[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"        "-oTLUSC-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/LUSC-TP/11541613/LUSC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LUSC-TP/11546294/transformed.cor.cli.txt"

nPatients in clinical file=422, in cluster file=501, common to both=420
[1]  80 420
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               81               339 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               81               339 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              178               242 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              178               242 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              184               236 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              184               236 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
              120               300 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
              120               300 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               91               329 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               91               329 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              269               151 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              269               151 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               30               390 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               30               390 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               20               400 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               20               400 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              265               155 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              265               155 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               79               341 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               79               341 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               90               330 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               90               330 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               77               343 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               77               343 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              206               214 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              206               214 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              191               229 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              191               229 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              108               312 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              108               312 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              217               203 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              217               203 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               47               373 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               47               373 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               77               343 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               77               343 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                63                357 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                63                357 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                36                384 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                36                384 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                64                356 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                64                356 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                78                342 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                78                342 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               194                226 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               194                226 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               132                288 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               132                288 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                32                388 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                32                388 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
               107                313 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
               107                313 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                92                328 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                92                328 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                72                348 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                72                348 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                73                347 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                73                347 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                58                362 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                58                362 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               134                286 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               134                286 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
               133                287 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
               133                287 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                98                322 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                98                322 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                97                323 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                97                323 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
               136                284 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
               136                284 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               216                204 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               216                204 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               208                212 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               208                212 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                48                372 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                48                372 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
               191                229 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
               191                229 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               67               353 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               67               353 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
              122               298 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
              122               298 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               47               373 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               47               373 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               16               404 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               16               404 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               31               389 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               31               389 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              262               158 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              262               158 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               60               360 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               60               360 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              260               160 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              260               160 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              245               175 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              245               175 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               65               355 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               65               355 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              244               176 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              244               176 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               95               325 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               95               325 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               97               323 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               97               323 
[1] "7P LOSS MUTATION ANALYSIS"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               49               371 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               49               371 
[1] "7Q LOSS MUTATION ANALYSIS"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               44               376 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               44               376 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              208               212 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              208               212 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               37               383 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               37               383 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              265               155 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              265               155 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              204               216 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              204               216 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               178                242 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               178                242 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               187                233 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               187                233 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               146                274 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               146                274 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               121                299 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               121                299 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                33                387 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                33                387 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                40                380 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                40                380 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               254                166 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               254                166 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               140                280 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               140                280 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               111                309 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               111                309 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
               131                289 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
               131                289 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               148                272 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               148                272 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               240                180 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               240                180 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                81                339 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                81                339 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               112                308 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               112                308 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               150                270 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               150                270 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
               137                283 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
               137                283 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                90                330 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                90                330 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                37                383 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                37                383 
[1] "20Q LOSS MUTATION ANALYSIS"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                39                381 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                39                381 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               222                198 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               222                198 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                77                343 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                77                343 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               87               333 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               87               333 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDISEASE"                  
 [6] "NEOPLASM.DISEASESTAGE"                 
 [7] "PATHOLOGY.T.STAGE"                     
 [8] "PATHOLOGY.N.STAGE"                     
 [9] "PATHOLOGY.M.STAGE"                     
[10] "DCCUPLOADDATE"                         
[11] "GENDER"                                
[12] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[13] "DAYSTOLASTKNOWNALIVE"                  
[14] "RADIATIONTHERAPY"                      
[15] "KARNOFSKYPERFORMANCESCORE"             
[16] "HISTOLOGICALTYPE"                      
[17] "RADIATIONS.RADIATION.REGIMENINDICATION"
[18] "NUMBERPACKYEARSSMOKED"                 
[19] "YEAROFTOBACCOSMOKINGONSET"             
[20] "COMPLETENESS.OF.RESECTION"             
[21] "RACE"                                  
[22] "ETHNICITY"                             
[23] "BATCHNUMBER"                           

Input Data has 23 rows and 420 columns.

[1] "Batch" "23"   
[1] "Last Follow UP"
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 
         370          136         2464         2417          146         1415 
TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 
         345          396         1810          862          758           50 
TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 
        1331          187           85         2754           92          827 
TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 
        3636         1426         3016         2134         1852         1058 
TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 TCGA-21-1083 
         474          965         3724          284         3644          267 
TCGA-21-5782 TCGA-21-5783 TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-21-A5DI 
         962           NA         1268         1032          329          979 
TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 
         608          223           NA          131         1953           53 
TCGA-22-1012 TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 
         429          822         1485          623         1067         1470 
TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 
         734           17         1161         1057          399           NA 
TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 
         587           NA          358          965         1975         1933 
TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 
         445         1346           24         1651         2170           NA 
TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 
         357          573          916         1912         1713          506 
TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 
          29         2524         3469         2979         1311         5287 
TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-33-4589 TCGA-33-6737 
        3149         4299          428           NA           NA           NA 
TCGA-33-6738 TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 
         822           80         1874          958          881         1000 
TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 
         951         1528         2062         1715           NA          707 
TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 
         365          428          941          552           NA           NA 
TCGA-34-8454 TCGA-34-8455 TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 
         166           NA          120           13           12          200 
TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 
         247          227          238          207           12          103 
TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 
        1454         2253         1361         2086           NA         2130 
TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 
        1849           52          740           59          833         1107 
TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 
         474         1084         1086          544           NA         1223 
TCGA-43-2578 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 
         684         1176          822         1007          349          849 
TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 
         376          757          310           NA           NA          212 
TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 
         236         2023          407          358           NA          353 
TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V TCGA-46-3765 TCGA-46-3766 TCGA-46-3767 
         296          432          366           NA           NA           NA 
TCGA-46-3768 TCGA-46-3769 TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 
          NA           NA          324          423           12           12 
TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 
         911          541           NA          923           NA           NA 
TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 
         881            3          555           62           26           30 
TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 
          13           30           44           40           26            6 
TCGA-56-7731 TCGA-56-7822 TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 TCGA-56-8624 
          NA            1           41          178           55           36 
TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW 
          63           17           16           34           38            2 
TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS 
          46           30           25            4            4            8 
TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-8392 
          NA           NA          378          911         2167           NA 
TCGA-58-8393 TCGA-58-A46J TCGA-58-A46K TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N 
        1058         2589           NA         1723         1072          910 
TCGA-60-2695 TCGA-60-2696 TCGA-60-2697 TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 
         642          109           NA          311           NA           NA 
TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 
        2820          661         2447         1505         2024         1260 
TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2715 TCGA-60-2716 TCGA-60-2719 
         274         1731         1531         1075         1475         1297 
TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 
          97          983          908         1092          717          816 
TCGA-60-2726 TCGA-63-5128 TCGA-63-5131 TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 
         358           NA           NA           NA           NA           NA 
TCGA-63-7022 TCGA-63-7023 TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 
          NA           NA           NA         1311           61          641 
TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 
          30           31           61           28           30           30 
TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 
         639          762           30           61           31           61 
TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 
          61           NA          700          578           NA           61 
TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 
         578           NA          121           NA          759           60 
TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 
         790         1217          699           NA          699           NA 
TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 
         913           NA         1645          122         1492           83 
TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J 
         202          211          244           96          121          104 
TCGA-70-6722 TCGA-70-6723 TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 
          NA           NA           NA           NA           NA           NA 
TCGA-77-7138 TCGA-77-7139 TCGA-77-7140 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 
          NA         2737           NA           15         1286           NA 
TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 
          NA           NA           NA          479           NA           NA 
TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 
        1641           NA         2522           NA           NA           NA 
TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8143 TCGA-77-8144 TCGA-77-8145 
          NA         3166           NA           NA          833           NA 
TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ 
         293           NA         1684         1092           10           NA 
TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA 
        4026         3576           NA           NA         1290         1280 
TCGA-77-A5GB TCGA-77-A5GF TCGA-77-A5GH TCGA-79-5596 TCGA-85-6175 TCGA-85-6560 
          NA          839          713           NA           NA          364 
TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 
         395           34           18           10           49            1 
TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 
          NA           35          911           60           26           60 
TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 
          16          960          428          513           13           11 
TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 
          13           54           60           55           67           54 
TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 
          61           61           22           21          445          424 
TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JB 
          NA            3          475           15           NA           NA 
TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z 
          NA           NA           NA           25           19           NA 
TCGA-85-A510 TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 
          NA           NA           NA           24           13          111 
TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 TCGA-90-7964 TCGA-90-A4ED 
         758          289           89          358          428          244 
TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 
         331          269           82          106          122          160 
TCGA-92-8065 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 TCGA-94-A4VJ TCGA-96-7544 
          70           87           NA          356          430         1213 
TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL TCGA-98-7454 
        1344          189          211          273          183          256 
TCGA-98-8020 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-J1-A4AH TCGA-L3-A4E7 
          NA          413          224          308          222           35 
TCGA-L3-A524 TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HE TCGA-NC-A5HG TCGA-NC-A5HI 
         449           36           83         1722         1548         1135 
Variable 1:'AGE':	nDistinctValues=45,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=138,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=269,	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=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=19,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=123,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 14:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=8,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'HISTOLOGICAL.TYPE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'NUMBERPACKYEARSSMOKED':	nDistinctValues=97,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'YEAROFTOBACCOSMOKINGONSET':	nDistinctValues=55,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'COMPLETENESS.OF.RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 22:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 23:'BATCH.NUMBER':	nDistinctValues=30,	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] "KARNOFSKY.PERFORMANCE.SCORE"           
 [8] "HISTOLOGICAL.TYPE"                     
 [9] "RADIATIONS.RADIATION.REGIMENINDICATION"
[10] "NUMBERPACKYEARSSMOKED"                 
[11] "COMPLETENESS.OF.RESECTION"             
[12] "RACE"                                  
[13] "ETHNICITY"                             
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 420 columns, 1 survival variables, and 13 non-survival variables.
AGE, nv=45, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=9, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
 98 254  48  20 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
 98 254  48  20 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
 T1  T2  T3  T4 
 98 254  48  20 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
 98 254  48  20 
PATHOLOGY.N.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
261 113  35   5 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
261 113  35   5 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
 N0  N1  N2  N3 
261 113  35   5 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
261 113  35   5 
PATHOLOGY.M.STAGE, nv=4, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY.PERFORMANCE.SCORE, nv=8, binary=FALSE, numeric=TRUE
HISTOLOGICAL.TYPE, nv=4, binary=FALSE, numeric=FALSE
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
NUMBERPACKYEARSSMOKED, nv=97, binary=FALSE, numeric=TRUE
COMPLETENESS.OF.RESECTION, nv=4, binary=FALSE, numeric=FALSE
RACE, nv=3, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1P GAIN MUTATION ANALYSIS
D1V1, survival
                   sevent
clus2                 0   1
  1P GAIN MUTATED    51  22
  1P GAIN WILD-TYPE 214 101
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               73               315 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               22               101 
$`1P GAIN MUTATED`
TCGA-18-3414 TCGA-21-1070 TCGA-21-1081 TCGA-21-1082 TCGA-21-5787 TCGA-22-1011 
         396         3636          284         3644          329           53 
TCGA-22-1012 TCGA-22-1016 TCGA-22-5481 TCGA-22-5483 TCGA-33-4533 TCGA-33-4582 
         429          822         1952          573         1940         1966 
TCGA-33-6738 TCGA-34-2608 TCGA-34-5231 TCGA-34-5240 TCGA-37-3792 TCGA-37-4130 
         822         1000         1528          365           12          247 
TCGA-37-4132 TCGA-37-4141 TCGA-39-5021 TCGA-39-5022 TCGA-39-5035 TCGA-39-5037 
         227           12         1947         1996          474         1086 
TCGA-39-5040 TCGA-43-2578 TCGA-43-3920 TCGA-43-6143 TCGA-43-6770 TCGA-46-6025 
        1964          684         1007          376          310          324 
TCGA-52-7809 TCGA-52-7810 TCGA-56-8504 TCGA-58-A46N TCGA-60-2695 TCGA-60-2708 
        1948          923          178          910          642         1963 
TCGA-60-2719 TCGA-60-2722 TCGA-60-2723 TCGA-60-2725 TCGA-60-2726 TCGA-66-2734 
        1297          908         1092          816          358         1311 
TCGA-66-2742 TCGA-66-2755 TCGA-66-2759 TCGA-66-2763 TCGA-66-2771 TCGA-66-2782 
         641           28          762           30          578         1954 
TCGA-66-2783 TCGA-68-8251 TCGA-68-A59I TCGA-77-7138 TCGA-77-7141 TCGA-77-7338 
         759           96          121         1959           15         1952 
TCGA-77-8145 TCGA-77-A5G8 TCGA-77-A5GB TCGA-77-A5GH TCGA-85-6560 TCGA-85-6798 
        1943         1290         1939          713          364           34 
TCGA-85-7699 TCGA-85-7844 TCGA-85-8072 TCGA-85-A4CL TCGA-85-A4QQ TCGA-85-A50M 
           1          911          513           15         1960           19 
TCGA-85-A512 TCGA-90-7964 TCGA-90-A4ED TCGA-92-8064 TCGA-96-8169 TCGA-J1-A4AH 
        1987          428          244          160          189          222 
TCGA-NC-A5HG 
        1548 

$`1P GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 
         370          136         2464         2417          146         1415 
TCGA-18-3412 TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 
         345         1810          862          758           50         1331 
TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1071 
         187           85         2754           92          827         1426 
TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 
        3016         2134         1852         1058          474          965 
TCGA-21-1080 TCGA-21-1083 TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 TCGA-21-A5DI 
        3724          267          962         1268         1032          979 
TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1017 
         608          223         1945          131         1952         1485 
TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 
         623         1067         1470          734           17         1161 
TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-4613 TCGA-22-5471 
        1057          399         1946          587          358          965 
TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 
        1964         1933          445         1346           24         1651 
TCGA-22-5480 TCGA-22-5482 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 
        1952          357          916         1912         1713          506 
TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4583 
          29         2524         2979         1311         5287         1941 
TCGA-33-4586 TCGA-33-4587 TCGA-33-4589 TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 
         428         1970         1948           80         1874          958 
TCGA-34-2605 TCGA-34-2609 TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 TCGA-34-5241 
         881          951         2062         1715          707          428 
TCGA-34-5927 TCGA-34-5928 TCGA-34-8454 TCGA-37-3783 TCGA-37-3789 TCGA-37-4129 
         941          552          166          120           13          200 
TCGA-37-4133 TCGA-37-4135 TCGA-37-5819 TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 
         238          207          103         1454         2253         1361 
TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 
        1964         1849           52          740           59          833 
TCGA-39-5034 TCGA-39-5036 TCGA-39-5039 TCGA-43-2576 TCGA-43-2581 TCGA-43-3394 
        1107         1084          544         1223         1176          822 
TCGA-43-5668 TCGA-43-5670 TCGA-43-6647 TCGA-43-6771 TCGA-43-7656 TCGA-43-7657 
         349          849          757         1936          212          236 
TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 
        1970          407          358         1971          353          296 
TCGA-43-A56U TCGA-43-A56V TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 
         432          366          423           12           12          911 
TCGA-52-7622 TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 
         541         1958         1967          881            3          555 
TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 
          62           26           30           13           30           44 
TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-8503 
          40           26            6         1961            1           41 
TCGA-56-8622 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 
          55           36           63           17           16           34 
TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK 
          38            2           46           30           25            4 
TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-8393 
           4            8          378          911         2167         1058 
TCGA-58-A46J TCGA-58-A46L TCGA-58-A46M TCGA-60-2696 TCGA-60-2698 TCGA-60-2703 
        2589         1723         1072          109          311         1950 
TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 
        1943         1958          661         1505         1963         1260 
TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2715 TCGA-60-2716 TCGA-60-2720 
         274         1731         1531         1075         1475           97 
TCGA-60-2721 TCGA-60-2724 TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 
         983          717         1973         1957         1955         1947 
TCGA-63-7023 TCGA-66-2727 TCGA-66-2737 TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 
        1952         1967           61           30           31           61 
TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 
          30           30          639           61           31           61 
TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 
          61         1947          700         1946           61          578 
TCGA-66-2780 TCGA-66-2781 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 
        1956          121           60          790         1217          699 
TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 
        1955          699         1977          913         1952         1645 
TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 
         122         1492           83          202          211          244 
TCGA-68-A59J TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7139 
         104         1950         1941         1942         1952         1968 
TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 
        1286         1954         1942         1954          479         1960 
TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 
        1945         1641         1953         1945         1941         1941 
TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8144 TCGA-77-8148 
        1947         1946         1951         1962          833          293 
TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 
        1961         1684         1092           10         1953         1942 
TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5GA TCGA-77-A5GF TCGA-85-6561 
        1959         1955         1963         1280          839          395 
TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7710 TCGA-85-7843 TCGA-85-7950 
          18           10           49         1965           35           60 
TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8276 
          26           60           16          960          428           13 
TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 
          11           13           54           60           55           67 
TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 
          54           61           61           22           21          445 
TCGA-85-8582 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4PA TCGA-85-A4QR TCGA-85-A50Z 
         424            3          475         1972           25         1973 
TCGA-85-A510 TCGA-85-A511 TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 
        1967         1972           24           13          111          758 
TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 
         289           89          358          331          269           82 
TCGA-92-7341 TCGA-92-8063 TCGA-92-8065 TCGA-94-7033 TCGA-94-7943 TCGA-94-A4VJ 
         106          122           70           87          356          430 
TCGA-96-7544 TCGA-96-7545 TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL TCGA-98-7454 
        1213         1344          211          273          183          256 
TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 
         413          224          308           35          449           36 
TCGA-MF-A522 TCGA-NC-A5HE TCGA-NC-A5HI 
          83         1722         1135 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                1                 1 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             3644              5287 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
              684               623 
[1] "1.0 - 3644.0 (684.0)" "1.0 - 5287.0 (623.0)"
[1] "hr=" "1.1"
D1V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  1P GAIN MUTATED         0        9       35        1         8        12
  1P GAIN WILD-TYPE       1       63      102        0        44        59
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  1P GAIN MUTATED            9          3        4
  1P GAIN WILD-TYPE         48         17        2
D1V3, multiclass
            clus
vv           1P GAIN MUTATED 1P GAIN WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                 9                63
  STAGE IB                35               102
  STAGE II                 1                 0
  STAGE IIA                8                44
  STAGE IIB               12                59
  STAGE IIIA               9                48
  STAGE IIIB               3                17
  STAGE IV                 4                 2
[1] 9 2
[1] 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    16  54   6   5
  1P GAIN WILD-TYPE  82 200  42  15
D1V4, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  T1              16                82
  T2              54               200
  T3               6                42
  T4               5                15
[1] 4 2
[1] 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    55  18   6   1
  1P GAIN WILD-TYPE 206  95  29   4
D1V5, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  N0              55               206
  N1              18                95
  N2               6                29
  N3               1                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A  MX
  1P GAIN MUTATED    70   3   1   7
  1P GAIN WILD-TYPE 288   2   0  43
D1V6, multiclass
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  M0               70               288
  M1                3                 2
  M1A               1                 0
  MX                7                43
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V7, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    21  60
  1P GAIN WILD-TYPE  86 253
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     21   60
  1P GAIN WILD-TYPE   86  253
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE              21                86
  MALE                60               253
[1] 2 2
[1] FALSE
D1V8, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  1P GAIN MUTATED                                       7
  1P GAIN WILD-TYPE                                     5
                   vv
clus                LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  1P GAIN MUTATED                                        0
  1P GAIN WILD-TYPE                                      6
                   vv
clus                LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  1P GAIN MUTATED                                         0
  1P GAIN WILD-TYPE                                       1
                   vv
clus                LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  1P GAIN MUTATED                                                            74
  1P GAIN WILD-TYPE                                                         327
D1V9, multiclass
                                                             clus
vv                                                            1P GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     7
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    0
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              74
                                                             clus
vv                                                            1P GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       5
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               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"
D1V10, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     2  79
  1P GAIN WILD-TYPE  11 328
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      2   79
  1P GAIN WILD-TYPE   11  328
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  NO                2                11
  YES              79               328
[1] 2 2
[1] FALSE
D1V11, continuous
                   vv
clus                 R0  R1  R2  RX
  1P GAIN MUTATED    64   3   1   3
  1P GAIN WILD-TYPE 278   5   3  15
D1V12, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  R0              64               278
  R1               3                 5
  R2               1                 3
  RX               3                15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1P GAIN MUTATED       2                         6    60
  1P GAIN WILD-TYPE     7                        11   238
D1V13, multiclass
                           clus
vv                          1P GAIN MUTATED 1P GAIN WILD-TYPE
  ASIAN                                   2                 7
  BLACK OR AFRICAN AMERICAN               6                11
  WHITE                                  60               238
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V14, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     1  60
  1P GAIN WILD-TYPE   7 207
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      1   60
  1P GAIN WILD-TYPE    7  207
                        clus
vv                       1P GAIN MUTATED 1P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 7
  NOT HISPANIC OR LATINO              60               207
[1] 2 2
[1] FALSE

