)"
[1] "hr=" "1.3"
D75V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  19Q LOSS MUTATED         1        8        20        31         1
  19Q LOSS WILD-TYPE      23       55        51       161         8
D75V3, multiclass
           clus
vv          19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  STAGE I                  1                 23
  STAGE II                 8                 55
  STAGE III               20                 51
  STAGE IVA               31                161
  STAGE IVB                1                  8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  19Q LOSS MUTATED     4  18  21  18
  19Q LOSS WILD-TYPE  36  90  64 113
D75V4, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  T1                4                 36
  T2               18                 90
  T3               21                 64
  T4               18                113
[1] 4 2
[1] 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    18  13  24   1
  19Q LOSS WILD-TYPE 118  43 105   6
D75V5, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  N0               18                118
  N1               13                 43
  N2               24                105
  N3                1                  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"
D75V6, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED   19  5
  19Q LOSS WILD-TYPE 89 43
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     19    5
  19Q LOSS WILD-TYPE   89   43
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  M0               19                 89
  MX                5                 43
[1] 2 2
[1] FALSE
D75V7, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    16  52
  19Q LOSS WILD-TYPE 105 244
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     16   52
  19Q LOSS WILD-TYPE  105  244
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE               16                105
  MALE                 52                244
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  19Q LOSS MUTATED                                      67
  19Q LOSS WILD-TYPE                                   343
                    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                                                   5
D75V8, multiclass
                                                             clus
vv                                                            19Q LOSS 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                        1
                                                             clus
vv                                                            19Q LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      343
  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"
D75V9, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    15  53
  19Q LOSS WILD-TYPE  64 285
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     15   53
  19Q LOSS WILD-TYPE   64  285
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  NO                15                 64
  YES               53                285
[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                                1     8
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19Q LOSS MUTATED                          10    53
  19Q LOSS WILD-TYPE                        23   308
D75V12, multiclass
                                  clus
vv                                 19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           2                  8
  BLACK OR AFRICAN AMERICAN                      10                 23
  WHITE                                          53                308
[1] 4 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     4  61
  19Q LOSS WILD-TYPE  14 320
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      4   61
  19Q LOSS WILD-TYPE   14  320
                        clus
vv                       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                 14
  NOT HISPANIC OR LATINO               61                320
[1] 2 2
[1] FALSE

Clustering(76) Variable = 20P LOSS MUTATION ANALYSIS
D76V1, survival
                    sevent
clus2                  0   1
  20P LOSS MUTATED    26  12
  20P LOSS WILD-TYPE 231  86
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                38                317 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                12                 86 
$`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 
         424          394          119          348          548          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         1724         1976         1955 
TCGA-CV-7435 TCGA-D6-6823 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-F7-7848 TCGA-F7-8298 
        1959          701          575          775          564          490 
TCGA-F7-A623 TCGA-HD-7917 
           6           37 

$`20P LOSS WILD-TYPE`
TCGA-BA-4078 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5557 
         276          248          722         1762          725          623 
TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6872 TCGA-BA-7269 
        1636         1747          190          644          384          236 
TCGA-BA-A4IF TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BB-4217 
         895          513          351          216          182          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-7870 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-8596 
         423          687         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          485          142 
TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
         452          613          392          462          993          642 
TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 
         369          395          240         1960         1330          811 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 
        1268         1988          488          512          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-6012 TCGA-CN-6013 TCGA-CN-6016 
         413          290          630          629          433          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-6996 TCGA-CN-6997 
         424          224          318          611          432          429 
TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V 
          46          443          447          225          526          484 
TCGA-CN-A63Y TCGA-CN-A641 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 
         175          367         1466         1207          654         1660 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 
        1422          896         1399          317          341          129 
TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 
         870         1000         1057          985         1959         1959 
TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 
         815         1461         1378         1007          509         1309 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CA 
         901          877          968         1960          613         1963 
TCGA-CQ-A4CB TCGA-CQ-A4CE TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 
         545          393          303          608         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-6477 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 
        1050         1125          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-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-7382 TCGA-CR-7385 
         759          889          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-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-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-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-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 
        1959         3837         1970         1970         1936         1959 
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-7261 TCGA-CV-7406 TCGA-CV-7410 
         797         1967         1960         1099         1974         1948 
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-7440 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A461 
        1984         1958         1981          851         1945         1954 
TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 
        1970          750          717          317          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-DQ-5624 
         568          106          128          112          104         1778 
TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7591 
        1081          516         1030          548         1965          622 
TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-8489 
         299          369          368          324          340          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-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-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-A61L TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T 
         412          440          351          360          224          210 
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-P3-A5Q5 TCGA-P3-A5QA TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX 
         254          910         1652          721         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 
         245          218          228          225           64 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 6                  2 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
              1983               3837 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             569.5              630.0 
[1] "6.0 - 1983.0 (569.5)" "2.0 - 3837.0 (630.0)"
[1] "hr=" "1.1"
D76V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  20P LOSS MUTATED         3        6         5        20         0
  20P LOSS WILD-TYPE      21       57        66       172         9
D76V3, multiclass
           clus
vv          20P LOSS MUTATED 20P LOSS WILD-TYPE
  STAGE I                  3                 21
  STAGE II                 6                 57
  STAGE III                5                 66
  STAGE IVA               20                172
  STAGE IVB                0                  9
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  20P LOSS MUTATED     4   9   8  13
  20P LOSS WILD-TYPE  36  99  77 118
D76V4, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  T1                4                 36
  T2                9                 99
  T3                8                 77
  T4               13                118
[1] 4 2
[1] 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    16   2  13   0
  20P LOSS WILD-TYPE 120  54 116   7
D76V5, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  N0               16                120
  N1                2                 54
  N2               13                116
  N3                0                  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"
D76V6, binary
                    cls
clus                  0  1
  20P LOSS MUTATED   13  2
  20P LOSS WILD-TYPE 95 46
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     13    2
  20P LOSS WILD-TYPE   95   46
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  M0               13                 95
  MX                2                 46
[1] 2 2
[1] FALSE
D76V7, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    11  31
  20P LOSS WILD-TYPE 110 265
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     11   31
  20P LOSS WILD-TYPE  110  265
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE               11                110
  MALE                 31                265
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  20P LOSS MUTATED                                      42
  20P LOSS WILD-TYPE                                   368
                    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                                                   6
D76V8, multiclass
                                                             clus
vv                                                            20P 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                        0
                                                             clus
vv                                                            20P LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      368
  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"
D76V9, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     9  33
  20P LOSS WILD-TYPE  70 305
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      9   33
  20P LOSS WILD-TYPE   70  305
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  NO                 9                 70
  YES               33                305
[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                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20P LOSS MUTATED                           5    36
  20P LOSS WILD-TYPE                        28   325
D76V12, multiclass
                                  clus
vv                                 20P LOSS MUTATED 20P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 10
  BLACK OR AFRICAN AMERICAN                       5                 28
  WHITE                                          36                325
[1] 4 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     1  40
  20P LOSS WILD-TYPE  17 341
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      1   40
  20P LOSS WILD-TYPE   17  341
                        clus
vv                       20P LOSS MUTATED 20P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 17
  NOT HISPANIC OR LATINO               40                341
[1] 2 2
[1] FALSE

Clustering(77) Variable = 20Q LOSS MUTATION ANALYSIS
D77V1, survival
                    sevent
clus2                  0   1
  20Q LOSS MUTATED    16   7
  20Q LOSS WILD-TYPE 241  91
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                23                332 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 7                 91 
$`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-7383 
        1081          608         2562         1125          105         1954 
TCGA-CR-7402 TCGA-CV-5440 TCGA-CV-7091 TCGA-CV-7101 TCGA-CV-7235 TCGA-CV-7254 
         911         1978         1959         1939         1724         1976 
TCGA-CV-7418 TCGA-CV-7435 TCGA-D6-6826 TCGA-DQ-7590 TCGA-HD-7917 
        1955         1959          154          775           37 

$`20Q LOSS 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-5153 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 
         722         1762          520          725          623         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-A4IF TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BA-A6DE TCGA-BB-4217 
         895          513          351          216          182          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-7870 TCGA-BB-7871 TCGA-BB-7872 