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                 0   1
  1Q GAIN MUTATED   116  52
  1Q GAIN WILD-TYPE 149  71
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              168               220 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               52                71 
$`1Q GAIN MUTATED`
TCGA-18-3406 TCGA-18-3408 TCGA-18-3411 TCGA-18-3414 TCGA-18-3415 TCGA-18-3417 
         370         2464         1415          396         1810          758 
TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 TCGA-21-1077 
          92         3636         1426         3016         2134         1058 
TCGA-21-1081 TCGA-21-1082 TCGA-21-5784 TCGA-21-5787 TCGA-22-0940 TCGA-22-1011 
         284         3644         1268          329          608           53 
TCGA-22-1012 TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 TCGA-22-4594 TCGA-22-4596 
         429          822         1485          623         1470           17 
TCGA-22-4599 TCGA-22-4607 TCGA-22-5473 TCGA-22-5474 TCGA-22-5479 TCGA-22-5480 
        1161          587         1933          445         1651         1952 
TCGA-22-5481 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-A5C4 TCGA-33-4533 
        1952          573          916         1912           29         1940 
TCGA-33-4538 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 
        2979         5287         1966         1941          428         1970 
TCGA-33-6738 TCGA-34-2596 TCGA-34-2600 TCGA-34-2608 TCGA-34-5231 TCGA-34-5239 
         822           80         1874         1000         1528          707 
TCGA-34-5240 TCGA-34-5928 TCGA-37-3783 TCGA-37-3792 TCGA-37-4132 TCGA-37-4133 
         365          552          120           12          227          238 
TCGA-37-4141 TCGA-39-5016 TCGA-39-5021 TCGA-39-5022 TCGA-39-5035 TCGA-39-5037 
          12         2253         1947         1996          474         1086 
TCGA-39-5040 TCGA-43-2578 TCGA-43-2581 TCGA-43-3920 TCGA-43-6143 TCGA-43-6770 
        1964          684         1176         1007          376          310 
TCGA-43-7657 TCGA-43-A475 TCGA-46-6025 TCGA-51-4080 TCGA-52-7622 TCGA-52-7809 
         236          296          324           12          541         1948 
TCGA-52-7810 TCGA-56-7223 TCGA-56-7582 TCGA-56-8504 TCGA-56-8622 TCGA-56-A4BX 
         923           30           26          178           55           46 
TCGA-56-A5DR TCGA-58-8388 TCGA-58-8393 TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 
           4          378         1058         1072          910          642 
TCGA-60-2698 TCGA-60-2707 TCGA-60-2708 TCGA-60-2722 TCGA-60-2723 TCGA-60-2725 
         311          661         1963          908         1092          816 
TCGA-60-2726 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2755 TCGA-66-2756 
         358         1311           61          641           28           30 
TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 
         639          762           30          700          578         1946 
TCGA-66-2777 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2787 
          61          121         1954          759           60         1217 
TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-77-6843 TCGA-77-6845 TCGA-77-7138 
          96          121          104         1941         1952         1959 
TCGA-77-7139 TCGA-77-7141 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8008 
        1968           15         1952         1954          479         1945 
TCGA-77-8009 TCGA-77-8145 TCGA-77-8148 TCGA-77-8156 TCGA-77-A5G8 TCGA-77-A5GA 
        1641         1943          293           10         1290         1280 
TCGA-77-A5GB TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6560 TCGA-85-6798 TCGA-85-7696 
        1939          839          713          364           34           18 
TCGA-85-7699 TCGA-85-7844 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 
           1          911           26           60           16          960 
TCGA-85-8072 TCGA-85-8277 TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 TCGA-85-8664 
         513           11           55           67           54            3 
TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4QQ TCGA-85-A50M TCGA-85-A511 TCGA-85-A512 
         475           15         1960           19         1972         1987 
TCGA-85-A5B5 TCGA-90-7767 TCGA-90-7964 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q 
         111           89          428          244          331          269 
TCGA-92-7340 TCGA-92-7341 TCGA-92-8064 TCGA-94-7943 TCGA-94-A4VJ TCGA-96-8169 
          82          106          160          356          430          189 
TCGA-96-A4JL TCGA-J1-A4AH TCGA-L3-A524 TCGA-MF-A522 TCGA-NC-A5HE TCGA-NC-A5HG 
         183          222          449           83         1722         1548 

$`1Q GAIN WILD-TYPE`
TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3412 TCGA-18-3416 TCGA-18-3419 
         136         2417          146          345          862           50 
TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5595 TCGA-21-1076 
        1331          187           85         2754          827         1852 
TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 TCGA-21-1083 TCGA-21-5782 TCGA-21-5786 
         474          965         3724          267          962         1032 
TCGA-21-A5DI TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-4593 
         979          223         1945          131         1952         1067 
TCGA-22-4595 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 TCGA-22-4613 TCGA-22-5471 
         734         1057          399         1946          358          965 
TCGA-22-5472 TCGA-22-5477 TCGA-22-5478 TCGA-22-5482 TCGA-22-5491 TCGA-22-5492 
        1964         1346           24          357         1713          506 
TCGA-33-4532 TCGA-33-4547 TCGA-33-4589 TCGA-34-2604 TCGA-34-2605 TCGA-34-2609 
        2524         1311         1948          958          881          951 
TCGA-34-5232 TCGA-34-5234 TCGA-34-5241 TCGA-34-5927 TCGA-34-8454 TCGA-37-3789 
        2062         1715          428          941          166           13 
TCGA-37-4129 TCGA-37-4130 TCGA-37-4135 TCGA-37-5819 TCGA-39-5011 TCGA-39-5019 
         200          247          207          103         1454         1361 
TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 
        1964         1849           52          740           59          833 
TCGA-39-5034 TCGA-39-5036 TCGA-39-5039 TCGA-43-2576 TCGA-43-3394 TCGA-43-5668 
        1107         1084          544         1223          822          349 
TCGA-43-5670 TCGA-43-6647 TCGA-43-6771 TCGA-43-7656 TCGA-43-7658 TCGA-43-8115 
         849          757         1936          212         1970          407 
TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56U TCGA-43-A56V TCGA-46-6026 
         358         1971          353          432          366          423 
TCGA-51-4079 TCGA-51-4081 TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 
          12          911         1958         1967          881            3 
TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 TCGA-56-7579 
         555           62           26           30           13           44 
TCGA-56-7580 TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-8503 TCGA-56-8624 
          40            6         1961            1           41           36 
TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW 
          63           17           16           34           38            2 
TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DS TCGA-58-8390 TCGA-58-8391 
          30           25            4            8          911         2167 
TCGA-58-A46J TCGA-58-A46L TCGA-60-2696 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 
        2589         1723          109         1950         1943         1958 
TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 
        1505         1963         1260          274         1731         1531 
TCGA-60-2715 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2724 
        1075         1475         1297           97          983          717 
TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 TCGA-66-2727 
        1973         1957         1955         1947         1952         1967 
TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2757 TCGA-66-2765 TCGA-66-2766 
          30           31           61           30           61           31 
TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 TCGA-66-2778 TCGA-66-2780 TCGA-66-2786 
          61           61         1947          578         1956          790 
TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 
         699         1955          699         1977          913         1952 
TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 
        1645          122         1492           83          202          211 
TCGA-68-8250 TCGA-77-6842 TCGA-77-6844 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 
         244         1950         1942         1286         1954         1942 
TCGA-77-8007 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 
        1960         1953         1945         1941         1941         1947 
TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8144 TCGA-77-8150 TCGA-77-8153 
        1946         1951         1962          833         1961         1684 
TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 
        1092         1953         1942         1959         1955         1963 
TCGA-85-6561 TCGA-85-7697 TCGA-85-7698 TCGA-85-7710 TCGA-85-7843 TCGA-85-7950 
         395           10           49         1965           35           60 
TCGA-85-8071 TCGA-85-8276 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8354 
         428           13           13           54           60           61 
TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-A4PA 
          61           22           21          445          424         1972 
TCGA-85-A4QR TCGA-85-A50Z TCGA-85-A510 TCGA-85-A513 TCGA-85-A53L TCGA-90-6837 
          25         1973         1967           24           13          758 
TCGA-90-7766 TCGA-90-7769 TCGA-92-8063 TCGA-92-8065 TCGA-94-7033 TCGA-96-7544 
         289          358          122           70           87         1213 
TCGA-96-7545 TCGA-96-8170 TCGA-96-A4JK TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 
        1344          211          273          256          413          224 
TCGA-98-8023 TCGA-L3-A4E7 TCGA-LA-A446 TCGA-NC-A5HI 
         308           35           36         1135 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                1                 1 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             5287              3724 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            582.5             748.5 
[1] "1.0 - 5287.0 (582.5)" "1.0 - 3724.0 (748.5)"
[1] "hr=" "1"  
D2V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  1Q GAIN MUTATED         0       24       69        1        20        30
  1Q GAIN WILD-TYPE       1       48       68        0        32        41
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  1Q GAIN MUTATED           22          7        5
  1Q GAIN WILD-TYPE         35         13        1
D2V3, multiclass
            clus
vv           1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                24                48
  STAGE IB                69                68
  STAGE II                 1                 0
  STAGE IIA               20                32
  STAGE IIB               30                41
  STAGE IIIA              22                35
  STAGE IIIB               7                13
  STAGE IV                 5                 1
[1] 9 2
[1] 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    33 115  21   9
  1Q GAIN WILD-TYPE  65 139  27  11
D2V4, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T1              33                65
  T2             115               139
  T3              21                27
  T4               9                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  1Q GAIN MUTATED   113  50  12   1
  1Q GAIN WILD-TYPE 148  63  23   4
D2V5, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  N0             113               148
  N1              50                63
  N2              12                23
  N3               1                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A  MX
  1Q GAIN MUTATED   152   4   1  20
  1Q GAIN WILD-TYPE 206   1   0  30
D2V6, multiclass
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  M0              152               206
  M1                4                 1
  M1A               1                 0
  MX               20                30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V7, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    42 136
  1Q GAIN WILD-TYPE  65 177
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     42  136
  1Q GAIN WILD-TYPE   65  177
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE              42                65
  MALE               136               177
[1] 2 2
[1] FALSE
D2V8, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  1Q GAIN MUTATED                                      10
  1Q GAIN WILD-TYPE                                     2
                   vv
clus                LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  1Q GAIN MUTATED                                        0
  1Q GAIN WILD-TYPE                                      6
                   vv
clus                LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  1Q GAIN MUTATED                                         1
  1Q GAIN WILD-TYPE                                       0
                   vv
clus                LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  1Q GAIN MUTATED                                                           167
  1Q GAIN WILD-TYPE                                                         234
D2V9, multiclass
                                                             clus
vv                                                            1Q GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                    10
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    0
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             167
                                                             clus
vv                                                            1Q GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       2
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               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"
D2V10, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED     3 175
  1Q GAIN WILD-TYPE  10 232
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      3  175
  1Q GAIN WILD-TYPE   10  232
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO                3                10
  YES             175               232
[1] 2 2
[1] FALSE
D2V11, continuous
                   vv
clus                 R0  R1  R2  RX
  1Q GAIN MUTATED   149   5   1   6
  1Q GAIN WILD-TYPE 193   3   3  12
D2V12, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  R0             149               193
  R1               5                 3
  R2               1                 3
  RX               6                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1Q GAIN MUTATED       3                         7   131
  1Q GAIN WILD-TYPE     6                        10   167
D2V13, multiclass
                           clus
vv                          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  ASIAN                                   3                 6
  BLACK OR AFRICAN AMERICAN               7                10
  WHITE                                 131               167
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V14, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED     4 115
  1Q GAIN WILD-TYPE   4 152
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      4  115
  1Q GAIN WILD-TYPE    4  152
                        clus
vv                       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                 4
  NOT HISPANIC OR LATINO             115               152
[1] 2 2
[1] FALSE

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                 0   1
  2P GAIN MUTATED   119  49
  2P GAIN WILD-TYPE 146  74
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              168               220 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               49                74 
$`2P GAIN MUTATED`
TCGA-18-3409 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3417 
        2417         1415          345          396         1810          758 
TCGA-18-3419 TCGA-18-3421 TCGA-21-1072 TCGA-21-1076 TCGA-21-1079 TCGA-21-1081 
          50         1331         3016         1852          965          284 
TCGA-21-1083 TCGA-21-5786 TCGA-21-A5DI TCGA-22-4591 TCGA-22-4595 TCGA-22-4599 
         267         1032          979          623          734         1161 
TCGA-22-4604 TCGA-22-4605 TCGA-22-5471 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 
         399         1946          965         1933          445         1346 
TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5483 TCGA-22-5489 TCGA-22-5491 
          24         1651         1952          573         1912         1713 
TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-33-6738 
          29         2524         5287         1966         1941          822 
TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 TCGA-34-5231 TCGA-34-5240 
          80         1874          958          881         1528          365 
TCGA-34-5241 TCGA-34-5928 TCGA-34-8454 TCGA-37-3792 TCGA-37-4130 TCGA-37-4133 
         428          552          166           12          247          238 
TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5027 TCGA-39-5035 TCGA-39-5036 
        1454         2253         1361         1849          474         1084 
TCGA-39-5037 TCGA-39-5040 TCGA-43-2576 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 
        1086         1964         1223         1176          822         1007 
TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 TCGA-43-7658 TCGA-43-8115 TCGA-46-6025 
         349          849          376         1970          407          324 
TCGA-51-4080 TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 TCGA-56-1622 TCGA-56-5898 
          12         1948          923         1958          881          555 
TCGA-56-6546 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7582 TCGA-56-7730 
          26           13           30           44           26            6 
TCGA-56-8504 TCGA-56-8628 TCGA-56-8629 TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY 
         178           16           34            2           46           30 
TCGA-56-A5DS TCGA-58-8391 TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2698 
           8         2167         1723         1072          910          311 
TCGA-60-2703 TCGA-60-2708 TCGA-60-2711 TCGA-60-2712 TCGA-60-2719 TCGA-60-2724 
        1950         1963         1260          274         1297          717 
TCGA-60-2726 TCGA-63-6202 TCGA-63-7023 TCGA-66-2737 TCGA-66-2758 TCGA-66-2759 
         358         1973         1952           61          639          762 
TCGA-66-2767 TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2787 
          61          700          578         1946           61         1217 
TCGA-66-2789 TCGA-66-2792 TCGA-66-2793 TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 
        1955          913         1952          122         1492           83 
TCGA-68-7756 TCGA-68-A59I TCGA-77-6842 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 
         202          121         1950         1952         1959         1968 
TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-8009 TCGA-77-8130 
          15         1286         1954         1942         1641         1945 
TCGA-77-8136 TCGA-77-8139 TCGA-77-8148 TCGA-77-8150 TCGA-77-8156 TCGA-77-A5G1 
        1947         1951          293         1961           10         1942 
TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6560 TCGA-85-6798 
        1290         1280          839          713          364           34 
TCGA-85-7696 TCGA-85-7843 TCGA-85-7844 TCGA-85-8052 TCGA-85-8070 TCGA-85-8072 
          18           35          911           16          960          513 
TCGA-85-8277 TCGA-85-8350 TCGA-85-8354 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4QR 
          11           60           61            3          475           25 
TCGA-85-A50M TCGA-85-A510 TCGA-85-A5B5 TCGA-90-7767 TCGA-90-7769 TCGA-90-7964 
          19         1967          111           89          358          428 
TCGA-90-A4EE TCGA-92-7341 TCGA-94-7943 TCGA-94-A4VJ TCGA-96-7545 TCGA-96-8169 
         331          106          356          430         1344          189 
TCGA-96-A4JK TCGA-98-7454 TCGA-J1-A4AH TCGA-L3-A524 TCGA-MF-A522 TCGA-NC-A5HG 
         273          256          222          449           83         1548 

$`2P GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3410 TCGA-18-3416 TCGA-18-4083 
         370          136         2464          146          862          187 
TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1070 TCGA-21-1071 
          85         2754           92          827         3636         1426 
TCGA-21-1075 TCGA-21-1077 TCGA-21-1078 TCGA-21-1080 TCGA-21-1082 TCGA-21-5782 
        2134         1058          474         3724         3644          962 
TCGA-21-5784 TCGA-21-5787 TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 
        1268          329          608          223         1945          131 
TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-1017 TCGA-22-4593 
        1952           53          429          822         1485         1067 
TCGA-22-4594 TCGA-22-4596 TCGA-22-4601 TCGA-22-4607 TCGA-22-4613 TCGA-22-5472 
        1470           17         1057          587          358         1964 
TCGA-22-5481 TCGA-22-5482 TCGA-22-5485 TCGA-22-5492 TCGA-33-4533 TCGA-33-4538 
        1952          357          916          506         1940         2979 
TCGA-33-4547 TCGA-33-4586 TCGA-33-4587 TCGA-33-4589 TCGA-34-2608 TCGA-34-2609 
        1311          428         1970         1948         1000          951 
TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 TCGA-34-5927 TCGA-37-3783 TCGA-37-3789 
        2062         1715          707          941          120           13 
TCGA-37-4129 TCGA-37-4132 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5021 
         200          227          207           12          103         1947 
TCGA-39-5022 TCGA-39-5024 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 
        1996         1964           52          740           59          833 
TCGA-39-5034 TCGA-39-5039 TCGA-43-2578 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 
        1107          544          684          757          310         1936 
TCGA-43-7656 TCGA-43-7657 TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 
         212          236          358         1971          353          296 
TCGA-43-A56U TCGA-43-A56V TCGA-46-6026 TCGA-51-4079 TCGA-51-4081 TCGA-52-7622 
         432          366          423           12          911          541 
TCGA-52-7812 TCGA-56-5897 TCGA-56-6545 TCGA-56-7221 TCGA-56-7580 TCGA-56-7731 
        1967            3           62           30           40         1961 
TCGA-56-7822 TCGA-56-8503 TCGA-56-8622 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 
           1           41           55           36           63           17 
TCGA-56-A49D TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR TCGA-58-8388 TCGA-58-8390 
          38           25            4            4          378          911 
TCGA-58-8393 TCGA-58-A46J TCGA-60-2695 TCGA-60-2696 TCGA-60-2704 TCGA-60-2706 
        1058         2589          642          109         1943         1958 
TCGA-60-2707 TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 TCGA-60-2714 TCGA-60-2715 
         661         1505         1963         1731         1531         1075 
TCGA-60-2716 TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 TCGA-60-2725 
        1475           97          983          908         1092          816 
TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-66-2727 TCGA-66-2734 TCGA-66-2742 
        1957         1955         1947         1967         1311          641 
TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 
          30           31           61           28           30           30 
TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2768 TCGA-66-2769 TCGA-66-2778 
          30           61           31           61         1947          578 
TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 
        1956          121         1954          759           60          790 
TCGA-66-2788 TCGA-66-2790 TCGA-66-2791 TCGA-66-2794 TCGA-68-7757 TCGA-68-8250 
         699          699         1977         1645          211          244 
TCGA-68-8251 TCGA-68-A59J TCGA-77-6843 TCGA-77-6844 TCGA-77-7338 TCGA-77-7463 
          96          104         1941         1942         1952         1954 
TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 TCGA-77-8128 TCGA-77-8131 TCGA-77-8133 
         479         1960         1945         1953         1941         1941 
TCGA-77-8138 TCGA-77-8140 TCGA-77-8144 TCGA-77-8145 TCGA-77-8153 TCGA-77-8154 
        1946         1962          833         1943         1684         1092 
TCGA-77-A5FZ TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5GB TCGA-85-6561 
        1953         1959         1955         1963         1939          395 
TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7950 TCGA-85-8048 
          10           49            1         1965           60           26 
TCGA-85-8049 TCGA-85-8071 TCGA-85-8276 TCGA-85-8287 TCGA-85-8288 TCGA-85-8351 
          60          428           13           13           54           55 
TCGA-85-8352 TCGA-85-8353 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 
          67           54           61           22           21          445 
TCGA-85-8582 TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50Z TCGA-85-A511 
         424           15         1972         1960         1973         1972 
TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L TCGA-90-6837 TCGA-90-7766 TCGA-90-A4ED 
        1987           24           13          758          289          244 
TCGA-90-A59Q TCGA-92-7340 TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 
         269           82          122          160           70           87 
TCGA-96-7544 TCGA-96-8170 TCGA-96-A4JL TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 
        1213          211          183          413          224          308 
TCGA-L3-A4E7 TCGA-LA-A446 TCGA-NC-A5HE TCGA-NC-A5HI 
          35           36         1722         1135 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                2                 1 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             5287              3724 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            725.5             582.5 
[1] "2.0 - 5287.0 (725.5)" "1.0 - 3724.0 (582.5)"
[1] "hr=" "1.1"
D3V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  2P GAIN MUTATED         1       24       58        1        25        34
  2P GAIN WILD-TYPE       0       48       79        0        27        37
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  2P GAIN MUTATED           26         10        3
  2P GAIN WILD-TYPE         31         10        3
D3V3, multiclass
            clus
vv           2P GAIN MUTATED 2P GAIN WILD-TYPE
  STAGE I                  1                 0
  STAGE IA                24                48
  STAGE IB                58                79
  STAGE II                 1                 0
  STAGE IIA               25                27
  STAGE IIB               34                37
  STAGE IIIA              26                31
  STAGE IIIB              10                10
  STAGE IV                 3                 3
[1] 9 2
[1] 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    37 109  27  11
  2P GAIN WILD-TYPE  61 145  21   9
D3V4, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  T1              37                61
  T2             109               145
  T3              27                21
  T4              11                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  2P GAIN MUTATED   109  60  12   2
  2P GAIN WILD-TYPE 152  53  23   3
D3V5, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  N0             109               152
  N1              60                53
  N2              12                23
  N3               2                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A  MX
  2P GAIN MUTATED   158   2   1  20
  2P GAIN WILD-TYPE 200   3   0  30
D3V6, multiclass
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  M0              158               200
  M1                2                 3
  M1A               1                 0
  MX               20                30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V7, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    35 149
  2P GAIN WILD-TYPE  72 164
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     35  149
  2P GAIN WILD-TYPE   72  164
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE              35                72
  MALE               149               164
[1] 2 2
[1] FALSE
D3V8, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  2P GAIN MUTATED                                      10
  2P GAIN WILD-TYPE                                     2
                   vv
clus                LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  2P GAIN MUTATED                                        1
  2P GAIN WILD-TYPE                                      5
                   vv
clus                LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  2P GAIN MUTATED                                         0
  2P GAIN WILD-TYPE                                       1
                   vv
clus                LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  2P GAIN MUTATED                                                           173
  2P GAIN WILD-TYPE                                                         228
D3V9, multiclass
                                                             clus
vv                                                            2P GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                    10
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             173
                                                             clus
vv                                                            2P GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       2
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               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"
D3V10, binary
                   cls
clus                  0   1
  2P GAIN MUTATED     8 176
  2P GAIN WILD-TYPE   5 231
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      8  176
  2P GAIN WILD-TYPE    5  231
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  NO                8                 5
  YES             176               231
[1] 2 2
[1] FALSE
D3V11, continuous
                   vv
clus                 R0  R1  R2  RX
  2P GAIN MUTATED   154   1   1   5
  2P GAIN WILD-TYPE 188   7   3  13
D3V12, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  R0             154               188
  R1               1                 7
  R2               1                 3
  RX               5                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2P GAIN MUTATED       4                         4   140
  2P GAIN WILD-TYPE     5                        13   158
D3V13, multiclass
                           clus
vv                          2P GAIN MUTATED 2P GAIN WILD-TYPE
  ASIAN                                   4                 5
  BLACK OR AFRICAN AMERICAN               4                13
  WHITE                                 140               158
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V14, binary
                   cls
clus                  0   1
  2P GAIN MUTATED     1 122
  2P GAIN WILD-TYPE   7 145
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      1  122
  2P GAIN WILD-TYPE    7  145
                        clus
vv                       2P GAIN MUTATED 2P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 7
  NOT HISPANIC OR LATINO             122               145
[1] 2 2
[1] FALSE