         536          423          687         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          485 
TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 
         142          452          613          462          993          642 
TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 
         369          395          240         1960         1330          811 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 
        1268         1988          488          512          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          413 
TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 
         290          630          424          629          433          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-6994 
         424          224          318          611          394          119 
TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63T 
         432          429           46          443          447          225 
TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 TCGA-CQ-5323 
         526          484          348          175          367         1466 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 
        1207          654         1660         1422          896         1399 
TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 
         317          341          129          870         1000         1057 
TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7064 
         985         1959         1959          815         1461         1378 
TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 
        1007          509         1309          901          877          968 
TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE 
        1960          613         1963          545          548          393 
TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 
         391          303          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-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-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-5441 TCGA-CV-5442 TCGA-CV-5443 
        1438          584          546         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-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-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 
        3837         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-7261 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7422 
        1967         1960         1099         1974         1948         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-A461 TCGA-CV-A6JD 
        1958         1981          851         1945         1954         1970 
TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CX-7082 TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 
         750          717          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-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-DQ-5624 TCGA-DQ-5625 
         106          128          112          104         1778         1081 
TCGA-DQ-5629 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7591 
         516         1030          548         1965          575          622 
TCGA-DQ-7592 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 
         299          369          368          324          340          564 
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-HD-7229 TCGA-HD-7753 TCGA-HD-7754 
         133          414          403            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-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-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A 
         360          224          210           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         1652 
TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T4 
         721         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-A6IJ 
         225           64 

  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                37                  2 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
              2562               3837 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
              1081                613 
[1] "37.0 - 2562.0 (1081.0)" "2.0 - 3837.0 (613.0)"  
[1] "hr=" "1.2"
D77V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  20Q LOSS MUTATED         2        5         4         6         0
  20Q LOSS WILD-TYPE      22       58        67       186         9
D77V3, multiclass
           clus
vv          20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  STAGE I                  2                 22
  STAGE II                 5                 58
  STAGE III                4                 67
  STAGE IVA                6                186
  STAGE IVB                0                  9
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  20Q LOSS MUTATED     2   7   3   5
  20Q LOSS WILD-TYPE  38 101  82 126
D77V4, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  T1                2                 38
  T2                7                101
  T3                3                 82
  T4                5                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
  20Q LOSS MUTATED     7   3   4   0
  20Q LOSS WILD-TYPE 129  53 125   7
D77V5, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  N0                7                129
  N1                3                 53
  N2                4                125
  N3                0                  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"
D77V6, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     4   1
  20Q LOSS WILD-TYPE 104  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      4    1
  20Q LOSS WILD-TYPE  104   47
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  M0                4                104
  MX                1                 47
[1] 2 2
[1] FALSE
D77V7, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     6  19
  20Q LOSS WILD-TYPE 115 277
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      6   19
  20Q LOSS WILD-TYPE  115  277
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  FEMALE                6                115
  MALE                 19                277
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  20Q LOSS MUTATED                                      24
  20Q LOSS WILD-TYPE                                   386
                    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                                                   5
D77V8, multiclass
                                                             clus
vv                                                            20Q LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     24
  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                                      386
  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"
D77V9, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     4  21
  20Q LOSS WILD-TYPE  75 317
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      4   21
  20Q LOSS WILD-TYPE   75  317
     clus
vv    20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  NO                 4                 75
  YES               21                317
[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                                1    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20Q LOSS MUTATED                           3    22