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                 0   1
  2Q GAIN MUTATED    74  38
  2Q GAIN WILD-TYPE 191  85
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
              112               276 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               38                85 
$`2Q GAIN MUTATED`
TCGA-18-3409 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 TCGA-21-1072 TCGA-21-1081 
        2417         1415          345          396         3016          284 
TCGA-21-1083 TCGA-21-A5DI TCGA-22-4595 TCGA-22-4605 TCGA-22-5474 TCGA-22-5477 
         267          979          734         1946          445         1346 
TCGA-22-5480 TCGA-22-5483 TCGA-22-5489 TCGA-22-5491 TCGA-33-4532 TCGA-33-4566 
        1952          573         1912         1713         2524         5287 
TCGA-33-4582 TCGA-33-4583 TCGA-33-4587 TCGA-33-6738 TCGA-34-2596 TCGA-34-2600 
        1966         1941         1970          822           80         1874 
TCGA-34-2604 TCGA-34-2605 TCGA-34-5240 TCGA-34-5241 TCGA-37-3792 TCGA-37-4130 
         958          881          365          428           12          247 
TCGA-37-4133 TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5035 TCGA-39-5036 
         238         1454         2253         1361          474         1084 
TCGA-39-5037 TCGA-39-5040 TCGA-43-2576 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 
        1086         1964         1223         1176          822         1007 
TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 TCGA-51-4080 TCGA-52-7809 TCGA-52-7810 
         349          849          376           12         1948          923 
TCGA-52-7811 TCGA-56-1622 TCGA-56-5898 TCGA-56-6546 TCGA-56-7222 TCGA-56-7223 
        1958          881          555           26           13           30 
TCGA-56-7582 TCGA-56-7730 TCGA-56-8504 TCGA-56-8629 TCGA-56-A4BX TCGA-56-A5DS 
          26            6          178           34           46            8 
TCGA-58-8391 TCGA-58-A46M TCGA-58-A46N TCGA-60-2703 TCGA-60-2708 TCGA-60-2711 
        2167         1072          910         1950         1963         1260 
TCGA-60-2712 TCGA-60-2719 TCGA-60-2726 TCGA-63-6202 TCGA-66-2759 TCGA-66-2770 
         274         1297          358         1973          762          700 
TCGA-66-2773 TCGA-66-2792 TCGA-66-2793 TCGA-68-7755 TCGA-68-7756 TCGA-77-6842 
        1946          913         1952           83          202         1950 
TCGA-77-6845 TCGA-77-7139 TCGA-77-7142 TCGA-77-8009 TCGA-77-8130 TCGA-77-8139 
        1952         1968         1286         1641         1945         1951 
TCGA-77-8145 TCGA-77-8150 TCGA-77-8156 TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G8 
        1943         1961           10         1942         1959         1290 
TCGA-77-A5GA TCGA-77-A5GH TCGA-85-6560 TCGA-85-7843 TCGA-85-7844 TCGA-85-8070 
        1280          713          364           35          911          960 
TCGA-85-8277 TCGA-85-8287 TCGA-85-8350 TCGA-85-8354 TCGA-85-8666 TCGA-85-A4QR 
          11           13           60           61          475           25 
TCGA-85-A50M TCGA-85-A510 TCGA-90-7769 TCGA-90-7964 TCGA-90-A4EE TCGA-92-7341 
          19         1967          358          428          331          106 
TCGA-96-7545 TCGA-J1-A4AH TCGA-MF-A522 TCGA-NC-A5HG 
        1344          222           83         1548 

$`2Q GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3410 TCGA-18-3415 TCGA-18-3416 
         370          136         2464          146         1810          862 
TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 
         758           50         1331          187           85         2754 
TCGA-18-5592 TCGA-18-5595 TCGA-21-1070 TCGA-21-1071 TCGA-21-1075 TCGA-21-1076 
          92          827         3636         1426         2134         1852 
TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 TCGA-21-1082 TCGA-21-5782 
        1058          474          965         3724         3644          962 
TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 
        1268         1032          329          608          223         1945 
TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-1017 
         131         1952           53          429          822         1485 
TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 
         623         1067         1470           17         1161         1057 
TCGA-22-4604 TCGA-22-4607 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 
         399          587          358          965         1964         1933 
TCGA-22-5478 TCGA-22-5479 TCGA-22-5481 TCGA-22-5482 TCGA-22-5485 TCGA-22-5492 
          24         1651         1952          357          916          506 
TCGA-22-A5C4 TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 TCGA-33-4586 TCGA-33-4589 
          29         1940         2979         1311          428         1948 
TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 
        1000          951         1528         2062         1715          707 
TCGA-34-5927 TCGA-34-5928 TCGA-34-8454 TCGA-37-3783 TCGA-37-3789 TCGA-37-4129 
         941          552          166          120           13          200 
TCGA-37-4132 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5021 TCGA-39-5022 
         227          207           12          103         1947         1996 
TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 
        1964         1849           52          740           59          833 
TCGA-39-5034 TCGA-39-5039 TCGA-43-2578 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 
        1107          544          684          757          310         1936 
TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 
         212          236         1970          407          358         1971 
TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V TCGA-46-6025 TCGA-46-6026 
         353          296          432          366          324          423 
TCGA-51-4079 TCGA-51-4081 TCGA-52-7622 TCGA-52-7812 TCGA-56-5897 TCGA-56-6545 
          12          911          541         1967            3           62 
TCGA-56-7221 TCGA-56-7579 TCGA-56-7580 TCGA-56-7731 TCGA-56-7822 TCGA-56-8503 
          30           44           40         1961            1           41 
TCGA-56-8622 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-A49D 
          55           36           63           17           16           38 
TCGA-56-A4BW TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR TCGA-58-8388 
           2           30           25            4            4          378 
TCGA-58-8390 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46L TCGA-60-2695 TCGA-60-2696 
         911         1058         2589         1723          642          109 
TCGA-60-2698 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2709 TCGA-60-2710 
         311         1943         1958          661         1505         1963 
TCGA-60-2713 TCGA-60-2714 TCGA-60-2715 TCGA-60-2716 TCGA-60-2720 TCGA-60-2721 
        1731         1531         1075         1475           97          983 
TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-63-7020 TCGA-63-7021 
         908         1092          717          816         1957         1955 
TCGA-63-7022 TCGA-63-7023 TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 
        1947         1952         1967         1311           61          641 
TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 
          30           31           61           28           30           30 
TCGA-66-2758 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 
         639           30           61           31           61           61 
TCGA-66-2769 TCGA-66-2771 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 
        1947          578           61          578         1956          121 
TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 
        1954          759           60          790         1217          699 
TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 
        1955          699         1977         1645          122         1492 
TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-77-6843 
         211          244           96          121          104         1941 
TCGA-77-6844 TCGA-77-7138 TCGA-77-7141 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 
        1942         1959           15         1954         1942         1952 
TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 TCGA-77-8128 TCGA-77-8131 
        1954          479         1960         1945         1953         1941 
TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8140 TCGA-77-8144 TCGA-77-8148 
        1941         1947         1946         1962          833          293 
TCGA-77-8153 TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5GB 
        1684         1092         1953         1955         1963         1939 
TCGA-77-A5GF TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 
         839          395           34           18           10           49 
TCGA-85-7699 TCGA-85-7710 TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 
           1         1965           60           26           60           16 
TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 TCGA-85-8288 TCGA-85-8351 TCGA-85-8352 
         428          513           13           54           55           67 
TCGA-85-8353 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 
          54           61           22           21          445          424 
TCGA-85-8664 TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50Z TCGA-85-A511 
           3           15         1972         1960         1973         1972 
TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7766 
        1987           24           13          111          758          289 
TCGA-90-7767 TCGA-90-A4ED TCGA-90-A59Q TCGA-92-7340 TCGA-92-8063 TCGA-92-8064 
          89          244          269           82          122          160 
TCGA-92-8065 TCGA-94-7033 TCGA-94-7943 TCGA-94-A4VJ TCGA-96-7544 TCGA-96-8169 
          70           87          356          430         1213          189 
TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 
         211          273          183          256          413          224 
TCGA-98-8023 TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-NC-A5HE TCGA-NC-A5HI 
         308           35          449           36         1722         1135 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                6                 1 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             5287              3724 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            910.5             527.0 
[1] "6.0 - 5287.0 (910.5)" "1.0 - 3724.0 (527.0)"
[1] "hr=" "1.1"
D4V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  2Q GAIN MUTATED         1       14       40        1        18        22
  2Q GAIN WILD-TYPE       0       58       97        0        34        49
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  2Q GAIN MUTATED           15          5        2
  2Q GAIN WILD-TYPE         42         15        4
D4V3, multiclass
            clus
vv           2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  STAGE I                  1                 0
  STAGE IA                14                58
  STAGE IB                40                97
  STAGE II                 1                 0
  STAGE IIA               18                34
  STAGE IIB               22                49
  STAGE IIIA              15                42
  STAGE IIIB               5                15
  STAGE IV                 2                 4
[1] 9 2
[1] 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    24  74  14   8
  2Q GAIN WILD-TYPE  74 180  34  12
D4V4, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  T1              24                74
  T2              74               180
  T3              14                34
  T4               8                12
[1] 4 2
[1] 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    75  37   8   0
  2Q GAIN WILD-TYPE 186  76  27   5
D4V5, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  N0              75               186
  N1              37                76
  N2               8                27
  N3               0                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A  MX
  2Q GAIN MUTATED    99   1   1  16
  2Q GAIN WILD-TYPE 259   4   0  34
D4V6, multiclass
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  M0               99               259
  M1                1                 4
  M1A               1                 0
  MX               16                34
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V7, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    23  97
  2Q GAIN WILD-TYPE  84 216
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     23   97
  2Q GAIN WILD-TYPE   84  216
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE              23                84
  MALE                97               216
[1] 2 2
[1] FALSE
D4V8, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  2Q GAIN MUTATED                                       8
  2Q GAIN WILD-TYPE                                     4
                   vv
clus                LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  2Q GAIN MUTATED                                        1
  2Q GAIN WILD-TYPE                                      5
                   vv
clus                LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  2Q GAIN MUTATED                                         1
  2Q GAIN WILD-TYPE                                       0
                   vv
clus                LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  2Q GAIN MUTATED                                                           110
  2Q GAIN WILD-TYPE                                                         291
D4V9, multiclass
                                                             clus
vv                                                            2Q GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     8
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             110
                                                             clus
vv                                                            2Q GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       4
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               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"
D4V10, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED     6 114
  2Q GAIN WILD-TYPE   7 293
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      6  114
  2Q GAIN WILD-TYPE    7  293
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  NO                6                 7
  YES             114               293
[1] 2 2
[1] FALSE
D4V11, continuous
                   vv
clus                 R0  R1  R2  RX
  2Q GAIN MUTATED   100   1   0   2
  2Q GAIN WILD-TYPE 242   7   4  16
D4V12, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  R0             100               242
  R1               1                 7
  R2               0                 4
  RX               2                16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2Q GAIN MUTATED       3                         3    94
  2Q GAIN WILD-TYPE     6                        14   204
D4V13, multiclass
                           clus
vv                          2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  ASIAN                                   3                 6
  BLACK OR AFRICAN AMERICAN               3                14
  WHITE                                  94               204
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V14, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED     1  84
  2Q GAIN WILD-TYPE   7 183
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      1   84
  2Q GAIN WILD-TYPE    7  183
                        clus
vv                       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 7
  NOT HISPANIC OR LATINO              84               183
[1] 2 2
[1] FALSE

Clustering(5) Variable = 3P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                 0   1
  3P GAIN MUTATED    48  32
  3P GAIN WILD-TYPE 217  91
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               80               308 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               32                91 
$`3P GAIN MUTATED`
TCGA-18-3410 TCGA-18-3414 TCGA-21-1080 TCGA-21-1081 TCGA-22-1000 TCGA-22-1002 
         146          396         3724          284         1945          131 
TCGA-22-4593 TCGA-22-4595 TCGA-22-4601 TCGA-22-5477 TCGA-22-5485 TCGA-22-5489 
        1067          734         1057         1346          916         1912 
TCGA-22-5491 TCGA-33-4533 TCGA-33-4538 TCGA-33-4582 TCGA-33-4586 TCGA-34-2609 
        1713         1940         2979         1966          428          951 
TCGA-34-5232 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-37-3783 
        2062          365          428          941          552          120 
TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5029 TCGA-39-5030 TCGA-39-5037 
        1361         1947         1996          740           59         1086 
TCGA-39-5040 TCGA-43-3394 TCGA-43-5670 TCGA-43-6771 TCGA-43-A56V TCGA-46-6025 
        1964          822          849         1936          366          324 
TCGA-46-6026 TCGA-52-7810 TCGA-56-5898 TCGA-56-7223 TCGA-56-7730 TCGA-56-A49D 
         423          923          555           30            6           38 
TCGA-56-A4BW TCGA-56-A4ZK TCGA-56-A5DR TCGA-58-8393 TCGA-58-A46J TCGA-58-A46M 
           2            4            4         1058         2589         1072 
TCGA-60-2703 TCGA-60-2706 TCGA-60-2713 TCGA-60-2715 TCGA-63-7022 TCGA-66-2727 
        1950         1958         1731         1075         1947         1967 
TCGA-66-2756 TCGA-66-2766 TCGA-66-2771 TCGA-66-2777 TCGA-77-8008 TCGA-77-8009 
          30           31          578           61         1945         1641 
TCGA-77-8136 TCGA-77-8145 TCGA-77-8150 TCGA-77-A5G1 TCGA-77-A5G8 TCGA-77-A5GA 
        1947         1943         1961         1942         1290         1280 
TCGA-77-A5GB TCGA-77-A5GF TCGA-85-6561 TCGA-85-7696 TCGA-85-8049 TCGA-85-8350 
        1939          839          395           18           60           60 
TCGA-85-8352 TCGA-85-8580 TCGA-85-8582 TCGA-85-8664 TCGA-94-7033 TCGA-94-7943 
          67          445          424            3           87          356 
TCGA-96-7545 TCGA-J1-A4AH 
        1344          222 

$`3P GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3411 TCGA-18-3412 
         370          136         2464         2417         1415          345 
TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4083 
        1810          862          758           50         1331          187 
TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1070 TCGA-21-1071 
          85         2754           92          827         3636         1426 
TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 
        3016         2134         1852         1058          474          965 
TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 
        3644          267          962         1268         1032          329 
TCGA-21-A5DI TCGA-22-0940 TCGA-22-0944 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 
         979          608          223         1952           53          429 
TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 TCGA-22-4594 TCGA-22-4596 TCGA-22-4599 
         822         1485          623         1470           17         1161 
TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 
         399         1946          587          358          965         1964 
TCGA-22-5473 TCGA-22-5474 TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 
        1933          445           24         1651         1952         1952 
TCGA-22-5482 TCGA-22-5483 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4547 
         357          573          506           29         2524         1311 
TCGA-33-4566 TCGA-33-4583 TCGA-33-4587 TCGA-33-4589 TCGA-33-6738 TCGA-34-2596 
        5287         1941         1970         1948          822           80 
TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 TCGA-34-5231 TCGA-34-5234 
        1874          958          881         1000         1528         1715 
TCGA-34-5239 TCGA-34-8454 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 
         707          166           13           12          200          247 
TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5011 
         227          238          207           12          103         1454 
TCGA-39-5016 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5031 TCGA-39-5034 
        2253         1964         1849           52          833         1107 
TCGA-39-5035 TCGA-39-5036 TCGA-39-5039 TCGA-43-2576 TCGA-43-2578 TCGA-43-2581 
         474         1084          544         1223          684         1176 
TCGA-43-3920 TCGA-43-5668 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-7656 
        1007          349          376          757          310          212 
TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 
         236         1970          407          358         1971          353 
TCGA-43-A475 TCGA-43-A56U TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 
         296          432           12           12          911          541 
TCGA-52-7809 TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-6545 
        1948         1958         1967          881            3           62 
TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 
          26           30           13           44           40           26 
TCGA-56-7731 TCGA-56-7822 TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 TCGA-56-8624 
        1961            1           41          178           55           36 
TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A4BX TCGA-56-A4BY 
          63           17           16           34           46           30 
TCGA-56-A4ZJ TCGA-56-A5DS TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-A46L 
          25            8          378          911         2167         1723 
TCGA-58-A46N TCGA-60-2695 TCGA-60-2696 TCGA-60-2698 TCGA-60-2704 TCGA-60-2707 
         910          642          109          311         1943          661 
TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 TCGA-60-2714 
        1963         1505         1963         1260          274         1531 
TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 
        1475         1297           97          983          908         1092 
TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 
         717          816          358         1973         1957         1955 
TCGA-63-7023 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 TCGA-66-2753 
        1952         1311           61          641           30           31 
TCGA-66-2754 TCGA-66-2755 TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 
          61           28           30          639          762           30 
TCGA-66-2765 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 TCGA-66-2773 
          61           61           61         1947          700         1946 
TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 
         578         1956          121         1954          759           60 
TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 
         790         1217          699         1955          699         1977 
TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 
         913         1952         1645          122         1492           83 
TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J 
         202          211          244           96          121          104 
TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 
        1950         1941         1942         1952         1959         1968 
TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 
          15         1286         1954         1942         1952         1954 
TCGA-77-7465 TCGA-77-8007 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 
         479         1960         1953         1945         1941         1941 
TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8144 TCGA-77-8148 TCGA-77-8153 
        1946         1951         1962          833          293         1684 
TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 
        1092           10         1953         1959         1955         1963 
TCGA-77-A5GH TCGA-85-6560 TCGA-85-6798 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 
         713          364           34           10           49            1 
TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8052 
        1965           35          911           60           26           16 
TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 
         960          428          513           13           11           13 
TCGA-85-8288 TCGA-85-8351 TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 
          54           55           54           61           61           22 
TCGA-85-8481 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR 
          21          475           15         1972         1960           25 
TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 
          19         1973         1967         1972         1987           24 
TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 
          13          111          758          289           89          358 
TCGA-90-7964 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 
         428          244          331          269           82          106 
TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-A4VJ TCGA-96-7544 TCGA-96-8169 
         122          160           70          430         1213          189 
TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 
         211          273          183          256          413          224 
TCGA-98-8023 TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HE 
         308           35          449           36           83         1722 
TCGA-NC-A5HG TCGA-NC-A5HI 
        1548         1135 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                2                 1 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             3724              5287 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            882.5             582.5 
[1] "2.0 - 3724.0 (882.5)" "1.0 - 5287.0 (582.5)"
[1] "hr=" "1.3"
D5V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  3P GAIN MUTATED         0       18       22        1         9        18
  3P GAIN WILD-TYPE       1       54      115        0        43        53
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  3P GAIN MUTATED           20          2        1
  3P GAIN WILD-TYPE         37         18        5
D5V3, multiclass
            clus
vv           3P GAIN MUTATED 3P GAIN WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                18                54
  STAGE IB                22               115
  STAGE II                 1                 0
  STAGE IIA                9                43
  STAGE IIB               18                53
  STAGE IIIA              20                37
  STAGE IIIB               2                18
  STAGE IV                 1                 5
[1] 9 2
[1] 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    22  52  12   5
  3P GAIN WILD-TYPE  76 202  36  15
D5V4, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  T1              22                76
  T2              52               202
  T3              12                36
  T4               5                15
[1] 4 2
[1] 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    50  26  12   0
  3P GAIN WILD-TYPE 211  87  23   5
D5V5, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  N0              50               211
  N1              26                87
  N2              12                23
  N3               0                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A  MX
  3P GAIN MUTATED    81   1   0   8
  3P GAIN WILD-TYPE 277   4   1  42
D5V6, multiclass
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  M0               81               277
  M1                1                 4
  M1A               0                 1
  MX                8                42
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V7, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    18  73
  3P GAIN WILD-TYPE  89 240
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     18   73
  3P GAIN WILD-TYPE   89  240
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE              18                89
  MALE                73               240
[1] 2 2
[1] FALSE
D5V8, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  3P GAIN MUTATED                                       2
  3P GAIN WILD-TYPE                                    10
                   vv
clus                LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  3P GAIN MUTATED                                        0
  3P GAIN WILD-TYPE                                      6
                   vv
clus                LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  3P GAIN MUTATED                                         0
  3P GAIN WILD-TYPE                                       1
                   vv
clus                LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  3P GAIN MUTATED                                                            89
  3P GAIN WILD-TYPE                                                         312
D5V9, multiclass
                                                             clus
vv                                                            3P GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     2
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    0
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              89
                                                             clus
vv                                                            3P GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      10
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               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"
D5V10, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     4  87
  3P GAIN WILD-TYPE   9 320
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      4   87
  3P GAIN WILD-TYPE    9  320
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  NO                4                 9
  YES              87               320
[1] 2 2
[1] FALSE
D5V11, continuous
                   vv
clus                 R0  R1  R2  RX
  3P GAIN MUTATED    69   3   1   4
  3P GAIN WILD-TYPE 273   5   3  14
D5V12, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  R0              69               273
  R1               3                 5
  R2               1                 3
  RX               4                14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3P GAIN MUTATED       3                         6    64
  3P GAIN WILD-TYPE     6                        11   234
D5V13, multiclass
                           clus
vv                          3P GAIN MUTATED 3P GAIN WILD-TYPE
  ASIAN                                   3                 6
  BLACK OR AFRICAN AMERICAN               6                11
  WHITE                                  64               234
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V14, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     2  60
  3P GAIN WILD-TYPE   6 207
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      2   60
  3P GAIN WILD-TYPE    6  207
                        clus
vv                       3P GAIN MUTATED 3P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 6
  NOT HISPANIC OR LATINO              60               207
[1] 2 2
[1] FALSE

Clustering(6) Variable = 3Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                 0   1
  3Q GAIN MUTATED   168  80
  3Q GAIN WILD-TYPE  97  43
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              248               140 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               80                43 
$`3Q GAIN MUTATED`
TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3414 TCGA-18-3417 TCGA-18-3419 
         136         2417          146          396          758           50 
TCGA-18-3421 TCGA-18-4086 TCGA-18-5595 TCGA-21-1070 TCGA-21-1071 TCGA-21-1076 
        1331           85          827         3636         1426         1852 
TCGA-21-1077 TCGA-21-1080 TCGA-21-1081 TCGA-21-1083 TCGA-21-5782 TCGA-21-5784 
        1058         3724          284          267          962         1268 
TCGA-21-5786 TCGA-21-5787 TCGA-21-A5DI TCGA-22-0940 TCGA-22-1000 TCGA-22-1002 
        1032          329          979          608         1945          131 
TCGA-22-1012 TCGA-22-4591 TCGA-22-4593 TCGA-22-4595 TCGA-22-4599 TCGA-22-4601 
         429          623         1067          734         1161         1057 
TCGA-22-4605 TCGA-22-4607 TCGA-22-4613 TCGA-22-5472 TCGA-22-5477 TCGA-22-5479 
        1946          587          358         1964         1346         1651 
TCGA-22-5480 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-33-4532 
        1952          916         1912         1713          506         2524 
TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4586 
        1940         2979         1311         5287         1966          428 
TCGA-33-4587 TCGA-33-4589 TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 TCGA-34-2608 
        1970         1948           80         1874          958         1000 
TCGA-34-2609 TCGA-34-5232 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 
         951         2062          365          428          941          552 
TCGA-37-3783 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 
         120          247          227          238          207           12 
TCGA-37-5819 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 
         103         2253         1361         1947         1996         1964 
TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5035 TCGA-39-5037 
          52          740           59          833          474         1086 
TCGA-39-5040 TCGA-43-2576 TCGA-43-2578 TCGA-43-3394 TCGA-43-3920 TCGA-43-5670 
        1964         1223          684          822         1007          849 
TCGA-43-6143 TCGA-43-6771 TCGA-43-7657 TCGA-43-7658 TCGA-43-8118 TCGA-43-A56V 
         376         1936          236         1970         1971          366 
TCGA-46-6025 TCGA-46-6026 TCGA-51-4080 TCGA-51-4081 TCGA-52-7809 TCGA-52-7810 
         324          423           12          911         1948          923 
TCGA-56-5897 TCGA-56-5898 TCGA-56-7223 TCGA-56-7580 TCGA-56-7730 TCGA-56-7731 
           3          555           30           40            6         1961 
TCGA-56-7822 TCGA-56-8504 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 
           1          178           36           63           17           16 
TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK 
          34           38            2           30           25            4 
TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8390 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46M 
           4            8          911         1058         2589         1072 
TCGA-58-A46N TCGA-60-2695 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 
         910          642         1950         1943         1958          661 
TCGA-60-2708 TCGA-60-2710 TCGA-60-2712 TCGA-60-2713 TCGA-60-2715 TCGA-60-2721 
        1963         1963          274         1731         1075          983 
TCGA-60-2723 TCGA-60-2724 TCGA-60-2726 TCGA-63-7020 TCGA-63-7022 TCGA-66-2727 
        1092          717          358         1957         1947         1967 
TCGA-66-2734 TCGA-66-2742 TCGA-66-2744 TCGA-66-2755 TCGA-66-2756 TCGA-66-2758 
        1311          641           30           28           30          639 
TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2770 
         762           30           61           31           61          700 
TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 
         578         1946           61          578         1956          121 
TCGA-66-2783 TCGA-66-2786 TCGA-66-2787 TCGA-66-2789 TCGA-66-2790 TCGA-66-2800 
         759          790         1217         1955          699         1492 
TCGA-68-7755 TCGA-68-7756 TCGA-68-8250 TCGA-68-8251 TCGA-77-6842 TCGA-77-6845 
          83          202          244           96         1950         1952 
TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7338 
        1959         1968           15         1286         1954         1952 
TCGA-77-7463 TCGA-77-7465 TCGA-77-8008 TCGA-77-8009 TCGA-77-8133 TCGA-77-8136 
        1954          479         1945         1641         1941         1947 
TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 
        1946         1951         1962         1943          293         1961 
TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA 
        1942         1959         1955         1963         1290         1280 
TCGA-77-A5GB TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 
        1939          839          713          364          395           34 
TCGA-85-7696 TCGA-85-7697 TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 
          18           10         1965           35          911           60 
TCGA-85-8049 TCGA-85-8052 TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 
          60           16          513           13           11           13 
TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 TCGA-85-8355 
          54           60           55           67           54           61 
TCGA-85-8580 TCGA-85-8582 TCGA-85-8664 TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A510 
         445          424            3         1960           25         1967 
TCGA-85-A511 TCGA-85-A5B5 TCGA-90-7766 TCGA-90-7767 TCGA-90-7964 TCGA-90-A4EE 
        1972          111          289           89          428          331 
TCGA-90-A59Q TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 TCGA-94-7943 
         269          122          160           70           87          356 
TCGA-94-A4VJ TCGA-96-7544 TCGA-96-7545 TCGA-96-8170 TCGA-96-A4JK TCGA-98-8021 
         430         1213         1344          211          273          413 
TCGA-98-8022 TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-MF-A522 
         224          222           35          449           36           83 
TCGA-NC-A5HG TCGA-NC-A5HI 
        1548         1135 

$`3Q GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 TCGA-18-3415 TCGA-18-3416 
         370         2464         1415          345         1810          862 
TCGA-18-4083 TCGA-18-4721 TCGA-18-5592 TCGA-21-1072 TCGA-21-1075 TCGA-21-1078 
         187         2754           92         3016         2134          474 
TCGA-21-1079 TCGA-21-1082 TCGA-22-0944 TCGA-22-1005 TCGA-22-1011 TCGA-22-1016 
         965         3644          223         1952           53          822 
TCGA-22-1017 TCGA-22-4594 TCGA-22-4596 TCGA-22-4604 TCGA-22-5471 TCGA-22-5473 
        1485         1470           17          399          965         1933 
TCGA-22-5474 TCGA-22-5478 TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 TCGA-22-A5C4 
         445           24         1952          357          573           29 
TCGA-33-4583 TCGA-33-6738 TCGA-34-2605 TCGA-34-5231 TCGA-34-5234 TCGA-34-5239 
        1941          822          881         1528         1715          707 
TCGA-34-8454 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-39-5011 TCGA-39-5027 
         166           13           12          200         1454         1849 
TCGA-39-5034 TCGA-39-5036 TCGA-39-5039 TCGA-43-2581 TCGA-43-5668 TCGA-43-6647 
        1107         1084          544         1176          349          757 
TCGA-43-6770 TCGA-43-7656 TCGA-43-8115 TCGA-43-8116 TCGA-43-A474 TCGA-43-A475 
         310          212          407          358          353          296 
TCGA-43-A56U TCGA-51-4079 TCGA-52-7622 TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 
         432           12          541         1958         1967          881 
TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 TCGA-56-7579 TCGA-56-7582 
          62           26           30           13           44           26 
TCGA-56-8503 TCGA-56-8622 TCGA-56-A4BX TCGA-58-8388 TCGA-58-8391 TCGA-58-A46L 
          41           55           46          378         2167         1723 
TCGA-60-2696 TCGA-60-2698 TCGA-60-2709 TCGA-60-2711 TCGA-60-2714 TCGA-60-2716 
         109          311         1505         1260         1531         1475 
TCGA-60-2719 TCGA-60-2720 TCGA-60-2722 TCGA-60-2725 TCGA-63-6202 TCGA-63-7021 
        1297           97          908          816         1973         1955 
TCGA-63-7023 TCGA-66-2737 TCGA-66-2753 TCGA-66-2754 TCGA-66-2757 TCGA-66-2768 
        1952           61           31           61           30           61 
TCGA-66-2769 TCGA-66-2782 TCGA-66-2785 TCGA-66-2788 TCGA-66-2791 TCGA-66-2792 
        1947         1954           60          699         1977          913 
TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 TCGA-68-7757 TCGA-68-A59I TCGA-68-A59J 
        1952         1645          122          211          121          104 
TCGA-77-6843 TCGA-77-6844 TCGA-77-7337 TCGA-77-8007 TCGA-77-8128 TCGA-77-8130 
        1941         1942         1942         1960         1953         1945 
TCGA-77-8131 TCGA-77-8144 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ 
        1941          833         1684         1092           10         1953 
TCGA-85-7698 TCGA-85-7699 TCGA-85-8048 TCGA-85-8070 TCGA-85-8071 TCGA-85-8354 
          49            1           26          960          428           61 
TCGA-85-8479 TCGA-85-8481 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A50M 
          22           21          475           15         1972           19 
TCGA-85-A50Z TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L TCGA-90-6837 TCGA-90-7769 
        1973         1987           24           13          758          358 
TCGA-90-A4ED TCGA-92-7340 TCGA-92-7341 TCGA-96-8169 TCGA-96-A4JL TCGA-98-7454 
         244           82          106          189          183          256 
TCGA-98-8023 TCGA-NC-A5HE 
         308         1722 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                1                 1 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             5287              3644 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            691.5             508.0 
[1] "1.0 - 5287.0 (691.5)" "1.0 - 3644.0 (508.0)"
[1] "hr=" "1"  
D6V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  3Q GAIN MUTATED         1       50       85        1        29        44
  3Q GAIN WILD-TYPE       0       22       52        0        23        27
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  3Q GAIN MUTATED           40         12        6
  3Q GAIN WILD-TYPE         17          8        0
D6V3, multiclass
            clus
vv           3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  STAGE I                  1                 0
  STAGE IA                50                22
  STAGE IB                85                52
  STAGE II                 1                 0
  STAGE IIA               29                23
  STAGE IIB               44                27
  STAGE IIIA              40                17
  STAGE IIIB              12                 8
  STAGE IV                 6                 0
[1] 9 2
[1] 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    66 162  29  12
  3Q GAIN WILD-TYPE  32  92  19   8
D6V4, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  T1              66                32
  T2             162                92
  T3              29                19
  T4              12                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  3Q GAIN MUTATED   164  73  24   4
  3Q GAIN WILD-TYPE  97  40  11   1
D6V5, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  N0             164                97
  N1              73                40
  N2              24                11
  N3               4                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A  MX
  3Q GAIN MUTATED   228   5   1  33
  3Q GAIN WILD-TYPE 130   0   0  17
D6V6, multiclass
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  M0              228               130
  M1                5                 0
  M1A               1                 0
  MX               33                17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V7, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    70 199
  3Q GAIN WILD-TYPE  37 114
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     70  199
  3Q GAIN WILD-TYPE   37  114
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE              70                37
  MALE               199               114
[1] 2 2
[1] FALSE
D6V8, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  3Q GAIN MUTATED                                      10
  3Q GAIN WILD-TYPE                                     2
                   vv
clus                LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  3Q GAIN MUTATED                                        0
  3Q GAIN WILD-TYPE                                      6
                   vv
clus                LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  3Q GAIN MUTATED                                         1
  3Q GAIN WILD-TYPE                                       0
                   vv
clus                LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  3Q GAIN MUTATED                                                           258
  3Q GAIN WILD-TYPE                                                         143
D6V9, multiclass
                                                             clus
vv                                                            3Q GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                    10
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    0
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             258
                                                             clus
vv                                                            3Q GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       2
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               143
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V10, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    10 259
  3Q GAIN WILD-TYPE   3 148
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     10  259
  3Q GAIN WILD-TYPE    3  148
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  NO               10                 3
  YES             259               148
[1] 2 2
[1] FALSE
D6V11, continuous
                   vv
clus                 R0  R1  R2  RX
  3Q GAIN MUTATED   219   4   3  12
  3Q GAIN WILD-TYPE 123   4   1   6
D6V12, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  R0             219               123
  R1               4                 4
  R2               3                 1
  RX              12                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3Q GAIN MUTATED       4                        11   192
  3Q GAIN WILD-TYPE     5                         6   106
D6V13, multiclass
                           clus
vv                          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  ASIAN                                   4                 5
  BLACK OR AFRICAN AMERICAN              11                 6
  WHITE                                 192               106
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V14, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED     5 172
  3Q GAIN WILD-TYPE   3  95
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      5  172
  3Q GAIN WILD-TYPE    3   95
                        clus
vv                       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   5                 3
  NOT HISPANIC OR LATINO             172                95
[1] 2 2
[1] FALSE

Clustering(7) Variable = 4P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                 0   1
  4P GAIN MUTATED    13  14
  4P GAIN WILD-TYPE 252 109
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               27               361 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               14               109 
$`4P GAIN MUTATED`
TCGA-18-3409 TCGA-18-3410 TCGA-18-3416 TCGA-22-1017 TCGA-22-4591 TCGA-22-4601 
        2417          146          862         1485          623         1057 
TCGA-22-5478 TCGA-22-A5C4 TCGA-34-2596 TCGA-34-2609 TCGA-37-4130 TCGA-43-2576 
          24           29           80          951          247         1223 
TCGA-43-3920 TCGA-43-8116 TCGA-56-1622 TCGA-60-2715 TCGA-63-6202 TCGA-66-2763 
        1007          358          881         1075         1973           30 
TCGA-68-8250 TCGA-77-6842 TCGA-77-7337 TCGA-77-8007 TCGA-77-A5G6 TCGA-90-7767 
         244         1950         1942         1960         1955           89 
TCGA-94-A4VJ TCGA-96-7545 TCGA-98-8022 
         430         1344          224 

$`4P GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 
         370          136         2464         1415          345          396 
TCGA-18-3415 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 
        1810          758           50         1331          187           85 
TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 
        2754           92          827         3636         1426         3016 
TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 
        2134         1852         1058          474          965         3724 
TCGA-21-1081 TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 
         284         3644          267          962         1268         1032 
TCGA-21-5787 TCGA-21-A5DI TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 
         329          979          608          223         1945          131 
TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-4593 TCGA-22-4594 
        1952           53          429          822         1067         1470 
TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 
         734           17         1161          399         1946          587 
TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 
         358          965         1964         1933          445         1346 
TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 
        1651         1952         1952          357          573          916 
TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-33-4532 TCGA-33-4533 TCGA-33-4538 
        1912         1713          506         2524         1940         2979 
TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 
        1311         5287         1966         1941          428         1970 
TCGA-33-4589 TCGA-33-6738 TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 
        1948          822         1874          958          881         1000 
TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 
        1528         2062         1715          707          365          428 
TCGA-34-5927 TCGA-34-5928 TCGA-34-8454 TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 
         941          552          166          120           13           12 
TCGA-37-4129 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 
         200          227          238          207           12          103 
TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 
        1454         2253         1361         1947         1996         1964 
TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 
        1849           52          740           59          833         1107 
TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 TCGA-39-5040 TCGA-43-2578 
         474         1084         1086          544         1964          684 
TCGA-43-2581 TCGA-43-3394 TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 
        1176          822          349          849          376          757 
TCGA-43-6770 TCGA-43-6771 TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 
         310         1936          212          236         1970          407 
TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V TCGA-46-6025 
        1971          353          296          432          366          324 
TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 
         423           12           12          911          541         1948 
TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 
         923         1958         1967            3          555           62 
TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 
          26           30           13           30           44           40 
TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-8503 TCGA-56-8504 
          26            6         1961            1           41          178 
TCGA-56-8622 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 
          55           36           63           17           16           34 
TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK 
          38            2           46           30           25            4 
TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-8393 
           4            8          378          911         2167         1058 
TCGA-58-A46J TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 TCGA-60-2696 
        2589         1723         1072          910          642          109 
TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 
         311         1950         1943         1958          661         1963 
TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 
        1505         1963         1260          274         1731         1531 
TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 
        1475         1297           97          983          908         1092 
TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 
         717          816          358         1957         1955         1947 
TCGA-63-7023 TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 
        1952         1967         1311           61          641           30 
TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 
          31           61           28           30           30          639 
TCGA-66-2759 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 
         762           61           31           61           61         1947 
TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 
         700          578         1946           61          578         1956 
TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 
         121         1954          759           60          790         1217 
TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 
         699         1955          699         1977          913         1952 
TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 
        1645          122         1492           83          202          211 
TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 
          96          121          104         1941         1942         1952 
TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7338 
        1959         1968           15         1286         1954         1952 
TCGA-77-7463 TCGA-77-7465 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 
        1954          479         1945         1641         1953         1945 
TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 
        1941         1941         1947         1946         1951         1962 
TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 
         833         1943          293         1961         1684         1092 
TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G7 TCGA-77-A5G8 
          10         1953         1942         1959         1963         1290 
TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6560 TCGA-85-6561 
        1280         1939          839          713          364          395 
TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 
          34           18           10           49            1         1965 
TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 
          35          911           60           26           60           16 
TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 
         960          428          513           13           11           13 
TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 TCGA-85-8354 
          54           60           55           67           54           61 
TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8664 
          61           22           21          445          424            3 
TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M 
         475           15         1972         1960           25           19 
TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L 
        1973         1967         1972         1987           24           13 
TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7766 TCGA-90-7769 TCGA-90-7964 TCGA-90-A4ED 
         111          758          289          358          428          244 
TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 
         331          269           82          106          122          160 
TCGA-92-8065 TCGA-94-7033 TCGA-94-7943 TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 
          70           87          356         1213          189          211 
TCGA-96-A4JK TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8023 TCGA-J1-A4AH 
         273          183          256          413          308          222 
TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HE TCGA-NC-A5HG 
          35          449           36           83         1722         1548 
TCGA-NC-A5HI 
        1135 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               24                 1 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             2417              5287 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
              881               639 
[1] "24.0 - 2417.0 (881.0)" "1.0 - 5287.0 (639.0)" 
[1] "hr=" "1.7"
D7V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  4P GAIN MUTATED         0        7        5        0         3         8
  4P GAIN WILD-TYPE       1       65      132        1        49        63
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  4P GAIN MUTATED            6          0        0
  4P GAIN WILD-TYPE         51         20        6
D7V3, multiclass
            clus
vv           4P GAIN MUTATED 4P GAIN WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                 7                65
  STAGE IB                 5               132
  STAGE II                 0                 1
  STAGE IIA                3                49
  STAGE IIB                8                63
  STAGE IIIA               6                51
  STAGE IIIB               0                20
  STAGE IV                 0                 6
[1] 9 2
[1] 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     9  16   3   2
  4P GAIN WILD-TYPE  89 238  45  18
D7V4, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  T1               9                89
  T2              16               238
  T3               3                45
  T4               2                18
[1] 4 2
[1] 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    19   8   3   0
  4P GAIN WILD-TYPE 242 105  32   5
D7V5, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  N0              19               242
  N1               8               105
  N2               3                32
  N3               0                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A  MX
  4P GAIN MUTATED    27   0   0   3
  4P GAIN WILD-TYPE 331   5   1  47
D7V6, multiclass
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  M0               27               331
  M1                0                 5
  M1A               0                 1
  MX                3                47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V7, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     4  26
  4P GAIN WILD-TYPE 103 287
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      4   26
  4P GAIN WILD-TYPE  103  287
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE               4               103
  MALE                26               287
[1] 2 2
[1] FALSE
D7V8, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  4P GAIN MUTATED                                       1
  4P GAIN WILD-TYPE                                    11
                   vv
clus                LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  4P GAIN MUTATED                                        0
  4P GAIN WILD-TYPE                                      6
                   vv
clus                LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  4P GAIN MUTATED                                         0
  4P GAIN WILD-TYPE                                       1
                   vv
clus                LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  4P GAIN MUTATED                                                            29
  4P GAIN WILD-TYPE                                                         372
D7V9, multiclass
                                                             clus
vv                                                            4P GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    0
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              29
                                                             clus
vv                                                            4P GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      11
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               372
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V10, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     1  29
  4P GAIN WILD-TYPE  12 378
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      1   29
  4P GAIN WILD-TYPE   12  378
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  NO                1                12
  YES              29               378
[1] 2 2
[1] FALSE
D7V11, continuous
                   vv
clus                 R0  R1  R2  RX
  4P GAIN MUTATED    23   1   0   2
  4P GAIN WILD-TYPE 319   7   4  16
D7V12, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  R0              23               319
  R1               1                 7
  R2               0                 4
  RX               2                16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4P GAIN MUTATED       1                         2    19
  4P GAIN WILD-TYPE     8                        15   279
D7V13, multiclass
                           clus
vv                          4P GAIN MUTATED 4P GAIN WILD-TYPE
  ASIAN                                   1                 8
  BLACK OR AFRICAN AMERICAN               2                15
  WHITE                                  19               279
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V14, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     0  18
  4P GAIN WILD-TYPE   8 249
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      0   18
  4P GAIN WILD-TYPE    8  249
                        clus
vv                       4P GAIN MUTATED 4P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 8
  NOT HISPANIC OR LATINO              18               249
[1] 2 2
[1] FALSE

Clustering(8) Variable = 4Q GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                 0   1
  4Q GAIN MUTATED     8  10
  4Q GAIN WILD-TYPE 257 113
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               18               370 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               10               113 
$`4Q GAIN MUTATED`
TCGA-18-3409 TCGA-18-3410 TCGA-18-3416 TCGA-22-4593 TCGA-22-4601 TCGA-22-5478 
        2417          146          862         1067         1057           24 
TCGA-22-A5C4 TCGA-33-6738 TCGA-34-2596 TCGA-34-2609 TCGA-43-2576 TCGA-43-3920 
          29          822           80          951         1223         1007 
TCGA-56-1622 TCGA-56-7579 TCGA-60-2715 TCGA-77-7337 TCGA-85-A5B5 TCGA-96-7545 
         881           44         1075         1942          111         1344 