  20Q LOSS WILD-TYPE                        30   339
D77V12, multiclass
                                  clus
vv                                 20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           0                 10
  BLACK OR AFRICAN AMERICAN                       3                 30
  WHITE                                          22                339
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V13, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     0  24
  20Q LOSS WILD-TYPE  18 357
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      0   24
  20Q LOSS WILD-TYPE   18  357
                        clus
vv                       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 18
  NOT HISPANIC OR LATINO               24                357
[1] 2 2
[1] FALSE

Clustering(78) Variable = 21Q LOSS MUTATION ANALYSIS
D78V1, survival
                    sevent
clus2                  0   1
  21Q LOSS MUTATED    95  42
  21Q LOSS WILD-TYPE 162  56
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               137                218 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                42                 56 
$`21Q LOSS MUTATED`
TCGA-BA-4075 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6871 
         283         1636         1747          190          451           63 
TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BB-7862 TCGA-BB-7864 TCGA-BB-8596 TCGA-BB-8601 
         513          351          536          687         1955          624 
TCGA-C9-A47Z TCGA-CN-4725 TCGA-CN-4728 TCGA-CN-4736 TCGA-CN-4738 TCGA-CN-4739 
           5          485          613          395         1960         1330 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5370 TCGA-CN-5374 
        1268         1988         1977         1980         1975          290 
TCGA-CN-6010 TCGA-CN-6012 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6021 TCGA-CN-6022 
         630          629           45          432         1970          202 
TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CN-A49B TCGA-CN-A63T 
         119          432          429           46          447          225 
TCGA-CN-A63W TCGA-CQ-5323 TCGA-CQ-5330 TCGA-CQ-5332 TCGA-CQ-6223 TCGA-CQ-6224 
         348         1466          896          317         1057          985 
TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7069 TCGA-CQ-A4C6 
         815         1378         1007          509          901          968 
TCGA-CQ-A4C7 TCGA-CQ-A4C9 TCGA-CQ-A4CA TCGA-CQ-A4CE TCGA-CQ-A4CH TCGA-CQ-A4CI 
        1960          613         1963          393          303          608 
TCGA-CR-5247 TCGA-CR-6477 TCGA-CR-6484 TCGA-CR-6491 TCGA-CR-7365 TCGA-CR-7367 
         358          514          354          350         1191         1440 
TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7373 TCGA-CR-7388 TCGA-CR-7399 
        1960          105         1979          889         1951          181 
TCGA-CV-5431 TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5976 
         522          546         1978         2437          519         1478 
TCGA-CV-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6934 TCGA-CV-6941 
        1840          215         1315         1665         1948         1959 
TCGA-CV-6954 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7097 TCGA-CV-7101 
        1957         1959         3837         1959         1970         1939 
TCGA-CV-7180 TCGA-CV-7235 TCGA-CV-7242 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7254 
        1987         1724         1095          797         1967         1976 
TCGA-CV-7261 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7432 TCGA-CV-7435 TCGA-CV-7440 
        1099         1957         1947         1937         1959         1981 
TCGA-CV-A6JN TCGA-CX-7082 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6823 
         717          317          237          828          773          701 
TCGA-D6-6826 TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-DQ-5624 TCGA-DQ-5629 TCGA-DQ-7588 
         154          112          104         1778          516         1965 
TCGA-DQ-7592 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61W TCGA-F7-A620 
         299           15           92          585           14           13 
TCGA-H7-8501 TCGA-H7-8502 TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-8634 TCGA-HD-A633 
          58          133            2            5           24           49 
TCGA-HD-A6HZ TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61L 
         111          588          360          412          440          351 
TCGA-KU-A66T TCGA-MT-A51X TCGA-P3-A5QA TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 
         210           34         1652         1954          578         1917 
TCGA-P3-A6T4 TCGA-P3-A6T8 TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6IJ 
        1968          400          218          228           64 

$`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-A6DB TCGA-BA-A6DE 
         384          113          236          895          216          182 
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-7863 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-7872 
         310          423          638         1153          428          436 
TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4729 
           4          799          721          142          452          392 
TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4737 TCGA-CN-4740 
         462          993          642          369          240          811 
TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5366 
         488          512          173         1980         1081         1966 
TCGA-CN-5367 TCGA-CN-5373 TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 
        1966          413          424          433          594          629 
TCGA-CN-6020 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 
          98          424          224          318          611          394 
TCGA-CN-A498 TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A641 TCGA-CQ-5324 
         443          526          484          175          367         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-6227 TCGA-CQ-6228 TCGA-CQ-7063 TCGA-CQ-7068 
         870         1000         1959         1959         1461         1309 
TCGA-CQ-7071 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CG TCGA-CR-5243 TCGA-CR-5248 
         877          545          548          391         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-6487 TCGA-CR-6488 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7368 
         234          379          479         1956         1435         1245 
TCGA-CR-7372 TCGA-CR-7374 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 
         759           30          972         1968         1036          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-7401 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5434 
        1077          911         1472         1955         1950         3295 
TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5970 
        1438          584         2886         2327         1958          406 
TCGA-CV-5971 TCGA-CV-5973 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6441 TCGA-CV-6935 
         701         2641          641         1899         1970         1969 
TCGA-CV-6936 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-6960 