$`4Q GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 
         370          136         2464         1415          345          396 
TCGA-18-3415 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 
        1810          758           50         1331          187           85 
TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 
        2754           92          827         3636         1426         3016 
TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 
        2134         1852         1058          474          965         3724 
TCGA-21-1081 TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 
         284         3644          267          962         1268         1032 
TCGA-21-5787 TCGA-21-A5DI TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 
         329          979          608          223         1945          131 
TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 
        1952           53          429          822         1485          623 
TCGA-22-4594 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4604 TCGA-22-4605 
        1470          734           17         1161          399         1946 
TCGA-22-4607 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 
         587          358          965         1964         1933          445 
TCGA-22-5477 TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 
        1346         1651         1952         1952          357          573 
TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-33-4532 TCGA-33-4533 
         916         1912         1713          506         2524         1940 
TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 
        2979         1311         5287         1966         1941          428 
TCGA-33-4587 TCGA-33-4589 TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 
        1970         1948         1874          958          881         1000 
TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 
        1528         2062         1715          707          365          428 
TCGA-34-5927 TCGA-34-5928 TCGA-34-8454 TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 
         941          552          166          120           13           12 
TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 
         200          247          227          238          207           12 
TCGA-37-5819 TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 
         103         1454         2253         1361         1947         1996 
TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 
        1964         1849           52          740           59          833 
TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 TCGA-39-5040 
        1107          474         1084         1086          544         1964 
TCGA-43-2578 TCGA-43-2581 TCGA-43-3394 TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 
         684         1176          822          349          849          376 
TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 
         757          310         1936          212          236         1970 
TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U 
         407          358         1971          353          296          432 
TCGA-43-A56V TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 
         366          324          423           12           12          911 
TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 TCGA-56-5897 
         541         1948          923         1958         1967            3 
TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 
         555           62           26           30           13           30 
TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-8503 
          40           26            6         1961            1           41 
TCGA-56-8504 TCGA-56-8622 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 
         178           55           36           63           17           16 
TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ 
          34           38            2           46           30           25 
TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 
           4            4            8          378          911         2167 
TCGA-58-8393 TCGA-58-A46J TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 
        1058         2589         1723         1072          910          642 
TCGA-60-2696 TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 
         109          311         1950         1943         1958          661 
TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 
        1963         1505         1963         1260          274         1731 
TCGA-60-2714 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 
        1531         1475         1297           97          983          908 
TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 TCGA-63-7020 
        1092          717          816          358         1973         1957 
TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 
        1955         1947         1952         1967         1311           61 
TCGA-66-2742 TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 
         641           30           31           61           28           30 
TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 
          30          639          762           30           61           31 
TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 
          61           61         1947          700          578         1946 
TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 
          61          578         1956          121         1954          759 
TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 
          60          790         1217          699         1955          699 
TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 
        1977          913         1952         1645          122         1492 
TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I 
          83          202          211          244           96          121 
TCGA-68-A59J TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 
         104         1950         1941         1942         1952         1959 
TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7338 TCGA-77-7463 
        1968           15         1286         1954         1952         1954 
TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 
         479         1960         1945         1641         1953         1945 
TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 
        1941         1941         1947         1946         1951         1962 
TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 
         833         1943          293         1961         1684         1092 
TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 
          10         1953         1942         1959         1955         1963 
TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6560 
        1290         1280         1939          839          713          364 
TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 
         395           34           18           10           49            1 
TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 
        1965           35          911           60           26           60 
TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 
          16          960          428          513           13           11 
TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 
          13           54           60           55           67           54 
TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 
          61           61           22           21          445          424 
TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR 
           3          475           15         1972         1960           25 
TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 
          19         1973         1967         1972         1987           24 
TCGA-85-A53L TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 TCGA-90-7964 
          13          758          289           89          358          428 
TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 
         244          331          269           82          106          122 
TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 TCGA-94-7943 TCGA-94-A4VJ TCGA-96-7544 
         160           70           87          356          430         1213 
TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 
         189          211          273          183          256          413 
TCGA-98-8022 TCGA-98-8023 TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 
         224          308          222           35          449           36 
TCGA-MF-A522 TCGA-NC-A5HE TCGA-NC-A5HG TCGA-NC-A5HI 
          83         1722         1548         1135 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               24                 1 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
             2417              5287 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            916.0             615.5 
[1] "24.0 - 2417.0 (916.0)" "1.0 - 5287.0 (615.5)" 
[1] "hr=" "2.4"
D8V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  4Q GAIN MUTATED         0        3        3        0         3         5
  4Q GAIN WILD-TYPE       1       69      134        1        49        66
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  4Q GAIN MUTATED            5          0        0
  4Q GAIN WILD-TYPE         52         20        6
D8V3, multiclass
            clus
vv           4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                 3                69
  STAGE IB                 3               134
  STAGE II                 0                 1
  STAGE IIA                3                49
  STAGE IIB                5                66
  STAGE IIIA               5                52
  STAGE IIIB               0                20
  STAGE IV                 0                 6
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  4Q GAIN MUTATED     5  12   2   1
  4Q GAIN WILD-TYPE  93 242  46  19
D8V4, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  T1               5                93
  T2              12               242
  T3               2                46
  T4               1                19
[1] 4 2
[1] 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    12   6   2   0
  4Q GAIN WILD-TYPE 249 107  33   5
D8V5, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  N0              12               249
  N1               6               107
  N2               2                33
  N3               0                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A  MX
  4Q GAIN MUTATED    18   0   0   2
  4Q GAIN WILD-TYPE 340   5   1  48
D8V6, multiclass
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  M0               18               340
  M1                0                 5
  M1A               0                 1
  MX                2                48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V7, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     2  18
  4Q GAIN WILD-TYPE 105 295
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      2   18
  4Q GAIN WILD-TYPE  105  295
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE               2               105
  MALE                18               295
[1] 2 2
[1] FALSE
D8V8, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  4Q GAIN MUTATED                                       1
  4Q GAIN WILD-TYPE                                    11
                   vv
clus                LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  4Q GAIN MUTATED                                        0
  4Q GAIN WILD-TYPE                                      6
                   vv
clus                LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  4Q GAIN MUTATED                                         0
  4Q GAIN WILD-TYPE                                       1
                   vv
clus                LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  4Q GAIN MUTATED                                                            19
  4Q GAIN WILD-TYPE                                                         382
D8V9, multiclass
                                                             clus
vv                                                            4Q GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    0
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              19
                                                             clus
vv                                                            4Q GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      11
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               382
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V10, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     1  19
  4Q GAIN WILD-TYPE  12 388
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      1   19
  4Q GAIN WILD-TYPE   12  388
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  NO                1                12
  YES              19               388
[1] 2 2
[1] FALSE
D8V11, continuous
                   vv
clus                 R0  R1  R2  RX
  4Q GAIN MUTATED    17   0   0   1
  4Q GAIN WILD-TYPE 325   8   4  17
D8V12, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  R0              17               325
  R1               0                 8
  R2               0                 4
  RX               1                17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4Q GAIN MUTATED       0                         1    14
  4Q GAIN WILD-TYPE     9                        16   284
D8V13, multiclass
                           clus
vv                          4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  ASIAN                                   0                 9
  BLACK OR AFRICAN AMERICAN               1                16
  WHITE                                  14               284
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V14, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     0  11
  4Q GAIN WILD-TYPE   8 256
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      0   11
  4Q GAIN WILD-TYPE    8  256
                        clus
vv                       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 8
  NOT HISPANIC OR LATINO              11               256
[1] 2 2
[1] FALSE

Clustering(9) Variable = 5P GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                 0   1
  5P GAIN MUTATED   165  77
  5P GAIN WILD-TYPE 100  46
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              242               146 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               77                46 
$`5P GAIN MUTATED`
TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3417 TCGA-18-3421 
        1415          345          396         1810          758         1331 
TCGA-18-5592 TCGA-21-1071 TCGA-21-1072 TCGA-21-1077 TCGA-21-1080 TCGA-21-1081 
          92         1426         3016         1058         3724          284 
TCGA-21-1083 TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-21-A5DI 
         267          962         1268         1032          329          979 
TCGA-22-0940 TCGA-22-0944 TCGA-22-1002 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 
         608          223          131           53          429          822 
TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 
         623         1067         1470          734           17         1161 
TCGA-22-4601 TCGA-22-4613 TCGA-22-5471 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 
        1057          358          965         1933          445         1346 
TCGA-22-5478 TCGA-22-5482 TCGA-22-5483 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4533 
          24          357          573          506           29         1940 
TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-33-4587 TCGA-33-6738 TCGA-34-2596 
        5287         1966         1941         1970          822           80 
TCGA-34-2600 TCGA-34-2604 TCGA-34-2608 TCGA-34-2609 TCGA-34-5239 TCGA-34-5240 
        1874          958         1000          951          707          365 
TCGA-34-5241 TCGA-34-5928 TCGA-37-3783 TCGA-37-3792 TCGA-37-4133 TCGA-37-4135 
         428          552          120           12          238          207 
TCGA-37-4141 TCGA-37-5819 TCGA-39-5011 TCGA-39-5016 TCGA-39-5021 TCGA-39-5022 
          12          103         1454         2253         1947         1996 
TCGA-39-5024 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5035 TCGA-39-5036 
        1964          740           59          833          474         1084 
TCGA-39-5039 TCGA-43-2576 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 
         544         1223         1176          822         1007          349 
TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 
         849          376          757          212          236         1970 
TCGA-43-8116 TCGA-43-A474 TCGA-43-A56U TCGA-43-A56V TCGA-46-6025 TCGA-46-6026 
         358          353          432          366          324          423 
TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 TCGA-52-7811 TCGA-56-1622 TCGA-56-6545 
         911          541         1948         1958          881           62 
TCGA-56-6546 TCGA-56-7222 TCGA-56-7580 TCGA-56-7582 TCGA-56-7731 TCGA-56-7822 
          26           13           40           26         1961            1 
TCGA-56-8503 TCGA-56-8504 TCGA-56-8624 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 
          41          178           36           17           16           34 
TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A5DR TCGA-56-A5DS 
           2           46           30           25            4            8 
TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-A46J TCGA-58-A46M TCGA-58-A46N 
         378          911         2167         2589         1072          910 
TCGA-60-2695 TCGA-60-2703 TCGA-60-2704 TCGA-60-2711 TCGA-60-2712 TCGA-60-2714 
         642         1950         1943         1260          274         1531 
TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 
        1297           97          983         1092          717          816 
TCGA-60-2726 TCGA-63-6202 TCGA-63-7020 TCGA-63-7022 TCGA-66-2727 TCGA-66-2737 
         358         1973         1957         1947         1967           61 
TCGA-66-2742 TCGA-66-2744 TCGA-66-2753 TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 
         641           30           31           30           30          639 
TCGA-66-2759 TCGA-66-2766 TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 
         762           31         1947          700          578         1946 
TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2782 TCGA-66-2786 TCGA-66-2787 
          61          578         1956         1954          790         1217 
TCGA-66-2788 TCGA-66-2792 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-68-7756 
         699          913         1645          122         1492          202 
TCGA-68-7757 TCGA-68-A59I TCGA-68-A59J TCGA-77-6842 TCGA-77-6844 TCGA-77-6845 
         211          121          104         1950         1942         1952 
TCGA-77-7138 TCGA-77-7141 TCGA-77-7142 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 
        1959           15         1286         1942         1952         1954 
TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 
         479         1960         1945         1641         1953         1945 
TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8145 TCGA-77-8150 
        1941         1947         1946         1951         1943         1961 
TCGA-77-8156 TCGA-77-A5G1 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA 
          10         1942         1955         1963         1290         1280 
TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6560 TCGA-85-6798 TCGA-85-7696 TCGA-85-7699 
         839          713          364           34           18            1 
TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 TCGA-85-8048 TCGA-85-8071 TCGA-85-8072 
        1965           35          911           26          428          513 
TCGA-85-8277 TCGA-85-8287 TCGA-85-8350 TCGA-85-8351 TCGA-85-8479 TCGA-85-8481 
          11           13           60           55           22           21 
TCGA-85-8580 TCGA-85-8582 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4QQ TCGA-85-A4QR 
         445          424            3          475         1960           25 
TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-90-7766 TCGA-90-7767 
          19         1973         1967         1972          289           89 
TCGA-90-7769 TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-92-8064 
         358          331          269           82          106          160 
TCGA-94-A4VJ TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK 
         430         1213         1344          189          211          273 
TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 
         413          224          308          222           35          449 
TCGA-LA-A446 TCGA-MF-A522 
          36           83 

$`5P GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3416 
         370          136         2464         2417          146          862 
TCGA-18-3419 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5595 TCGA-21-1070 
          50          187           85         2754          827         3636 
TCGA-21-1075 TCGA-21-1076 TCGA-21-1078 TCGA-21-1079 TCGA-21-1082 TCGA-22-1000 
        2134         1852          474          965         3644         1945 
TCGA-22-1005 TCGA-22-1017 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-5472 
        1952         1485          399         1946          587         1964 
TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 
        1651         1952         1952          916         1912         1713 
TCGA-33-4532 TCGA-33-4538 TCGA-33-4547 TCGA-33-4586 TCGA-33-4589 TCGA-34-2605 
        2524         2979         1311          428         1948          881 
TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5927 TCGA-34-8454 TCGA-37-3789 
        1528         2062         1715          941          166           13 
TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-39-5019 TCGA-39-5027 TCGA-39-5028 
         200          247          227         1361         1849           52 
TCGA-39-5034 TCGA-39-5037 TCGA-39-5040 TCGA-43-2578 TCGA-43-6770 TCGA-43-6771 
        1107         1086         1964          684          310         1936 
TCGA-43-8115 TCGA-43-8118 TCGA-43-A475 TCGA-51-4079 TCGA-51-4080 TCGA-52-7810 
         407         1971          296           12           12          923 
TCGA-52-7812 TCGA-56-5897 TCGA-56-5898 TCGA-56-7221 TCGA-56-7223 TCGA-56-7579 
        1967            3          555           30           30           44 
TCGA-56-7730 TCGA-56-8622 TCGA-56-8625 TCGA-56-A49D TCGA-56-A4ZK TCGA-58-8393 
           6           55           63           38            4         1058 
TCGA-58-A46L TCGA-60-2696 TCGA-60-2698 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 
        1723          109          311         1958          661         1963 
TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 TCGA-60-2715 TCGA-60-2716 TCGA-60-2722 
        1505         1963         1731         1075         1475          908 
TCGA-63-7021 TCGA-63-7023 TCGA-66-2734 TCGA-66-2754 TCGA-66-2755 TCGA-66-2763 
        1955         1952         1311           61           28           30 
TCGA-66-2765 TCGA-66-2767 TCGA-66-2768 TCGA-66-2781 TCGA-66-2783 TCGA-66-2785 
          61           61           61          121          759           60 
TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 TCGA-66-2793 TCGA-68-7755 TCGA-68-8250 
        1955          699         1977         1952           83          244 
TCGA-68-8251 TCGA-77-6843 TCGA-77-7139 TCGA-77-7335 TCGA-77-8131 TCGA-77-8140 
          96         1941         1968         1954         1941         1962 
TCGA-77-8144 TCGA-77-8148 TCGA-77-8153 TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G3 
         833          293         1684         1092         1953         1959 
TCGA-77-A5GB TCGA-85-6561 TCGA-85-7697 TCGA-85-7698 TCGA-85-7950 TCGA-85-8049 
        1939          395           10           49           60           60 
TCGA-85-8052 TCGA-85-8070 TCGA-85-8276 TCGA-85-8288 TCGA-85-8352 TCGA-85-8353 
          16          960           13           54           67           54 
TCGA-85-8354 TCGA-85-8355 TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A512 TCGA-85-A513 
          61           61           15         1972         1987           24 
TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7964 TCGA-90-A4ED TCGA-92-8063 
          13          111          758          428          244          122 
TCGA-92-8065 TCGA-94-7033 TCGA-94-7943 TCGA-96-A4JL TCGA-98-7454 TCGA-NC-A5HE 
          70           87          356          183          256         1722 
TCGA-NC-A5HG TCGA-NC-A5HI 
        1548         1135 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                1                 3 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             5287              3644 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            593.0             758.5 
[1] "1.0 - 5287.0 (593.0)" "3.0 - 3644.0 (758.5)"
[1] "hr=" "1.2"
D9V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  5P GAIN MUTATED         1       46       86        1        33        47
  5P GAIN WILD-TYPE       0       26       51        0        19        24
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  5P GAIN MUTATED           34         11        5
  5P GAIN WILD-TYPE         23          9        1
D9V3, multiclass
            clus
vv           5P GAIN MUTATED 5P GAIN WILD-TYPE
  STAGE I                  1                 0
  STAGE IA                46                26
  STAGE IB                86                51
  STAGE II                 1                 0
  STAGE IIA               33                19
  STAGE IIB               47                24
  STAGE IIIA              34                23
  STAGE IIIB              11                 9
  STAGE IV                 5                 1
[1] 9 2
[1] 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    58 166  28  13
  5P GAIN WILD-TYPE  40  88  20   7
D9V4, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  T1              58                40
  T2             166                88
  T3              28                20
  T4              13                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  5P GAIN MUTATED   170  69  24   1
  5P GAIN WILD-TYPE  91  44  11   4
D9V5, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  N0             170                91
  N1              69                44
  N2              24                11
  N3               1                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A  MX
  5P GAIN MUTATED   225   4   1  33
  5P GAIN WILD-TYPE 133   1   0  17
D9V6, multiclass
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  M0              225               133
  M1                4                 1
  M1A               1                 0
  MX               33                17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V7, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    67 198
  5P GAIN WILD-TYPE  40 115
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     67  198
  5P GAIN WILD-TYPE   40  115
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE              67                40
  MALE               198               115
[1] 2 2
[1] FALSE
D9V8, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  5P GAIN MUTATED                                       8
  5P GAIN WILD-TYPE                                     4
                   vv
clus                LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  5P GAIN MUTATED                                        2
  5P GAIN WILD-TYPE                                      4
                   vv
clus                LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  5P GAIN MUTATED                                         1
  5P GAIN WILD-TYPE                                       0
                   vv
clus                LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  5P GAIN MUTATED                                                           254
  5P GAIN WILD-TYPE                                                         147
D9V9, multiclass
                                                             clus
vv                                                            5P GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     8
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             254
                                                             clus
vv                                                            5P GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       4
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               147
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V10, binary
                   cls
clus                  0   1
  5P GAIN MUTATED     7 258
  5P GAIN WILD-TYPE   6 149
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      7  258
  5P GAIN WILD-TYPE    6  149
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  NO                7                 6
  YES             258               149
[1] 2 2
[1] FALSE
D9V11, continuous
                   vv
clus                 R0  R1  R2  RX
  5P GAIN MUTATED   223   4   3   5
  5P GAIN WILD-TYPE 119   4   1  13
D9V12, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  R0             223               119
  R1               4                 4
  R2               3                 1
  RX               5                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5P GAIN MUTATED       3                         9   193
  5P GAIN WILD-TYPE     6                         8   105
D9V13, multiclass
                           clus
vv                          5P GAIN MUTATED 5P GAIN WILD-TYPE
  ASIAN                                   3                 6
  BLACK OR AFRICAN AMERICAN               9                 8
  WHITE                                 193               105
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V14, binary
                   cls
clus                  0   1
  5P GAIN MUTATED     3 171
  5P GAIN WILD-TYPE   5  96
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      3  171
  5P GAIN WILD-TYPE    5   96
                        clus
vv                       5P GAIN MUTATED 5P GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 5
  NOT HISPANIC OR LATINO             171                96
[1] 2 2
[1] FALSE

Clustering(10) Variable = 5Q GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                 0   1
  5Q GAIN MUTATED    46  28
  5Q GAIN WILD-TYPE 219  95
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               74               314 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               28                95 
$`5Q GAIN MUTATED`
TCGA-18-5592 TCGA-21-1071 TCGA-21-1083 TCGA-21-5782 TCGA-21-A5DI TCGA-22-1012 
          92         1426          267          962          979          429 
TCGA-22-1016 TCGA-22-4595 TCGA-22-4596 TCGA-22-5478 TCGA-22-5482 TCGA-22-5483 
         822          734           17           24          357          573 
TCGA-22-A5C4 TCGA-33-4582 TCGA-33-4583 TCGA-34-2596 TCGA-34-5241 TCGA-34-5928 
          29         1966         1941           80          428          552 
TCGA-37-3792 TCGA-37-5819 TCGA-39-5021 TCGA-39-5039 TCGA-43-3920 TCGA-43-6143 
          12          103         1947          544         1007          376 
TCGA-43-7657 TCGA-43-7658 TCGA-43-A56V TCGA-56-1622 TCGA-56-7222 TCGA-56-7580 
         236         1970          366          881           13           40 
TCGA-56-8503 TCGA-56-8624 TCGA-56-8626 TCGA-58-A46M TCGA-58-A46N TCGA-60-2703 
          41           36           17         1072          910         1950 
TCGA-60-2712 TCGA-60-2719 TCGA-60-2724 TCGA-60-2725 TCGA-66-2771 TCGA-66-2778 
         274         1297          717          816          578          578 
TCGA-66-2786 TCGA-66-2792 TCGA-77-6842 TCGA-77-6844 TCGA-77-7138 TCGA-77-7142 
         790          913         1950         1942         1959         1286 
TCGA-77-7337 TCGA-77-7463 TCGA-77-7465 TCGA-77-8008 TCGA-77-8130 TCGA-77-8133 
        1942         1954          479         1945         1945         1941 
TCGA-77-8150 TCGA-77-8156 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5GF TCGA-85-7699 
        1961           10         1955         1963          839            1 
TCGA-85-8048 TCGA-85-8350 TCGA-85-8582 TCGA-85-A4QQ TCGA-85-A510 TCGA-90-7769 
          26           60          424         1960         1967          358 
TCGA-90-A59Q TCGA-92-7340 TCGA-96-8169 TCGA-96-8170 TCGA-J1-A4AH TCGA-L3-A4E7 
         269           82          189          211          222           35 
TCGA-LA-A446 TCGA-MF-A522 
          36           83 

$`5Q GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 
         370          136         2464         2417          146         1415 
TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 
         345          396         1810          862          758           50 
TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5595 TCGA-21-1070 
        1331          187           85         2754          827         3636 
TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 
        3016         2134         1852         1058          474          965 
TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 
        3724          284         3644         1268         1032          329 
TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 
         608          223         1945          131         1952           53 
TCGA-22-1017 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4599 TCGA-22-4601 
        1485          623         1067         1470         1161         1057 
TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 
         399         1946          587          358          965         1964 
TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 
        1933          445         1346         1651         1952         1952 
TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-33-4532 TCGA-33-4533 
         916         1912         1713          506         2524         1940 
TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4586 TCGA-33-4587 TCGA-33-4589 
        2979         1311         5287          428         1970         1948 
TCGA-33-6738 TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 
         822         1874          958          881         1000          951 
TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 TCGA-34-5927 
        1528         2062         1715          707          365          941 
TCGA-34-8454 TCGA-37-3783 TCGA-37-3789 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 
         166          120           13          200          247          227 
TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 
         238          207           12         1454         2253         1361 
TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 
        1996         1964         1849           52          740           59 
TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-39-5040 
         833         1107          474         1084         1086         1964 
TCGA-43-2576 TCGA-43-2578 TCGA-43-2581 TCGA-43-3394 TCGA-43-5668 TCGA-43-5670 
        1223          684         1176          822          349          849 
TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-7656 TCGA-43-8115 TCGA-43-8116 
         757          310         1936          212          407          358 
TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U TCGA-46-6025 TCGA-46-6026 
        1971          353          296          432          324          423 
TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 
          12           12          911          541         1948          923 
TCGA-52-7811 TCGA-52-7812 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 
        1958         1967            3          555           62           26 
TCGA-56-7221 TCGA-56-7223 TCGA-56-7579 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 
          30           30           44           26            6         1961 
TCGA-56-7822 TCGA-56-8504 TCGA-56-8622 TCGA-56-8625 TCGA-56-8628 TCGA-56-8629 
           1          178           55           63           16           34 
TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK 
          38            2           46           30           25            4 
TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-8393 
           4            8          378          911         2167         1058 
TCGA-58-A46J TCGA-58-A46L TCGA-60-2695 TCGA-60-2696 TCGA-60-2698 TCGA-60-2704 
        2589         1723          642          109          311         1943 
TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 
        1958          661         1963         1505         1963         1260 
TCGA-60-2713 TCGA-60-2714 TCGA-60-2715 TCGA-60-2716 TCGA-60-2720 TCGA-60-2721 
        1731         1531         1075         1475           97          983 
TCGA-60-2722 TCGA-60-2723 TCGA-60-2726 TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 
         908         1092          358         1973         1957         1955 
TCGA-63-7022 TCGA-63-7023 TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 
        1947         1952         1967         1311           61          641 
TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 
          30           31           61           28           30           30 
TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 
         639          762           30           61           31           61 
TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 TCGA-66-2773 TCGA-66-2777 TCGA-66-2780 
          61         1947          700         1946           61         1956 
TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2787 TCGA-66-2788 
         121         1954          759           60         1217          699 
TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 
        1955          699         1977         1952         1645          122 
TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 
        1492           83          202          211          244           96 
TCGA-68-A59I TCGA-68-A59J TCGA-77-6843 TCGA-77-6845 TCGA-77-7139 TCGA-77-7141 
         121          104         1941         1952         1968           15 
TCGA-77-7335 TCGA-77-7338 TCGA-77-8007 TCGA-77-8009 TCGA-77-8128 TCGA-77-8131 
        1954         1952         1960         1641         1953         1941 
TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8144 TCGA-77-8145 
        1947         1946         1951         1962          833         1943 
TCGA-77-8148 TCGA-77-8153 TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 
         293         1684         1092         1953         1942         1959 
TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GH TCGA-85-6560 TCGA-85-6561 
        1290         1280         1939          713          364          395 
TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7710 TCGA-85-7843 
          34           18           10           49         1965           35 
TCGA-85-7844 TCGA-85-7950 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 
         911           60           60           16          960          428 
TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 TCGA-85-8351 
         513           13           11           13           54           55 
TCGA-85-8352 TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 
          67           54           61           61           22           21 
TCGA-85-8580 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A4QR 
         445            3          475           15         1972           25 
TCGA-85-A50M TCGA-85-A50Z TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L 
          19         1973         1972         1987           24           13 
TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 TCGA-90-7964 TCGA-90-A4ED 
         111          758          289           89          428          244 
TCGA-90-A4EE TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 
         331          106          122          160           70           87 
TCGA-94-7943 TCGA-94-A4VJ TCGA-96-7544 TCGA-96-7545 TCGA-96-A4JK TCGA-96-A4JL 
         356          430         1213         1344          273          183 
TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-L3-A524 TCGA-NC-A5HE 
         256          413          224          308          449         1722 
TCGA-NC-A5HG TCGA-NC-A5HI 
        1548         1135 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                1                 1 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             1970              5287 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            562.5             691.5 
[1] "1.0 - 1970.0 (562.5)" "1.0 - 5287.0 (691.5)"
[1] "hr=" "1.5"
D10V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  5Q GAIN MUTATED         1       13       25        0        10        18
  5Q GAIN WILD-TYPE       0       59      112        1        42        53
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  5Q GAIN MUTATED            9          1        1
  5Q GAIN WILD-TYPE         48         19        5
D10V3, multiclass
            clus
vv           5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  STAGE I                  1                 0
  STAGE IA                13                59
  STAGE IB                25               112
  STAGE II                 0                 1
  STAGE IIA               10                42
  STAGE IIB               18                53
  STAGE IIIA               9                48
  STAGE IIIB               1                19
  STAGE IV                 1                 5
[1] 9 2
[1] 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    19  49  10   1
  5Q GAIN WILD-TYPE  79 205  38  19
D10V4, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T1              19                79
  T2              49               205
  T3              10                38
  T4               1                19
[1] 4 2
[1] 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    49  23   5   1
  5Q GAIN WILD-TYPE 212  90  30   4
D10V5, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  N0              49               212
  N1              23                90
  N2               5                30
  N3               1                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A  MX
  5Q GAIN MUTATED    67   1   0   9
  5Q GAIN WILD-TYPE 291   4   1  41
D10V6, multiclass
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  M0               67               291
  M1                1                 4
  M1A               0                 1
  MX                9                41
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V7, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    19  60
  5Q GAIN WILD-TYPE  88 253
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     19   60
  5Q GAIN WILD-TYPE   88  253
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE              19                88
  MALE                60               253
[1] 2 2
[1] FALSE
D10V8, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  5Q GAIN MUTATED                                       2
  5Q GAIN WILD-TYPE                                    10
                   vv
clus                LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  5Q GAIN MUTATED                                        0
  5Q GAIN WILD-TYPE                                      6
                   vv
clus                LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  5Q GAIN MUTATED                                         0
  5Q GAIN WILD-TYPE                                       1
                   vv
clus                LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  5Q GAIN MUTATED                                                            77
  5Q GAIN WILD-TYPE                                                         324
D10V9, multiclass
                                                             clus
vv                                                            5Q GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     2
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    0
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              77
                                                             clus
vv                                                            5Q GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      10
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               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"
D10V10, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     2  77
  5Q GAIN WILD-TYPE  11 330
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      2   77
  5Q GAIN WILD-TYPE   11  330
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  NO                2                11
  YES              77               330
[1] 2 2
[1] FALSE
D10V11, continuous
                   vv
clus                 R0  R1  R2  RX
  5Q GAIN MUTATED    66   1   1   1
  5Q GAIN WILD-TYPE 276   7   3  17
D10V12, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  R0              66               276
  R1               1                 7
  R2               1                 3
  RX               1                17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5Q GAIN MUTATED       0                         2    60
  5Q GAIN WILD-TYPE     9                        15   238
D10V13, multiclass
                           clus
vv                          5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  ASIAN                                   0                 9
  BLACK OR AFRICAN AMERICAN               2                15
  WHITE                                  60               238
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V14, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     0  49
  5Q GAIN WILD-TYPE   8 218
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      0   49
  5Q GAIN WILD-TYPE    8  218
                        clus
vv                       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 8
  NOT HISPANIC OR LATINO              49               218
[1] 2 2
[1] FALSE

Clustering(11) Variable = 6P GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                 0   1
  6P GAIN MUTATED    60  23
  6P GAIN WILD-TYPE 205 100
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               83               305 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               23               100 
$`6P GAIN MUTATED`
TCGA-18-3409 TCGA-21-1072 TCGA-21-1077 TCGA-21-1079 TCGA-21-1082 TCGA-21-1083 
        2417         3016         1058          965         3644          267 
TCGA-21-5786 TCGA-21-5787 TCGA-22-1002 TCGA-22-4601 TCGA-22-4605 TCGA-22-4607 
        1032          329          131         1057         1946          587 
TCGA-22-5482 TCGA-33-4533 TCGA-33-4582 TCGA-33-4587 TCGA-33-4589 TCGA-34-2609 
         357         1940         1966         1970         1948          951 
TCGA-34-5928 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-39-5019 
         552          227          238          207           12         1361 
TCGA-39-5022 TCGA-43-2578 TCGA-43-5670 TCGA-43-6770 TCGA-46-6026 TCGA-52-7809 
        1996          684          849          310          423         1948 
TCGA-52-7810 TCGA-56-1622 TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-56-7730 
         923          881          555           62           26            6 
TCGA-56-7822 TCGA-56-8629 TCGA-56-A49D TCGA-58-8393 TCGA-60-2703 TCGA-60-2714 
           1           34           38         1058         1950         1531 
TCGA-60-2715 TCGA-60-2719 TCGA-60-2723 TCGA-60-2725 TCGA-63-6202 TCGA-66-2734 
        1075         1297         1092          816         1973         1311 
TCGA-66-2754 TCGA-66-2757 TCGA-66-2759 TCGA-66-2765 TCGA-66-2766 TCGA-66-2769 
          61           30          762           61           31         1947 
TCGA-66-2777 TCGA-66-2781 TCGA-66-2791 TCGA-66-2793 TCGA-68-8251 TCGA-77-7141 
          61          121         1977         1952           96           15 
TCGA-77-7142 TCGA-77-7465 TCGA-77-8130 TCGA-77-8156 TCGA-85-6560 TCGA-85-6798 
        1286          479         1945           10          364           34 
TCGA-85-7699 TCGA-85-7843 TCGA-85-8052 TCGA-85-8072 TCGA-85-8276 TCGA-85-8287 
           1           35           16          513           13           13 
TCGA-85-8353 TCGA-85-8582 TCGA-90-A4EE TCGA-90-A59Q TCGA-94-7943 TCGA-98-7454 
          54          424          331          269          356          256 
TCGA-98-8022 TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HE TCGA-NC-A5HG 
         224           36           83         1722         1548 

$`6P GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3410 TCGA-18-3411 TCGA-18-3412 
         370          136         2464          146         1415          345 
TCGA-18-3414 TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 
         396         1810          862          758           50         1331 
TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1070 
         187           85         2754           92          827         3636 
TCGA-21-1071 TCGA-21-1075 TCGA-21-1076 TCGA-21-1078 TCGA-21-1080 TCGA-21-1081 
        1426         2134         1852          474         3724          284 
TCGA-21-5782 TCGA-21-5784 TCGA-21-A5DI TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 
         962         1268          979          608          223         1945 
TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 
        1952           53          429          822         1485          623 
TCGA-22-4593 TCGA-22-4594 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4604 
        1067         1470          734           17         1161          399 
TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 
         358          965         1964         1933          445         1346 
TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 TCGA-22-5483 TCGA-22-5485 
          24         1651         1952         1952          573          916 
TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4538 
        1912         1713          506           29         2524         2979 
TCGA-33-4547 TCGA-33-4566 TCGA-33-4583 TCGA-33-4586 TCGA-33-6738 TCGA-34-2596 
        1311         5287         1941          428          822           80 
TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 
        1874          958          881         1000         1528         2062 
TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-8454 
        1715          707          365          428          941          166 
TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-5819 
         120           13           12          200          247          103 
TCGA-39-5011 TCGA-39-5016 TCGA-39-5021 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 
        1454         2253         1947         1964         1849           52 
TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 
         740           59          833         1107          474         1084 
TCGA-39-5037 TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 TCGA-43-2581 TCGA-43-3394 
        1086          544         1964         1223         1176          822 
TCGA-43-3920 TCGA-43-5668 TCGA-43-6143 TCGA-43-6647 TCGA-43-6771 TCGA-43-7656 
        1007          349          376          757         1936          212 
TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 
         236         1970          407          358         1971          353 
TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V TCGA-46-6025 TCGA-51-4079 TCGA-51-4080 
         296          432          366          324           12           12 
TCGA-51-4081 TCGA-52-7622 TCGA-52-7811 TCGA-52-7812 TCGA-56-5897 TCGA-56-7221 
         911          541         1958         1967            3           30 
TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7731 
          13           30           44           40           26         1961 
TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 
          41          178           55           36           63           17 
TCGA-56-8628 TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK 
          16            2           46           30           25            4 
TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-A46J 
           4            8          378          911         2167         2589 
TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 TCGA-60-2696 TCGA-60-2698 
        1723         1072          910          642          109          311 
TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 
        1943         1958          661         1963         1505         1963 
TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2716 TCGA-60-2720 TCGA-60-2721 
        1260          274         1731         1475           97          983 
TCGA-60-2722 TCGA-60-2724 TCGA-60-2726 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 
         908          717          358         1957         1955         1947 
TCGA-63-7023 TCGA-66-2727 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 TCGA-66-2753 
        1952         1967           61          641           30           31 
TCGA-66-2755 TCGA-66-2756 TCGA-66-2758 TCGA-66-2763 TCGA-66-2767 TCGA-66-2768 
          28           30          639           30           61           61 
TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2778 TCGA-66-2780 TCGA-66-2782 
         700          578         1946          578         1956         1954 
TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 
         759           60          790         1217          699         1955 
TCGA-66-2790 TCGA-66-2792 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 
         699          913         1645          122         1492           83 
TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 TCGA-68-A59I TCGA-68-A59J TCGA-77-6842 
         202          211          244          121          104         1950 
TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7335 
        1941         1942         1952         1959         1968         1954 
TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 
        1942         1952         1954         1960         1945         1641 
TCGA-77-8128 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 
        1953         1941         1941         1947         1946         1951 
TCGA-77-8140 TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 
        1962          833         1943          293         1961         1684 
TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 
        1092         1953         1942         1959         1955         1963 
TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6561 
        1290         1280         1939          839          713          395 
TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7710 TCGA-85-7844 TCGA-85-7950 
          18           10           49         1965          911           60 
TCGA-85-8048 TCGA-85-8049 TCGA-85-8070 TCGA-85-8071 TCGA-85-8277 TCGA-85-8288 
          26           60          960          428           11           54 
TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 
          60           55           67           61           61           22 
TCGA-85-8481 TCGA-85-8580 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4PA 
          21          445            3          475           15         1972 
TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 
        1960           25           19         1973         1967         1972 
TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7766 
        1987           24           13          111          758          289 
TCGA-90-7767 TCGA-90-7769 TCGA-90-7964 TCGA-90-A4ED TCGA-92-7340 TCGA-92-7341 
          89          358          428          244           82          106 
TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 TCGA-94-A4VJ TCGA-96-7544 
         122          160           70           87          430         1213 
TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL TCGA-98-8021 
        1344          189          211          273          183          413 
TCGA-98-8023 TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 TCGA-NC-A5HI 
         308          222           35          449         1135 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                1                 2 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             3644              5287 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              479               700 
[1] "1.0 - 3644.0 (479.0)" "2.0 - 5287.0 (700.0)"
[1] "hr=" "1"  
D11V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  6P GAIN MUTATED         0       14       28        1        13        14
  6P GAIN WILD-TYPE       1       58      109        0        39        57
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  6P GAIN MUTATED           12          6        1
  6P GAIN WILD-TYPE         45         14        5
D11V3, multiclass
            clus
vv           6P GAIN MUTATED 6P GAIN WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                14                58
  STAGE IB                28               109
  STAGE II                 1                 0
  STAGE IIA               13                39
  STAGE IIB               14                57
  STAGE IIIA              12                45
  STAGE IIIB               6                14
  STAGE IV                 1                 5
[1] 9 2
[1] 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    18  59   7   6
  6P GAIN WILD-TYPE  80 195  41  14
D11V4, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  T1              18                80
  T2              59               195
  T3               7                41
  T4               6                14
[1] 4 2
[1] 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    61  20   7   1
  6P GAIN WILD-TYPE 200  93  28   4
D11V5, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  N0              61               200
  N1              20                93
  N2               7                28
  N3               1                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A  MX
  6P GAIN MUTATED    79   1   0  10
  6P GAIN WILD-TYPE 279   4   1  40
D11V6, multiclass
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  M0               79               279
  M1                1                 4
  M1A               0                 1
  MX               10                40
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V7, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    21  69
  6P GAIN WILD-TYPE  86 244
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     21   69
  6P GAIN WILD-TYPE   86  244
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE              21                86
  MALE                69               244
[1] 2 2
[1] FALSE
D11V8, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  6P GAIN MUTATED                                       4
  6P GAIN WILD-TYPE                                     8
                   vv
clus                LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  6P GAIN MUTATED                                        1
  6P GAIN WILD-TYPE                                      5
                   vv
clus                LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  6P GAIN MUTATED                                         1
  6P GAIN WILD-TYPE                                       0
                   vv
clus                LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  6P GAIN MUTATED                                                            84
  6P GAIN WILD-TYPE                                                         317
D11V9, multiclass
                                                             clus
vv                                                            6P GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     4
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              84
                                                             clus
vv                                                            6P GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       8
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               317
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V10, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     3  87
  6P GAIN WILD-TYPE  10 320
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      3   87
  6P GAIN WILD-TYPE   10  320
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  NO                3                10
  YES              87               320
[1] 2 2
[1] FALSE
D11V11, continuous
                   vv
clus                 R0  R1  R2  RX
  6P GAIN MUTATED    74   3   1   2
  6P GAIN WILD-TYPE 268   5   3  16
D11V12, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  R0              74               268
  R1               3                 5
  R2               1                 3
  RX               2                16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6P GAIN MUTATED       0                         5    69
  6P GAIN WILD-TYPE     9                        12   229
D11V13, multiclass
                           clus
vv                          6P GAIN MUTATED 6P GAIN WILD-TYPE
  ASIAN                                   0                 9
  BLACK OR AFRICAN AMERICAN               5                12
  WHITE                                  69               229
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V14, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     2  61
  6P GAIN WILD-TYPE   6 206
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      2   61
  6P GAIN WILD-TYPE    6  206
                        clus
vv                       6P GAIN MUTATED 6P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 6
  NOT HISPANIC OR LATINO              61               206
[1] 2 2
[1] FALSE

Clustering(12) Variable = 6Q GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                 0   1
  6Q GAIN MUTATED    53  17
  6Q GAIN WILD-TYPE 212 106
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               70               318 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               17               106 
$`6Q GAIN MUTATED`
TCGA-21-1072 TCGA-21-1082 TCGA-21-1083 TCGA-21-5786 TCGA-22-4605 TCGA-22-5477 
        3016         3644          267         1032         1946         1346 
TCGA-22-5482 TCGA-22-5483 TCGA-33-4533 TCGA-33-4547 TCGA-33-4587 TCGA-33-4589 
         357          573         1940         1311         1970         1948 
TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-39-5019 TCGA-43-2578 TCGA-43-3920 
         238          207           12         1361          684         1007 
TCGA-43-5670 TCGA-43-6770 TCGA-46-6026 TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 
         849          310          423         1948          923         1958 
TCGA-56-1622 TCGA-56-6545 TCGA-56-6546 TCGA-56-7822 TCGA-56-A49D TCGA-56-A5DR 
         881           62           26            1           38            4 
TCGA-58-8393 TCGA-60-2703 TCGA-60-2714 TCGA-60-2715 TCGA-60-2719 TCGA-60-2723 
        1058         1950         1531         1075         1297         1092 
TCGA-60-2725 TCGA-63-6202 TCGA-66-2734 TCGA-66-2757 TCGA-66-2759 TCGA-66-2765 
         816         1973         1311           30          762           61 
TCGA-66-2769 TCGA-66-2777 TCGA-66-2781 TCGA-66-2786 TCGA-66-2789 TCGA-66-2793 
        1947           61          121          790         1955         1952 
TCGA-68-8251 TCGA-77-7142 TCGA-77-7465 TCGA-77-8130 TCGA-85-6798 TCGA-85-7699 
          96         1286          479         1945           34            1 
TCGA-85-7843 TCGA-85-7950 TCGA-85-8276 TCGA-85-8287 TCGA-85-8352 TCGA-85-8353 
          35           60           13           13           67           54 
TCGA-85-8666 TCGA-90-A4EE TCGA-90-A59Q TCGA-94-7943 TCGA-94-A4VJ TCGA-98-7454 
         475          331          269          356          430          256 
TCGA-98-8022 TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HE 
         224           36           83         1722 

$`6Q GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 
         370          136         2464         2417          146         1415 
TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 
         345          396         1810          862          758           50 
TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 
        1331          187           85         2754           92          827 
TCGA-21-1070 TCGA-21-1071 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 
        3636         1426         2134         1852         1058          474 
TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 TCGA-21-5782 TCGA-21-5784 TCGA-21-5787 
         965         3724          284          962         1268          329 
TCGA-21-A5DI TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 
         979          608          223         1945          131         1952 
TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 TCGA-22-4593 
          53          429          822         1485          623         1067 
TCGA-22-4594 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 
        1470          734           17         1161         1057          399 
TCGA-22-4607 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 
         587          358          965         1964         1933          445 
TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 TCGA-22-5485 TCGA-22-5489 
          24         1651         1952         1952          916         1912 
TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4538 TCGA-33-4566 
        1713          506           29         2524         2979         5287 
TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-6738 TCGA-34-2596 TCGA-34-2600 
        1966         1941          428          822           80         1874 
TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 
         958          881         1000          951         1528         2062 
TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 
        1715          707          365          428          941          552 
TCGA-34-8454 TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 
         166          120           13           12          200          247 
TCGA-37-4132 TCGA-37-5819 TCGA-39-5011 TCGA-39-5016 TCGA-39-5021 TCGA-39-5022 
         227          103         1454         2253         1947         1996 
TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 
        1964         1849           52          740           59          833 
TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 TCGA-39-5040 
        1107          474         1084         1086          544         1964 
TCGA-43-2576 TCGA-43-2581 TCGA-43-3394 TCGA-43-5668 TCGA-43-6143 TCGA-43-6647 
        1223         1176          822          349          376          757 
TCGA-43-6771 TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 
        1936          212          236         1970          407          358 
TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V TCGA-46-6025 
        1971          353          296          432          366          324 
TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7812 TCGA-56-5897 
          12           12          911          541         1967            3 
TCGA-56-5898 TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 
         555           30           13           30           44           40 
TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 
          26            6         1961           41          178           55 
TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A4BW 
          36           63           17           16           34            2 
TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DS TCGA-58-8388 
          46           30           25            4            8          378 
TCGA-58-8390 TCGA-58-8391 TCGA-58-A46J TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N 
         911         2167         2589         1723         1072          910 
TCGA-60-2695 TCGA-60-2696 TCGA-60-2698 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 
         642          109          311         1943         1958          661 
TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 
        1963         1505         1963         1260          274         1731 
TCGA-60-2716 TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 TCGA-60-2724 TCGA-60-2726 
        1475           97          983          908          717          358 
TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 TCGA-66-2727 TCGA-66-2737 
        1957         1955         1947         1952         1967           61 
TCGA-66-2742 TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 
         641           30           31           61           28           30 
TCGA-66-2758 TCGA-66-2763 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2770 
         639           30           31           61           61          700 
TCGA-66-2771 TCGA-66-2773 TCGA-66-2778 TCGA-66-2780 TCGA-66-2782 TCGA-66-2783 
         578         1946          578         1956         1954          759 
TCGA-66-2785 TCGA-66-2787 TCGA-66-2788 TCGA-66-2790 TCGA-66-2791 TCGA-66-2792 
          60         1217          699          699         1977          913 
TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 
        1645          122         1492           83          202          211 
TCGA-68-8250 TCGA-68-A59I TCGA-68-A59J TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 
         244          121          104         1950         1941         1942 
TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 TCGA-77-7335 TCGA-77-7337 
        1952         1959         1968           15         1954         1942 
TCGA-77-7338 TCGA-77-7463 TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 
        1952         1954         1960         1945         1641         1953 
TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 
        1941         1941         1947         1946         1951         1962 
TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 
         833         1943          293         1961         1684         1092 
TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 
          10         1953         1942         1959         1955         1963 
TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6560 
        1290         1280         1939          839          713          364 
TCGA-85-6561 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7710 TCGA-85-7844 
         395           18           10           49         1965          911 
TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 
          26           60           16          960          428          513 
TCGA-85-8277 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8354 TCGA-85-8355 
          11           54           60           55           61           61 
TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8664 TCGA-85-A4CL 
          22           21          445          424            3           15 
TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 
        1972         1960           25           19         1973         1967 
TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 
        1972         1987           24           13          111          758 
TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 TCGA-90-7964 TCGA-90-A4ED TCGA-92-7340 
         289           89          358          428          244           82 
TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 TCGA-96-7544 
         106          122          160           70           87         1213 
TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL TCGA-98-8021 
        1344          189          211          273          183          413 
TCGA-98-8023 TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 TCGA-NC-A5HG TCGA-NC-A5HI 
         308          222           35          449         1548         1135 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                1                 2 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
             3644              5287 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            526.0             651.5 
[1] "1.0 - 3644.0 (526.0)" "2.0 - 5287.0 (651.5)"
[1] "hr=" "1.1"
D12V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  6Q GAIN MUTATED         0       13       29        1        10        11
  6Q GAIN WILD-TYPE       1       59      108        0        42        60
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  6Q GAIN MUTATED            7          6        0
  6Q GAIN WILD-TYPE         50         14        6
D12V3, multiclass
            clus
vv           6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                13                59
  STAGE IB                29               108
  STAGE II                 1                 0
  STAGE IIA               10                42
  STAGE IIB               11                60
  STAGE IIIA               7                50
  STAGE IIIB               6                14
  STAGE IV                 0                 6
[1] 9 2
[1] 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    17  49   6   5
  6Q GAIN WILD-TYPE  81 205  42  15
D12V4, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  T1              17                81
  T2              49               205
  T3               6                42
  T4               5                15
[1] 4 2
[1] 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    53  19   3   1
  6Q GAIN WILD-TYPE 208  94  32   4
D12V5, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  N0              53               208
  N1              19                94
  N2               3                32
  N3               1                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A  MX
  6Q GAIN MUTATED    67   0   0  10
  6Q GAIN WILD-TYPE 291   5   1  40
D12V6, multiclass
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  M0               67               291
  M1                0                 5
  M1A               0                 1
  MX               10                40
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V7, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    20  57
  6Q GAIN WILD-TYPE  87 256
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     20   57
  6Q GAIN WILD-TYPE   87  256
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE              20                87
  MALE                57               256
[1] 2 2
[1] FALSE
D12V8, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  6Q GAIN MUTATED                                       2
  6Q GAIN WILD-TYPE                                    10
                   vv
clus                LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  6Q GAIN MUTATED                                        0
  6Q GAIN WILD-TYPE                                      6
                   vv
clus                LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  6Q GAIN MUTATED                                         1
  6Q GAIN WILD-TYPE                                       0
                   vv
clus                LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  6Q GAIN MUTATED                                                            74
  6Q GAIN WILD-TYPE                                                         327
D12V9, multiclass
                                                             clus
vv                                                            6Q GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     2
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    0
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              74
                                                             clus
vv                                                            6Q GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      10
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               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"
D12V10, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     2  75
  6Q GAIN WILD-TYPE  11 332
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      2   75
  6Q GAIN WILD-TYPE   11  332
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  NO                2                11
  YES              75               332
[1] 2 2
[1] FALSE
D12V11, continuous
                   vv
clus                 R0  R1  R2  RX
  6Q GAIN MUTATED    62   2   1   3
  6Q GAIN WILD-TYPE 280   6   3  15
D12V12, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  R0              62               280
  R1               2                 6
  R2               1                 3
  RX               3                15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6Q GAIN MUTATED       0                         3    61
  6Q GAIN WILD-TYPE     9                        14   237
D12V13, multiclass
                           clus
vv                          6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  ASIAN                                   0                 9
  BLACK OR AFRICAN AMERICAN               3                14
  WHITE                                  61               237
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V14, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     3  52
  6Q GAIN WILD-TYPE   5 215
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      3   52
  6Q GAIN WILD-TYPE    5  215
                        clus
vv                       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 5
  NOT HISPANIC OR LATINO              52               215
[1] 2 2
[1] FALSE