        1952         3835         1948         1969         1966         1969 
TCGA-CV-7095 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7183 TCGA-CV-7238 
        1970         1936         1959         1945         1979         1444 
TCGA-CV-7243 TCGA-CV-7250 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7418 TCGA-CV-7427 
         954         1960         1974         1948         1955         1937 
TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-A45O TCGA-CV-A45Q 
        1973         1972         1984         1958          851         1945 
TCGA-CV-A461 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CX-7085 TCGA-D6-6517 TCGA-D6-6824 
        1954         1970          750          321          292           77 
TCGA-D6-6825 TCGA-D6-6827 TCGA-D6-8568 TCGA-D6-8569 TCGA-DQ-5625 TCGA-DQ-5630 
         491          568          106          128         1081         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-F7-7848 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A61S 
         324          340          564          490          658            3 
TCGA-F7-A61V TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-A6C4 TCGA-H7-A6C5 TCGA-HD-7754 
         384            6          407          414          403           25 
TCGA-HD-7917 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8635 TCGA-HD-A4C1 TCGA-HD-A634 
          37           55           44           25           11           10 
TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61O 
          33         1057          485          122          441          360 
TCGA-KU-A66S TCGA-MT-A51W TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G 
         224           14          392           56          111          112 
TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A6SW TCGA-QK-A64Z TCGA-QK-A652 
         254          910          721         1120          553          357 
TCGA-QK-A6IF TCGA-QK-A6II 
         245          225 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 2                  3 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              3837               3835 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             613.0              639.5 
[1] "2.0 - 3837.0 (613.0)" "3.0 - 3835.0 (639.5)"
[1] "hr=" "1.1"
D78V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  21Q LOSS MUTATED         7       26        29        75         5
  21Q LOSS WILD-TYPE      17       37        42       117         4
D78V3, multiclass
           clus
vv          21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  STAGE I                  7                 17
  STAGE II                26                 37
  STAGE III               29                 42
  STAGE IVA               75                117
  STAGE IVB                5                  4
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  21Q LOSS MUTATED    9 46 37 51
  21Q LOSS WILD-TYPE 31 62 48 80
D78V4, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  T1                9                 31
  T2               46                 62
  T3               37                 48
  T4               51                 80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2 N3
  21Q LOSS MUTATED   47 26 51  4
  21Q LOSS WILD-TYPE 89 30 78  3
D78V5, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  N0               47                 89
  N1               26                 30
  N2               51                 78
  N3                4                  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"
D78V6, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED   41 24
  21Q LOSS WILD-TYPE 67 24
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     41   24
  21Q LOSS WILD-TYPE   67   24
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  M0               41                 67
  MX               24                 24
[1] 2 2
[1] FALSE
D78V7, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    44 115
  21Q LOSS WILD-TYPE  77 181
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     44  115
  21Q LOSS WILD-TYPE   77  181
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE               44                 77
  MALE                115                181
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  21Q LOSS MUTATED                                     158
  21Q LOSS WILD-TYPE                                   252
                    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                                                     1
  21Q LOSS WILD-TYPE                                                   5
D78V8, multiclass
                                                             clus
vv                                                            21Q LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                    158
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT                0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                        1
                                                             clus
vv                                                            21Q LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                      252
  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"
D78V9, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    27 132
  21Q LOSS WILD-TYPE  52 206
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     27  132
  21Q LOSS WILD-TYPE   52  206
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  NO                27                 52
  YES              132                206
[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                                0     3
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  21Q LOSS MUTATED                          17   129
  21Q LOSS WILD-TYPE                        16   232
D78V12, multiclass
                                  clus
vv                                 21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           7                  3
  BLACK OR AFRICAN AMERICAN                      17                 16
  WHITE                                         129                232
[1] 4 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     7 143
  21Q LOSS WILD-TYPE  11 238
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      7  143
  21Q LOSS WILD-TYPE   11  238
                        clus
vv                       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    7                 11
  NOT HISPANIC OR LATINO              143                238
[1] 2 2
[1] FALSE

Clustering(79) Variable = 22Q LOSS MUTATION ANALYSIS
D79V1, survival
                    sevent
clus2                  0   1
  22Q LOSS MUTATED    44  15
  22Q LOSS WILD-TYPE 213  83
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                59                296 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                15                 83 
$`22Q LOSS MUTATED`
TCGA-BA-4075 TCGA-BA-5149 TCGA-BA-5558 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-A6DE 
         283          248         1636          451           63          182 
TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-7861 TCGA-C9-A47Z TCGA-CN-4725 
        2878          278          140          310            5          485 
TCGA-CN-4730 TCGA-CN-5355 TCGA-CN-5370 TCGA-CN-6018 TCGA-CN-6021 TCGA-CN-6998 
         462          488         1975           45         1970           46 
TCGA-CN-A63W TCGA-CQ-5327 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-A4C7 TCGA-CQ-A4CA 