Clustering(13) Variable = 7P GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                 0   1
  7P GAIN MUTATED   134  57
  7P GAIN WILD-TYPE 131  66
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              191               197 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               57                66 
$`7P GAIN MUTATED`
TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 
         136         2464         2417         1415          345          396 
TCGA-18-3417 TCGA-18-3421 TCGA-18-4083 TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 
         758         1331          187         2754           92         3636 
TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1079 TCGA-21-1081 TCGA-21-1082 
        3016         2134         1852          965          284         3644 
TCGA-21-5784 TCGA-22-0944 TCGA-22-1011 TCGA-22-1012 TCGA-22-4591 TCGA-22-4593 
        1268          223           53          429          623         1067 
TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4604 TCGA-22-4605 TCGA-22-5471 
         734           17         1161          399         1946          965 
TCGA-22-5472 TCGA-22-5473 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5482 
        1964         1933         1346           24         1651          357 
TCGA-22-5483 TCGA-22-5491 TCGA-22-A5C4 TCGA-33-4533 TCGA-33-4538 TCGA-33-4566 
         573         1713           29         1940         2979         5287 
TCGA-33-4582 TCGA-33-4586 TCGA-33-4589 TCGA-34-2596 TCGA-34-2605 TCGA-34-2609 
        1966          428         1948           80          881          951 
TCGA-34-5231 TCGA-34-5234 TCGA-34-5240 TCGA-34-5241 TCGA-34-5928 TCGA-37-3783 
        1528         1715          365          428          552          120 
TCGA-37-3792 TCGA-37-4130 TCGA-37-4135 TCGA-37-4141 TCGA-39-5011 TCGA-39-5016 
          12          247          207           12         1454         2253 
TCGA-39-5019 TCGA-39-5031 TCGA-39-5035 TCGA-39-5037 TCGA-43-2576 TCGA-43-2581 
        1361          833          474         1086         1223         1176 
TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 TCGA-43-6647 TCGA-43-6771 
         822         1007          349          849          757         1936 
TCGA-43-7657 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56V TCGA-46-6025 TCGA-51-4079 
         236          353          296          366          324           12 
TCGA-51-4081 TCGA-52-7809 TCGA-56-7221 TCGA-56-7223 TCGA-56-7579 TCGA-56-7582 
         911         1948           30           30           44           26 
TCGA-56-8504 TCGA-56-8624 TCGA-56-8626 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX 
         178           36           17           38            2           46 
TCGA-56-A5DR TCGA-58-8391 TCGA-58-8393 TCGA-58-A46M TCGA-58-A46N TCGA-60-2704 
           4         2167         1058         1072          910         1943 
TCGA-60-2706 TCGA-60-2708 TCGA-60-2709 TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 
        1958         1963         1505         1260          274         1731 
TCGA-60-2714 TCGA-60-2719 TCGA-60-2722 TCGA-60-2723 TCGA-60-2726 TCGA-63-6202 
        1531         1297          908         1092          358         1973 
TCGA-63-7020 TCGA-63-7021 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 
        1957         1955         1311           61          641           30 
TCGA-66-2755 TCGA-66-2759 TCGA-66-2763 TCGA-66-2766 TCGA-66-2767 TCGA-66-2770 
          28          762           30           31           61          700 
TCGA-66-2771 TCGA-66-2777 TCGA-66-2780 TCGA-66-2782 TCGA-66-2785 TCGA-66-2787 
         578           61         1956         1954           60         1217 
TCGA-66-2791 TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-68-8250 TCGA-68-A59J 
        1977          122         1492           83          244          104 
TCGA-77-6845 TCGA-77-7138 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 
        1952         1959         1952         1954          479         1960 
TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8133 TCGA-77-8136 
        1945         1641         1953         1945         1941         1947 
TCGA-77-8139 TCGA-77-8148 TCGA-77-8150 TCGA-77-8156 TCGA-77-A5G3 TCGA-77-A5G6 
        1951          293         1961           10         1959         1955 
TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF TCGA-85-6561 
        1963         1290         1280         1939          839          395 
TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 
          34           18           10           35          911           60 
TCGA-85-8049 TCGA-85-8052 TCGA-85-8072 TCGA-85-8276 TCGA-85-8352 TCGA-85-8354 
          60           16          513           13           67           61 
TCGA-85-8664 TCGA-85-8666 TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A513 
           3          475         1960           25           19           24 
TCGA-85-A53L TCGA-90-7769 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7341 
          13          358          244          331          269          106 
TCGA-92-8064 TCGA-96-7545 TCGA-96-A4JK TCGA-96-A4JL TCGA-98-8023 TCGA-L3-A4E7 
         160         1344          273          183          308           35 
TCGA-L3-A524 TCGA-MF-A522 TCGA-NC-A5HE TCGA-NC-A5HG TCGA-NC-A5HI 
         449           83         1722         1548         1135 

$`7P GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3410 TCGA-18-3415 TCGA-18-3416 TCGA-18-3419 TCGA-18-4086 
         370          146         1810          862           50           85 
TCGA-18-5595 TCGA-21-1071 TCGA-21-1077 TCGA-21-1078 TCGA-21-1080 TCGA-21-1083 
         827         1426         1058          474         3724          267 
TCGA-21-5782 TCGA-21-5786 TCGA-21-5787 TCGA-21-A5DI TCGA-22-0940 TCGA-22-1000 
         962         1032          329          979          608         1945 
TCGA-22-1002 TCGA-22-1005 TCGA-22-1016 TCGA-22-1017 TCGA-22-4594 TCGA-22-4601 
         131         1952          822         1485         1470         1057 
TCGA-22-4607 TCGA-22-4613 TCGA-22-5474 TCGA-22-5480 TCGA-22-5481 TCGA-22-5485 
         587          358          445         1952         1952          916 
TCGA-22-5489 TCGA-22-5492 TCGA-33-4532 TCGA-33-4547 TCGA-33-4583 TCGA-33-4587 
        1912          506         2524         1311         1941         1970 
TCGA-33-6738 TCGA-34-2600 TCGA-34-2604 TCGA-34-2608 TCGA-34-5232 TCGA-34-5239 
         822         1874          958         1000         2062          707 
TCGA-34-5927 TCGA-34-8454 TCGA-37-3789 TCGA-37-4129 TCGA-37-4132 TCGA-37-4133 
         941          166           13          200          227          238 
TCGA-37-5819 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 
         103         1947         1996         1964         1849           52 
TCGA-39-5029 TCGA-39-5030 TCGA-39-5034 TCGA-39-5036 TCGA-39-5039 TCGA-39-5040 
         740           59         1107         1084          544         1964 
TCGA-43-2578 TCGA-43-6143 TCGA-43-6770 TCGA-43-7656 TCGA-43-7658 TCGA-43-8115 
         684          376          310          212         1970          407 
TCGA-43-8116 TCGA-43-8118 TCGA-43-A56U TCGA-46-6026 TCGA-51-4080 TCGA-52-7622 
         358         1971          432          423           12          541 
TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 
         923         1958         1967          881            3          555 
TCGA-56-6545 TCGA-56-6546 TCGA-56-7222 TCGA-56-7580 TCGA-56-7730 TCGA-56-7731 
          62           26           13           40            6         1961 
TCGA-56-7822 TCGA-56-8503 TCGA-56-8622 TCGA-56-8625 TCGA-56-8628 TCGA-56-8629 
           1           41           55           63           16           34 
TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DS TCGA-58-8388 TCGA-58-8390 
          30           25            4            8          378          911 
TCGA-58-A46J TCGA-58-A46L TCGA-60-2695 TCGA-60-2696 TCGA-60-2698 TCGA-60-2703 
        2589         1723          642          109          311         1950 
TCGA-60-2707 TCGA-60-2710 TCGA-60-2715 TCGA-60-2716 TCGA-60-2720 TCGA-60-2721 
         661         1963         1075         1475           97          983 
TCGA-60-2724 TCGA-60-2725 TCGA-63-7022 TCGA-63-7023 TCGA-66-2727 TCGA-66-2753 
         717          816         1947         1952         1967           31 
TCGA-66-2754 TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 TCGA-66-2765 TCGA-66-2768 
          61           30           30          639           61           61 
TCGA-66-2769 TCGA-66-2773 TCGA-66-2778 TCGA-66-2781 TCGA-66-2783 TCGA-66-2786 
        1947         1946          578          121          759          790 
TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 
         699         1955          699          913         1952         1645 
TCGA-68-7756 TCGA-68-7757 TCGA-68-8251 TCGA-68-A59I TCGA-77-6842 TCGA-77-6843 
         202          211           96          121         1950         1941 
TCGA-77-6844 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 
        1942         1968           15         1286         1954         1942 
TCGA-77-8131 TCGA-77-8138 TCGA-77-8140 TCGA-77-8144 TCGA-77-8145 TCGA-77-8153 
        1941         1946         1962          833         1943         1684 
TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5GH TCGA-85-6560 TCGA-85-7698 
        1092         1953         1942          713          364           49 
TCGA-85-7699 TCGA-85-7710 TCGA-85-8048 TCGA-85-8070 TCGA-85-8071 TCGA-85-8277 
           1         1965           26          960          428           11 
TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8353 TCGA-85-8355 
          13           54           60           55           54           61 
TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-A4CL TCGA-85-A4PA 
          22           21          445          424           15         1972 
TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A512 TCGA-85-A5B5 TCGA-90-6837 
        1973         1967         1972         1987          111          758 
TCGA-90-7766 TCGA-90-7767 TCGA-90-7964 TCGA-92-7340 TCGA-92-8063 TCGA-92-8065 
         289           89          428           82          122           70 
TCGA-94-7033 TCGA-94-7943 TCGA-94-A4VJ TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 
          87          356          430         1213          189          211 
TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-J1-A4AH TCGA-LA-A446 
         256          413          224          222           36 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                2                 1 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             5287              3724 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              734               608 
[1] "2.0 - 5287.0 (734.0)" "1.0 - 3724.0 (608.0)"
[1] "hr=" "1.2"
D13V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  7P GAIN MUTATED         0       23       74        0        27        43
  7P GAIN WILD-TYPE       1       49       63        1        25        28
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  7P GAIN MUTATED           27          7        3
  7P GAIN WILD-TYPE         30         13        3
D13V3, multiclass
            clus
vv           7P GAIN MUTATED 7P GAIN WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                23                49
  STAGE IB                74                63
  STAGE II                 0                 1
  STAGE IIA               27                25
  STAGE IIB               43                28
  STAGE IIIA              27                30
  STAGE IIIB               7                13
  STAGE IV                 3                 3
[1] 9 2
[1] 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    34 138  29   5
  7P GAIN WILD-TYPE  64 116  19  15
D13V4, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  T1              34                64
  T2             138               116
  T3              29                19
  T4               5                15
[1] 4 2
[1] 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   122  64  15   2
  7P GAIN WILD-TYPE 139  49  20   3
D13V5, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  N0             122               139
  N1              64                49
  N2              15                20
  N3               2                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A  MX
  7P GAIN MUTATED   178   3   0  22
  7P GAIN WILD-TYPE 180   2   1  28
D13V6, multiclass
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  M0              178               180
  M1                3                 2
  M1A               0                 1
  MX               22                28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V7, binary
                   cls
clus                  0   1
  7P GAIN MUTATED    46 160
  7P GAIN WILD-TYPE  61 153
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     46  160
  7P GAIN WILD-TYPE   61  153
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE              46                61
  MALE               160               153
[1] 2 2
[1] FALSE
D13V8, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  7P GAIN MUTATED                                       6
  7P GAIN WILD-TYPE                                     6
                   vv
clus                LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  7P GAIN MUTATED                                        1
  7P GAIN WILD-TYPE                                      5
                   vv
clus                LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  7P GAIN MUTATED                                         0
  7P GAIN WILD-TYPE                                       1
                   vv
clus                LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  7P GAIN MUTATED                                                           199
  7P GAIN WILD-TYPE                                                         202
D13V9, multiclass
                                                             clus
vv                                                            7P GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     6
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             199
                                                             clus
vv                                                            7P GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       6
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               202
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V10, binary
                   cls
clus                  0   1
  7P GAIN MUTATED     5 201
  7P GAIN WILD-TYPE   8 206
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      5  201
  7P GAIN WILD-TYPE    8  206
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  NO                5                 8
  YES             201               206
[1] 2 2
[1] FALSE
D13V11, continuous
                   vv
clus                 R0  R1  R2  RX
  7P GAIN MUTATED   173   4   1   7
  7P GAIN WILD-TYPE 169   4   3  11
D13V12, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  R0             173               169
  R1               4                 4
  R2               1                 3
  RX               7                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7P GAIN MUTATED       8                         9   138
  7P GAIN WILD-TYPE     1                         8   160
D13V13, multiclass
                           clus
vv                          7P GAIN MUTATED 7P GAIN WILD-TYPE
  ASIAN                                   8                 1
  BLACK OR AFRICAN AMERICAN               9                 8
  WHITE                                 138               160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V14, binary
                   cls
clus                  0   1
  7P GAIN MUTATED     2 128
  7P GAIN WILD-TYPE   6 139
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      2  128
  7P GAIN WILD-TYPE    6  139
                        clus
vv                       7P GAIN MUTATED 7P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 6
  NOT HISPANIC OR LATINO             128               139
[1] 2 2
[1] FALSE

Clustering(14) Variable = 7Q GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                 0   1
  7Q GAIN MUTATED   122  53
  7Q GAIN WILD-TYPE 143  70
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              175               213 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               53                70 
$`7Q GAIN MUTATED`
TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 
         136         2464         2417         1415          345          396 
TCGA-18-3417 TCGA-18-4083 TCGA-18-4721 TCGA-21-1070 TCGA-21-1075 TCGA-21-1076 
         758          187         2754         3636         2134         1852 
TCGA-21-1077 TCGA-21-1079 TCGA-21-1081 TCGA-21-5787 TCGA-21-A5DI TCGA-22-1011 
        1058          965          284          329          979           53 
TCGA-22-1012 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4595 TCGA-22-4596 
         429          623         1067         1470          734           17 
TCGA-22-4599 TCGA-22-4604 TCGA-22-4605 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 
        1161          399         1946          965         1964         1933 
TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5482 TCGA-22-5483 TCGA-22-5491 
        1346           24         1651          357          573         1713 
TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4533 TCGA-33-4538 TCGA-33-4586 TCGA-33-4589 
         506           29         1940         2979          428         1948 
TCGA-33-6738 TCGA-34-2596 TCGA-34-2600 TCGA-34-2605 TCGA-34-2609 TCGA-34-5231 
         822           80         1874          881          951         1528 
TCGA-34-5240 TCGA-34-5241 TCGA-34-5928 TCGA-37-3783 TCGA-37-4133 TCGA-37-4135 
         365          428          552          120          238          207 
TCGA-37-4141 TCGA-39-5011 TCGA-39-5019 TCGA-39-5027 TCGA-39-5031 TCGA-39-5035 
          12         1454         1361         1849          833          474 
TCGA-39-5037 TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 TCGA-43-6647 TCGA-43-7657 
        1086          822         1007          349          757          236 
TCGA-43-A474 TCGA-43-A475 TCGA-43-A56V TCGA-46-6025 TCGA-51-4079 TCGA-51-4081 
         353          296          366          324           12          911 
TCGA-52-7809 TCGA-52-7810 TCGA-56-5898 TCGA-56-7221 TCGA-56-7223 TCGA-56-7579 
        1948          923          555           30           30           44 
TCGA-56-7582 TCGA-56-8504 TCGA-56-A49D TCGA-56-A4BX TCGA-56-A5DR TCGA-58-8393 
          26          178           38           46            4         1058 
TCGA-58-A46M TCGA-58-A46N TCGA-60-2704 TCGA-60-2706 TCGA-60-2708 TCGA-60-2709 
        1072          910         1943         1958         1963         1505 
TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2719 TCGA-60-2722 
        1260          274         1731         1531         1297          908 
TCGA-60-2723 TCGA-60-2726 TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 TCGA-66-2734 
        1092          358         1973         1957         1955         1311 
TCGA-66-2737 TCGA-66-2742 TCGA-66-2755 TCGA-66-2758 TCGA-66-2763 TCGA-66-2766 
          61          641           28          639           30           31 
TCGA-66-2767 TCGA-66-2770 TCGA-66-2771 TCGA-66-2777 TCGA-66-2780 TCGA-66-2782 
          61          700          578           61         1956         1954 
TCGA-66-2785 TCGA-66-2787 TCGA-66-2791 TCGA-66-2792 TCGA-66-2794 TCGA-66-2795 
          60         1217         1977          913         1645          122 
TCGA-66-2800 TCGA-68-7755 TCGA-68-8250 TCGA-77-6845 TCGA-77-7141 TCGA-77-7338 
        1492           83          244         1952           15         1952 
TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 
        1954          479         1960         1641         1953         1945 
TCGA-77-8133 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8156 TCGA-77-A5G8 
        1941          293         1961         1684           10         1290 
TCGA-77-A5GA TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7843 TCGA-85-7950 
        1280          395           34           18           35           60 
TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 
          60           16          960          513           13           11 
TCGA-85-8352 TCGA-85-8354 TCGA-85-8666 TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M 
          67           61          475         1960           25           19 
TCGA-85-A512 TCGA-85-A5B5 TCGA-90-7769 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q 
        1987          111          358          244          331          269 
TCGA-92-7341 TCGA-96-7545 TCGA-96-8169 TCGA-96-A4JK TCGA-96-A4JL TCGA-98-8023 
         106         1344          189          273          183          308 
TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HE TCGA-NC-A5HG 
          35          449           36           83         1722         1548 
TCGA-NC-A5HI 
        1135 