         348         1660         1378         1007         1960         1963 
TCGA-CQ-A4CE TCGA-CR-5248 TCGA-CR-6488 TCGA-CR-6493 TCGA-CR-7373 TCGA-CR-7379 
         393         1663          379         1956          889         1036 
TCGA-CR-7398 TCGA-CR-7399 TCGA-CV-5973 TCGA-CV-5977 TCGA-CV-6003 TCGA-CV-6441 
         156          181         2641         1840         1665         1970 
TCGA-CV-6945 TCGA-CV-7091 TCGA-CV-7180 TCGA-CV-7432 TCGA-CX-7086 TCGA-D6-8569 
        1969         1959         1987         1937          237          128 
TCGA-D6-A4Z9 TCGA-DQ-5631 TCGA-DQ-7592 TCGA-DQ-7593 TCGA-F7-A50G TCGA-F7-A50J 
         112          548          299          369           15          585 
TCGA-F7-A623 TCGA-HD-A633 TCGA-IQ-7630 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-MT-A51W 
           6           49          485          588          360           14 
TCGA-MT-A67G TCGA-P3-A5QA TCGA-P3-A6T0 TCGA-QK-A6IH TCGA-QK-A6IJ 
         112         1652          578          228           64 

$`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-A6D8 
         644          384          113          236          895          513 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BB-4217 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7862 
         351          216          187          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-4726 
        1955          624            4          799          721          142 
TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4735 
         452          613          392          993          642          369 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-4741 
         395          240         1960         1330          811         1268 
TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5363 
        1988          512          173         1980         1081         1977 
TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6010 
        1980         1966         1966          413          290          630 
TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 
         424          629          433          594          629          432 
TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 
          98          202          424          224          318          611 
TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-A498 TCGA-CN-A49B 
         394          119          432          429          443          447 
TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A641 TCGA-CQ-5323 
         225          526          484          175          367         1466 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 
        1207          654         1422          896         1399          317 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 TCGA-CQ-6223 TCGA-CQ-6224 
         341          129          870         1000         1057          985 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7067 TCGA-CQ-7068 
        1959         1959          815         1461          509         1309 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD 
         901          877          968          613          545          548 
TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5249 
         391          303          608         2562          358         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-6491 TCGA-CR-6492 TCGA-CR-7364 TCGA-CR-7365 
         354          234          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-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-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-7401 TCGA-CR-7402 
         908          898          930          216         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-5976 TCGA-CV-5978 
        2437          519          406          701         1478          215 
TCGA-CV-5979 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 
        1315          641         1899         1948         1969         1952 
TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6960 
        1959         3835         1948         1966         1957         1969 
TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 
        1959         3837         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         1724         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-A461 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JN 
         851         1945         1954         1970          750          717 
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-D6-8568 TCGA-D6-A4ZB 
          77          491          154          568          106          104 
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-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 
         775          622          368          324          340          564 
TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50I TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A61W 
         490          658           92            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-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-A634 TCGA-HD-A6HZ TCGA-HD-A6I0 
          24           25           11           10          111           33 
TCGA-HL-7533 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61L 
        1057          122          441          412          440          351 
TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D 
         360          224          210           34          392           56 
TCGA-MT-A67F TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6SX 
         111          254          910          721         1120         1954 
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 
         218          225 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 5                  2 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              2878               3837 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               462                656 
[1] "5.0 - 2878.0 (462.0)" "2.0 - 3837.0 (656.0)"
[1] "hr=" "1.1"
D79V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  22Q LOSS MUTATED         3       12        15        24         1
  22Q LOSS WILD-TYPE      21       51        56       168         8
D79V3, multiclass
           clus
vv          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  STAGE I                  3                 21
  STAGE II                12                 51
  STAGE III               15                 56
  STAGE IVA               24                168
  STAGE IVB                1                  8
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  22Q LOSS MUTATED     6  18  16  15
  22Q LOSS WILD-TYPE  34  90  69 116
D79V4, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T1                6                 34
  T2               18                 90
  T3               16                 69
  T4               15                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
  22Q LOSS MUTATED    22  12  17   0
  22Q LOSS WILD-TYPE 114  44 112   7
D79V5, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  N0               22                114
  N1               12                 44
  N2               17                112
  N3                0                  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"
D79V6, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED   20  7
  22Q LOSS WILD-TYPE 88 41
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     20    7
  22Q LOSS WILD-TYPE   88   41
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  M0               20                 88
  MX                7                 41
[1] 2 2
[1] FALSE
D79V7, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    23  41
  22Q LOSS WILD-TYPE  98 255
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     23   41
  22Q LOSS WILD-TYPE   98  255
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE               23                 98
  MALE                 41                255
[1] 2 2
[1] FALSE
                    vv
clus                 HEAD AND NECK SQUAMOUS CELL CARCINOMA
  22Q LOSS MUTATED                                      64
  22Q LOSS WILD-TYPE                                   346
                    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                                                   6
D79V8, multiclass
                                                             clus
vv                                                            22Q LOSS MUTATED
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     64
  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                                      346
  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"
D79V9, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED     7  57
  22Q LOSS WILD-TYPE  72 281
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      7   57
  22Q LOSS WILD-TYPE   72  281
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  NO                 7                 72
  YES               57                281
[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                                0     7
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  22Q LOSS MUTATED                           5    52
  22Q LOSS WILD-TYPE                        28   309
D79V12, multiclass
                                  clus
vv                                 22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           3                  7
  BLACK OR AFRICAN AMERICAN                       5                 28
  WHITE                                          52                309
[1] 4 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     4  55
  22Q LOSS WILD-TYPE  14 326
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      4   55
  22Q LOSS WILD-TYPE   14  326
                        clus
vv                       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                 14
  NOT HISPANIC OR LATINO               55                326
[1] 2 2
[1] FALSE

Clustering(80) Variable = XQ LOSS MUTATION ANALYSIS
D80V1, survival
                   sevent
clus2                 0   1
  XQ LOSS MUTATED    38  19
  XQ LOSS WILD-TYPE 219  79
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               57               298 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               19                79 
$`XQ LOSS MUTATED`
TCGA-BA-4074 TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-6868 TCGA-BA-A6D8 TCGA-BA-A6DE 
         462          415          276          190          513          182 
TCGA-BB-7862 TCGA-BB-7871 TCGA-BB-8596 TCGA-CN-4725 TCGA-CN-4735 TCGA-CN-4736 
         536          428         1955          485          369          395 
TCGA-CN-5360 TCGA-CN-6010 TCGA-CN-6992 TCGA-CN-6997 TCGA-CQ-6218 TCGA-CQ-6221 
        1081          630          394          429          870         1000 
TCGA-CQ-6227 TCGA-CQ-7064 TCGA-CQ-7067 TCGA-CQ-A4CI TCGA-CR-5248 TCGA-CR-6472 
        1959         1378          509          608         1663         1050 
TCGA-CR-6487 TCGA-CR-7371 TCGA-CR-7374 TCGA-CR-7383 TCGA-CR-7388 TCGA-CR-7390 
         234         1979           30         1954         1951          907 
TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CV-5439 TCGA-CV-5973 TCGA-CV-5976 
         216          156          181          546         2641         1478 
TCGA-CV-6441 TCGA-CV-6935 TCGA-CV-6960 TCGA-CV-7095 TCGA-CV-7101 TCGA-CV-7235 
        1970         1969         1969         1970         1939         1724 
TCGA-CV-7418 TCGA-CV-7430 TCGA-CV-7435 TCGA-CX-7082 TCGA-D6-6827 TCGA-DQ-7588 
        1955         1972         1959          317          568         1965 
TCGA-F7-7848 TCGA-F7-A50G TCGA-F7-A61W TCGA-H7-A6C5 TCGA-MZ-A6I9 TCGA-P3-A5QA 
         564           15           14          403          254         1652 
TCGA-P3-A5QE TCGA-P3-A6T4 TCGA-QK-A6IH 
         721         1968          228 

$`XQ LOSS WILD-TYPE`
TCGA-BA-4075 TCGA-BA-4077 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 
         283         1983          248          722         1288         1762 
TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 TCGA-BA-6869 
         520          725          623         1636         1747          644 
TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A4IF 
         451           63          384          113          236          895 
TCGA-BA-A6DA TCGA-BA-A6DB TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 
         351          216          187         2878          278          140 
TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7866 
         133          558          310          423          687          638 
TCGA-BB-7870 TCGA-BB-7872 TCGA-BB-8601 TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 
        1153          436          624            5            4          799 
TCGA-CN-4723 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 TCGA-CN-4730 
         721          142          452          613          392          462 
TCGA-CN-4731 TCGA-CN-4733 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4740 
         993          642          240         1960         1330          811 
TCGA-CN-4741 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 
        1268         1988          488          512          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          413 
TCGA-CN-5374 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 
         290          424          629          433          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          424 
TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-6998 
         224          318          611          119          432           46 
TCGA-CN-A498 TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W 
         443          447          225          526          484          348 
TCGA-CN-A63Y TCGA-CN-A641 TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 
         175          367         1466         1207          654         1660 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-5333 TCGA-CQ-5334 
        1422          896         1399          317          341          129 
TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7065 
        1057          985         1959          815         1461         1007 
TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4C9 
        1309          901          877          968         1960          613 
TCGA-CQ-A4CA TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH 
        1963          545          548          393          391          303 
TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 
        2562          358         1152          799         1777         1521 
TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6478 TCGA-CR-6480 
        1966         1125         1971          514         1969          362 
TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6492 
         311          345          354          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-7372 TCGA-CR-7373 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 
         105          759          889          972         1968         1036 
TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7389 TCGA-CR-7391 TCGA-CR-7392 
         796          997         1430          392          913          946 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7401 TCGA-CR-7402 TCGA-CR-7404 
         908          898          930         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-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-5977 TCGA-CV-5978 TCGA-CV-5979 TCGA-CV-6003 
         406          701         1840          215         1315         1665 
TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6934 TCGA-CV-6936 TCGA-CV-6941 TCGA-CV-6942 
         641         1899         1948         1952         1959         3835 
TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6952 TCGA-CV-6954 TCGA-CV-6961 TCGA-CV-7090 
        1948         1969         1966         1957         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-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-7424 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 
        1947         1937         1973         1937         1984         1958 
TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45Q TCGA-CV-A461 TCGA-CV-A6JD TCGA-CV-A6JE 
        1981          851         1945         1954         1970          750 
TCGA-CV-A6JN TCGA-CX-7085 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6517 
         717          321          237          828          773          292 
TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-8568 TCGA-D6-8569 
         701           77          491          154          106          128 
TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5629 TCGA-DQ-5630 
         112          104         1778         1081          516         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-F7-8489 TCGA-F7-A50I 
         368          324          340          490          658           92 
TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A620 TCGA-F7-A623 TCGA-H7-7774 
         585            3          384           13            6          407 
TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A6C4 TCGA-HD-7229 TCGA-HD-7753 TCGA-HD-7754 
          58          133          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-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-MT-A51W TCGA-MT-A51X 
         351          360          224          210           14           34 
TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G TCGA-P3-A5Q5 TCGA-P3-A6SW 
         392           56          111          112          910         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-A6II TCGA-QK-A6IJ 
         245          218          225           64 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               14                 2 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             2641              3837 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
              608               629 
[1] "14.0 - 2641.0 (608.0)" "2.0 - 3837.0 (629.0)" 
[1] "hr=" "1.2"
D80V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  XQ LOSS MUTATED         6        7        10        29         2
  XQ LOSS WILD-TYPE      18       56        61       163         7
D80V3, multiclass
           clus
vv          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  STAGE I                 6                18
  STAGE II                7                56
  STAGE III              10                61
  STAGE IVA              29               163
  STAGE IVB               2                 7
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  XQ LOSS MUTATED     7  14  20  15
  XQ LOSS WILD-TYPE  33  94  65 116
D80V4, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T1               7                33
  T2              14                94
  T3              20                65
  T4              15               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
  XQ LOSS MUTATED    16   9  22   1
  XQ LOSS WILD-TYPE 120  47 107   6
D80V5, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  N0              16               120
  N1               9                47
  N2              22               107
  N3               1                 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"
D80V6, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED   16  6
  XQ LOSS WILD-TYPE 92 42
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     16    6
  XQ LOSS WILD-TYPE   92   42
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  M0              16                92
  MX               6                42
[1] 2 2
[1] FALSE
D80V7, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    24  41
  XQ LOSS WILD-TYPE  97 255
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     24   41
  XQ LOSS WILD-TYPE   97  255
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE              24                97
  MALE                41               255
[1] 2 2
[1] FALSE
                   vv
clus                HEAD AND NECK SQUAMOUS CELL CARCINOMA
  XQ LOSS MUTATED                                      63
  XQ LOSS WILD-TYPE                                   347
                   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                                                     2
  XQ LOSS WILD-TYPE                                                   4
D80V8, multiclass
                                                             clus
vv                                                            XQ 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                       2
                                                             clus
vv                                                            XQ LOSS WILD-TYPE
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                                     347
  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"
D80V9, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    11  54
  XQ LOSS WILD-TYPE  68 284
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     11   54
  XQ LOSS WILD-TYPE   68  284
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  NO               11                68
  YES              54               284
[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                                1     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XQ LOSS MUTATED                           4    58
  XQ LOSS WILD-TYPE                        29   303
D80V12, multiclass
                                  clus
vv                                 XQ LOSS MUTATED XQ LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                 9
  BLACK OR AFRICAN AMERICAN                      4                29
  WHITE                                         58               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"
D80V13, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     2  60
  XQ LOSS WILD-TYPE  16 321
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      2   60
  XQ LOSS WILD-TYPE   16  321
                        clus
vv                       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                16
  NOT HISPANIC OR LATINO              60               321
[1] 2 2
[1] FALSE