$`7Q GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3410 TCGA-18-3415 TCGA-18-3416 TCGA-18-3419 TCGA-18-3421 
         370          146         1810          862           50         1331 
TCGA-18-4086 TCGA-18-5592 TCGA-18-5595 TCGA-21-1071 TCGA-21-1072 TCGA-21-1078 
          85           92          827         1426         3016          474 
TCGA-21-1080 TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 
        3724         3644          267          962         1268         1032 
TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1016 
         608          223         1945          131         1952          822 
TCGA-22-1017 TCGA-22-4601 TCGA-22-4607 TCGA-22-4613 TCGA-22-5474 TCGA-22-5480 
        1485         1057          587          358          445         1952 
TCGA-22-5481 TCGA-22-5485 TCGA-22-5489 TCGA-33-4532 TCGA-33-4547 TCGA-33-4566 
        1952          916         1912         2524         1311         5287 
TCGA-33-4582 TCGA-33-4583 TCGA-33-4587 TCGA-34-2604 TCGA-34-2608 TCGA-34-5232 
        1966         1941         1970          958         1000         2062 
TCGA-34-5234 TCGA-34-5239 TCGA-34-5927 TCGA-34-8454 TCGA-37-3789 TCGA-37-3792 
        1715          707          941          166           13           12 
TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-5819 TCGA-39-5016 TCGA-39-5021 
         200          247          227          103         2253         1947 
TCGA-39-5022 TCGA-39-5024 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5034 
        1996         1964           52          740           59         1107 
TCGA-39-5036 TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 TCGA-43-2578 TCGA-43-2581 
        1084          544         1964         1223          684         1176 
TCGA-43-5670 TCGA-43-6143 TCGA-43-6770 TCGA-43-6771 TCGA-43-7656 TCGA-43-7658 
         849          376          310         1936          212         1970 
TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 TCGA-43-A56U TCGA-46-6026 TCGA-51-4080 
         407          358         1971          432          423           12 
TCGA-52-7622 TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-6545 
         541         1958         1967          881            3           62 
TCGA-56-6546 TCGA-56-7222 TCGA-56-7580 TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 
          26           13           40            6         1961            1 
TCGA-56-8503 TCGA-56-8622 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 
          41           55           36           63           17           16 
TCGA-56-8629 TCGA-56-A4BW TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DS 
          34            2           30           25            4            8 
TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-A46J TCGA-58-A46L TCGA-60-2695 
         378          911         2167         2589         1723          642 
TCGA-60-2696 TCGA-60-2698 TCGA-60-2703 TCGA-60-2707 TCGA-60-2710 TCGA-60-2715 
         109          311         1950          661         1963         1075 
TCGA-60-2716 TCGA-60-2720 TCGA-60-2721 TCGA-60-2724 TCGA-60-2725 TCGA-63-7022 
        1475           97          983          717          816         1947 
TCGA-63-7023 TCGA-66-2727 TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2756 
        1952         1967           30           31           61           30 
TCGA-66-2757 TCGA-66-2759 TCGA-66-2765 TCGA-66-2768 TCGA-66-2769 TCGA-66-2773 
          30          762           61           61         1947         1946 
TCGA-66-2778 TCGA-66-2781 TCGA-66-2783 TCGA-66-2786 TCGA-66-2788 TCGA-66-2789 
         578          121          759          790          699         1955 
TCGA-66-2790 TCGA-66-2793 TCGA-68-7756 TCGA-68-7757 TCGA-68-8251 TCGA-68-A59I 
         699         1952          202          211           96          121 
TCGA-68-A59J TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-7138 TCGA-77-7139 
         104         1950         1941         1942         1959         1968 
TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-8008 TCGA-77-8131 TCGA-77-8136 
        1286         1954         1942         1945         1941         1947 
TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8144 TCGA-77-8145 TCGA-77-8154 
        1946         1951         1962          833         1943         1092 
TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5GB 
        1953         1942         1959         1955         1963         1939 
TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6560 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 
         839          713          364           10           49            1 
TCGA-85-7710 TCGA-85-7844 TCGA-85-8048 TCGA-85-8071 TCGA-85-8287 TCGA-85-8288 
        1965          911           26          428           13           54 
TCGA-85-8350 TCGA-85-8351 TCGA-85-8353 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 
          60           55           54           61           22           21 
TCGA-85-8580 TCGA-85-8582 TCGA-85-8664 TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A50Z 
         445          424            3           15         1972         1973 
TCGA-85-A510 TCGA-85-A511 TCGA-85-A513 TCGA-85-A53L TCGA-90-6837 TCGA-90-7766 
        1967         1972           24           13          758          289 
TCGA-90-7767 TCGA-90-7964 TCGA-92-7340 TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 
          89          428           82          122          160           70 
TCGA-94-7033 TCGA-94-7943 TCGA-94-A4VJ TCGA-96-7544 TCGA-96-8170 TCGA-98-7454 
          87          356          430         1213          211          256 
TCGA-98-8021 TCGA-98-8022 TCGA-J1-A4AH 
         413          224          222 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                4                 1 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             3636              5287 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              623               684 
[1] "4.0 - 3636.0 (623.0)" "1.0 - 5287.0 (684.0)"
[1] "hr=" "1.1"
D14V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  7Q GAIN MUTATED         1       22       63        1        22        38
  7Q GAIN WILD-TYPE       0       50       74        0        30        33
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  7Q GAIN MUTATED           29          9        4
  7Q GAIN WILD-TYPE         28         11        2
D14V3, multiclass
            clus
vv           7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  STAGE I                  1                 0
  STAGE IA                22                50
  STAGE IB                63                74
  STAGE II                 1                 0
  STAGE IIA               22                30
  STAGE IIB               38                33
  STAGE IIIA              29                28
  STAGE IIIB               9                11
  STAGE IV                 4                 2
[1] 9 2
[1] 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    35 121  28   7
  7Q GAIN WILD-TYPE  63 133  20  13
D14V4, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T1              35                63
  T2             121               133
  T3              28                20
  T4               7                13
[1] 4 2
[1] 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   110  59  18   2
  7Q GAIN WILD-TYPE 151  54  17   3
D14V5, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  N0             110               151
  N1              59                54
  N2              18                17
  N3               2                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A  MX
  7Q GAIN MUTATED   165   4   0  19
  7Q GAIN WILD-TYPE 193   1   1  31
D14V6, multiclass
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  M0              165               193
  M1                4                 1
  M1A               0                 1
  MX               19                31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V7, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED    42 149
  7Q GAIN WILD-TYPE  65 164
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     42  149
  7Q GAIN WILD-TYPE   65  164
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE              42                65
  MALE               149               164
[1] 2 2
[1] FALSE
D14V8, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  7Q GAIN MUTATED                                       6
  7Q GAIN WILD-TYPE                                     6
                   vv
clus                LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  7Q GAIN MUTATED                                        1
  7Q GAIN WILD-TYPE                                      5
                   vv
clus                LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  7Q GAIN MUTATED                                         0
  7Q GAIN WILD-TYPE                                       1
                   vv
clus                LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  7Q GAIN MUTATED                                                           184
  7Q GAIN WILD-TYPE                                                         217
D14V9, multiclass
                                                             clus
vv                                                            7Q GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     6
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             184
                                                             clus
vv                                                            7Q GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       6
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V10, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED     5 186
  7Q GAIN WILD-TYPE   8 221
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      5  186
  7Q GAIN WILD-TYPE    8  221
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NO                5                 8
  YES             186               221
[1] 2 2
[1] FALSE
D14V11, continuous
                   vv
clus                 R0  R1  R2  RX
  7Q GAIN MUTATED   158   4   1   5
  7Q GAIN WILD-TYPE 184   4   3  13
D14V12, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  R0             158               184
  R1               4                 4
  R2               1                 3
  RX               5                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7Q GAIN MUTATED       6                         9   129
  7Q GAIN WILD-TYPE     3                         8   169
D14V13, multiclass
                           clus
vv                          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  ASIAN                                   6                 3
  BLACK OR AFRICAN AMERICAN               9                 8
  WHITE                                 129               169
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V14, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED     2 118
  7Q GAIN WILD-TYPE   6 149
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      2  118
  7Q GAIN WILD-TYPE    6  149
                        clus
vv                       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 6
  NOT HISPANIC OR LATINO             118               149
[1] 2 2
[1] FALSE

Clustering(15) Variable = 8P GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                 0   1
  8P GAIN MUTATED    70  33
  8P GAIN WILD-TYPE 195  90
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              103               285 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               33                90 
$`8P GAIN MUTATED`
TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 TCGA-18-3414 TCGA-18-3416 
         136         2417          146         1415          396          862 
TCGA-18-3421 TCGA-21-1070 TCGA-21-1075 TCGA-21-1079 TCGA-21-1082 TCGA-21-5784 
        1331         3636         2134          965         3644         1268 
TCGA-22-1011 TCGA-22-4596 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 TCGA-22-5479 
          53           17         1964         1933          445         1651 
TCGA-22-5482 TCGA-22-5489 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4533 TCGA-33-4583 
         357         1912           29         2524         1940         1941 
TCGA-33-4587 TCGA-34-2605 TCGA-34-5231 TCGA-34-5232 TCGA-34-5239 TCGA-37-4132 
        1970          881         1528         2062          707          227 
TCGA-37-5819 TCGA-39-5019 TCGA-39-5022 TCGA-39-5024 TCGA-39-5028 TCGA-39-5029 
         103         1361         1996         1964           52          740 
TCGA-39-5034 TCGA-39-5040 TCGA-43-2578 TCGA-43-3920 TCGA-43-5670 TCGA-43-6647 
        1107         1964          684         1007          849          757 
TCGA-43-A56V TCGA-52-7811 TCGA-56-7730 TCGA-56-7731 TCGA-56-A49D TCGA-56-A4ZK 
         366         1958            6         1961           38            4 
TCGA-56-A5DR TCGA-60-2695 TCGA-60-2708 TCGA-60-2712 TCGA-60-2714 TCGA-60-2719 
           4          642         1963          274         1531         1297 
TCGA-60-2720 TCGA-60-2722 TCGA-60-2725 TCGA-63-6202 TCGA-63-7020 TCGA-63-7023 
          97          908          816         1973         1957         1952 
TCGA-66-2742 TCGA-66-2744 TCGA-66-2756 TCGA-66-2763 TCGA-66-2767 TCGA-66-2770 
         641           30           30           30           61          700 
TCGA-66-2773 TCGA-66-2777 TCGA-66-2788 TCGA-66-2789 TCGA-66-2793 TCGA-66-2800 
        1946           61          699         1955         1952         1492 
TCGA-68-7756 TCGA-68-8251 TCGA-77-7139 TCGA-77-7141 TCGA-77-7335 TCGA-77-7463 
         202           96         1968           15         1954         1954 
TCGA-77-8007 TCGA-77-8136 TCGA-77-8138 TCGA-77-8150 TCGA-77-A5G7 TCGA-77-A5GH 
        1960         1947         1946         1961         1963          713 
TCGA-85-6560 TCGA-85-7699 TCGA-85-8052 TCGA-85-8287 TCGA-85-8481 TCGA-85-8580 
         364            1           16           13           21          445 
TCGA-85-8582 TCGA-85-8664 TCGA-85-A510 TCGA-85-A513 TCGA-90-7769 TCGA-90-A4EE 
         424            3         1967           24          358          331 
TCGA-92-7340 TCGA-94-7943 TCGA-96-7545 TCGA-96-8169 TCGA-98-8023 TCGA-L3-A4E7 
          82          356         1344          189          308           35 
TCGA-L3-A524 
         449 

$`8P GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3408 TCGA-18-3412 TCGA-18-3415 TCGA-18-3417 TCGA-18-3419 
         370         2464          345         1810          758           50 
TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1071 
         187           85         2754           92          827         1426 
TCGA-21-1072 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1080 TCGA-21-1081 
        3016         1852         1058          474         3724          284 
TCGA-21-1083 TCGA-21-5782 TCGA-21-5786 TCGA-21-5787 TCGA-21-A5DI TCGA-22-0940 
         267          962         1032          329          979          608 
TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1012 TCGA-22-1016 
         223         1945          131         1952          429          822 
TCGA-22-1017 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4595 TCGA-22-4599 
        1485          623         1067         1470          734         1161 
TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-4613 TCGA-22-5471 
        1057          399         1946          587          358          965 
TCGA-22-5477 TCGA-22-5478 TCGA-22-5480 TCGA-22-5481 TCGA-22-5483 TCGA-22-5485 
        1346           24         1952         1952          573          916 
TCGA-22-5491 TCGA-22-5492 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 
        1713          506         2979         1311         5287         1966 
TCGA-33-4586 TCGA-33-4589 TCGA-33-6738 TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 
         428         1948          822           80         1874          958 
TCGA-34-2608 TCGA-34-2609 TCGA-34-5234 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 
        1000          951         1715          365          428          941 
TCGA-34-5928 TCGA-34-8454 TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 
         552          166          120           13           12          200 
TCGA-37-4130 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-39-5011 TCGA-39-5016 
         247          238          207           12         1454         2253 
TCGA-39-5021 TCGA-39-5027 TCGA-39-5030 TCGA-39-5031 TCGA-39-5035 TCGA-39-5036 
        1947         1849           59          833          474         1084 
TCGA-39-5037 TCGA-39-5039 TCGA-43-2576 TCGA-43-2581 TCGA-43-3394 TCGA-43-5668 
        1086          544         1223         1176          822          349 
TCGA-43-6143 TCGA-43-6770 TCGA-43-6771 TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 
         376          310         1936          212          236         1970 
TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U 
         407          358         1971          353          296          432 
TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 
         324          423           12           12          911          541 
TCGA-52-7809 TCGA-52-7810 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 
        1948          923         1967          881            3          555 
TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 
          62           26           30           13           30           44 
TCGA-56-7580 TCGA-56-7582 TCGA-56-7822 TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 
          40           26            1           41          178           55 
TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A4BW 
          36           63           17           16           34            2 
TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A5DS TCGA-58-8388 TCGA-58-8390 
          46           30           25            8          378          911 
TCGA-58-8391 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N 
        2167         1058         2589         1723         1072          910 
TCGA-60-2696 TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 
         109          311         1950         1943         1958          661 
TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 TCGA-60-2713 TCGA-60-2715 TCGA-60-2716 
        1505         1963         1260         1731         1075         1475 
TCGA-60-2721 TCGA-60-2723 TCGA-60-2724 TCGA-60-2726 TCGA-63-7021 TCGA-63-7022 
         983         1092          717          358         1955         1947 
TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 
        1967         1311           61           31           61           28 
TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 TCGA-66-2765 TCGA-66-2766 TCGA-66-2768 
          30          639          762           61           31           61 
TCGA-66-2769 TCGA-66-2771 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 
        1947          578          578         1956          121         1954 
TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2790 TCGA-66-2791 
         759           60          790         1217          699         1977 
TCGA-66-2792 TCGA-66-2794 TCGA-66-2795 TCGA-68-7755 TCGA-68-7757 TCGA-68-8250 
         913         1645          122           83          211          244 
TCGA-68-A59I TCGA-68-A59J TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 
         121          104         1950         1941         1942         1952 
TCGA-77-7138 TCGA-77-7142 TCGA-77-7337 TCGA-77-7338 TCGA-77-7465 TCGA-77-8008 
        1959         1286         1942         1952          479         1945 
TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8139 
        1641         1953         1945         1941         1941         1951 
TCGA-77-8140 TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 TCGA-77-8153 TCGA-77-8154 
        1962          833         1943          293         1684         1092 
TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G8 
          10         1953         1942         1959         1955         1290 
TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 
        1280         1939          839          395           34           18 
TCGA-85-7697 TCGA-85-7698 TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 
          10           49         1965           35          911           60 
TCGA-85-8048 TCGA-85-8049 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 
          26           60          960          428          513           13 
TCGA-85-8277 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 
          11           54           60           55           67           54 
TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4PA 
          61           61           22          475           15         1972 
TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A511 TCGA-85-A512 
        1960           25           19         1973         1972         1987 
TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 TCGA-90-7964 
          13          111          758          289           89          428 
TCGA-90-A4ED TCGA-90-A59Q TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 
         244          269          106          122          160           70 
TCGA-94-7033 TCGA-94-A4VJ TCGA-96-7544 TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL 
          87          430         1213          211          273          183 
TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-J1-A4AH TCGA-LA-A446 TCGA-MF-A522 
         256          413          224          222           36           83 
TCGA-NC-A5HE TCGA-NC-A5HG TCGA-NC-A5HI 
        1722         1548         1135 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                1                 1 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             3644              5287 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              757               555 
[1] "1.0 - 3644.0 (757.0)" "1.0 - 5287.0 (555.0)"
[1] "hr=" "1.4"
D15V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  8P GAIN MUTATED         0       13       37        1         9        17
  8P GAIN WILD-TYPE       1       59      100        0        43        54
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  8P GAIN MUTATED           18          8        4
  8P GAIN WILD-TYPE         39         12        2
D15V3, multiclass
            clus
vv           8P GAIN MUTATED 8P GAIN WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                13                59
  STAGE IB                37               100
  STAGE II                 1                 0
  STAGE IIA                9                43
  STAGE IIB               17                54
  STAGE IIIA              18                39
  STAGE IIIB               8                12
  STAGE IV                 4                 2
[1] 9 2
[1] 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    21  66  11  10
  8P GAIN WILD-TYPE  77 188  37  10
D15V4, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  T1              21                77
  T2              66               188
  T3              11                37
  T4              10                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  8P GAIN MUTATED    66  27  10   2
  8P GAIN WILD-TYPE 195  86  25   3
D15V5, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  N0              66               195
  N1              27                86
  N2              10                25
  N3               2                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A  MX
  8P GAIN MUTATED    93   4   0  11
  8P GAIN WILD-TYPE 265   1   1  39
D15V6, multiclass
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  M0               93               265
  M1                4                 1
  M1A               0                 1
  MX               11                39
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V7, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    29  79
  8P GAIN WILD-TYPE  78 234
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     29   79
  8P GAIN WILD-TYPE   78  234
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE              29                78
  MALE                79               234
[1] 2 2
[1] FALSE
D15V8, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  8P GAIN MUTATED                                       2
  8P GAIN WILD-TYPE                                    10
                   vv
clus                LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  8P GAIN MUTATED                                        1
  8P GAIN WILD-TYPE                                      5
                   vv
clus                LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  8P GAIN MUTATED                                         1
  8P GAIN WILD-TYPE                                       0
                   vv
clus                LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  8P GAIN MUTATED                                                           104
  8P GAIN WILD-TYPE                                                         297
D15V9, multiclass
                                                             clus
vv                                                            8P GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     2
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             104
                                                             clus
vv                                                            8P GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      10
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               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"
D15V10, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     4 104
  8P GAIN WILD-TYPE   9 303
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      4  104
  8P GAIN WILD-TYPE    9  303
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  NO                4                 9
  YES             104               303
[1] 2 2
[1] FALSE
D15V11, continuous
                   vv
clus                 R0  R1  R2  RX
  8P GAIN MUTATED    91   2   0   1
  8P GAIN WILD-TYPE 251   6   4  17
D15V12, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  R0              91               251
  R1               2                 6
  R2               0                 4
  RX               1                17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8P GAIN MUTATED       3                         4    74
  8P GAIN WILD-TYPE     6                        13   224
D15V13, multiclass
                           clus
vv                          8P GAIN MUTATED 8P GAIN WILD-TYPE
  ASIAN                                   3                 6
  BLACK OR AFRICAN AMERICAN               4                13
  WHITE                                  74               224
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V14, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     3  67
  8P GAIN WILD-TYPE   5 200
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      3   67
  8P GAIN WILD-TYPE    5  200
                        clus
vv                       8P GAIN MUTATED 8P GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 5
  NOT HISPANIC OR LATINO              67               200
[1] 2 2
[1] FALSE

Clustering(16) Variable = 8Q GAIN MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                 0   1
  8Q GAIN MUTATED   130  68
  8Q GAIN WILD-TYPE 135  55
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              198               190 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               68                55 
$`8Q GAIN MUTATED`
TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 
         136         2417          146         1415          345          396 
TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4083 TCGA-18-5595 
         862          758           50         1331          187          827 
TCGA-21-1070 TCGA-21-1075 TCGA-21-1079 TCGA-21-1081 TCGA-21-1082 TCGA-21-1083 
        3636         2134          965          284         3644          267 
TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-21-A5DI TCGA-22-1011 TCGA-22-1016 
        1268         1032          329          979           53          822 
TCGA-22-1017 TCGA-22-4596 TCGA-22-4605 TCGA-22-4613 TCGA-22-5472 TCGA-22-5473 
        1485           17         1946          358         1964         1933 
TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5481 TCGA-22-5482 
         445         1346           24         1651         1952          357 
TCGA-22-5485 TCGA-22-5489 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4533 TCGA-33-4583 
         916         1912           29         2524         1940         1941 
TCGA-33-4587 TCGA-33-4589 TCGA-34-2605 TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 
        1970         1948          881          951         1528         2062 
TCGA-34-5239 TCGA-34-5241 TCGA-34-5928 TCGA-34-8454 TCGA-37-3789 TCGA-37-4132 
         707          428          552          166           13          227 
TCGA-37-5819 TCGA-39-5016 TCGA-39-5019 TCGA-39-5022 TCGA-39-5024 TCGA-39-5028 
         103         2253         1361         1996         1964           52 
TCGA-39-5029 TCGA-39-5034 TCGA-39-5035 TCGA-39-5040 TCGA-43-2576 TCGA-43-2578 
         740         1107          474         1964         1223          684 
TCGA-43-2581 TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 TCGA-43-6647 TCGA-43-6770 
        1176         1007          349          849          757          310 
TCGA-43-7657 TCGA-43-8118 TCGA-43-A475 TCGA-43-A56V TCGA-52-7810 TCGA-52-7811 
         236         1971          296          366          923         1958 
TCGA-56-1622 TCGA-56-5897 TCGA-56-6545 TCGA-56-6546 TCGA-56-7731 TCGA-56-7822 
         881            3           62           26         1961            1 
TCGA-56-8504 TCGA-56-8622 TCGA-56-8628 TCGA-56-A49D TCGA-56-A4BX TCGA-56-A4ZK 
         178           55           16           38           46            4 
TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8393 TCGA-58-A46J TCGA-58-A46M TCGA-60-2695 
           4            8         1058         2589         1072          642 
TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2707 TCGA-60-2708 TCGA-60-2712 
         311         1950         1943          661         1963          274 
TCGA-60-2713 TCGA-60-2714 TCGA-60-2719 TCGA-60-2720 TCGA-60-2722 TCGA-60-2723 
        1731         1531         1297           97          908         1092 
TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 TCGA-63-7023 TCGA-66-2734 
         717          816          358         1973         1952         1311 
TCGA-66-2742 TCGA-66-2744 TCGA-66-2753 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 
         641           30           31           28           30           30 
TCGA-66-2763 TCGA-66-2767 TCGA-66-2769 TCGA-66-2770 TCGA-66-2773 TCGA-66-2777 
          30           61         1947          700         1946           61 
TCGA-66-2782 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2792 TCGA-66-2793 
        1954          699         1955          699          913         1952 
TCGA-66-2800 TCGA-68-7756 TCGA-68-8251 TCGA-68-A59I TCGA-77-6844 TCGA-77-7139 
        1492          202           96          121         1942         1968 
TCGA-77-7141 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 
          15         1954         1942         1952         1954          479 
TCGA-77-8007 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 
        1960         1641         1953         1945         1941         1941 
TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8148 TCGA-77-8150 
        1947         1946         1951         1962          293         1961 
TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GH TCGA-85-6560 TCGA-85-6798 
        1955         1963         1290          713          364           34 
TCGA-85-7699 TCGA-85-7843 TCGA-85-7950 TCGA-85-8052 TCGA-85-8070 TCGA-85-8287 
           1           35           60           16          960           13 
TCGA-85-8350 TCGA-85-8353 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8664 
          60           54           21          445          424            3 
TCGA-85-8666 TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A510 TCGA-85-A511 TCGA-85-A513 
         475         1960           25         1967         1972           24 
TCGA-85-A5B5 TCGA-90-7767 TCGA-90-7769 TCGA-90-A4EE TCGA-92-7340 TCGA-92-7341 
         111           89          358          331           82          106 
TCGA-94-7943 TCGA-94-A4VJ TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK 
         356          430         1344          189          211          273 
TCGA-98-8022 TCGA-98-8023 TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 TCGA-NC-A5HG 
         224          308          222           35          449         1548 

$`8Q GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3408 TCGA-18-3415 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 
         370         2464         1810           85         2754           92 
TCGA-21-1071 TCGA-21-1072 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1080 
        1426         3016         1852         1058          474         3724 
TCGA-21-5782 TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 
         962          608          223         1945          131         1952 
TCGA-22-1012 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4595 TCGA-22-4599 
         429          623         1067         1470          734         1161 
TCGA-22-4601 TCGA-22-4604 TCGA-22-4607 TCGA-22-5471 TCGA-22-5480 TCGA-22-5483 
        1057          399          587          965         1952          573 
TCGA-22-5491 TCGA-22-5492 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 
        1713          506         2979         1311         5287         1966 
TCGA-33-4586 TCGA-33-6738 TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 TCGA-34-2608 
         428          822           80         1874          958         1000 
TCGA-34-5234 TCGA-34-5240 TCGA-34-5927 TCGA-37-3783 TCGA-37-3792 TCGA-37-4129 
        1715          365          941          120           12          200 
TCGA-37-4130 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-39-5011 TCGA-39-5021 
         247          238          207           12         1454         1947 
TCGA-39-5027 TCGA-39-5030 TCGA-39-5031 TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 
        1849           59          833         1084         1086          544 
TCGA-43-3394 TCGA-43-6143 TCGA-43-6771 TCGA-43-7656 TCGA-43-7658 TCGA-43-8115 
         822          376         1936          212         1970          407 
TCGA-43-8116 TCGA-43-A474 TCGA-43-A56U TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 
         358          353          432          324          423           12 
TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 TCGA-52-7812 TCGA-56-5898 
          12          911          541         1948         1967          555 
TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 
          30           13           30           44           40           26 
TCGA-56-7730 TCGA-56-8503 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8629 
           6           41           36           63           17           34 
TCGA-56-A4BW TCGA-56-A4BY TCGA-56-A4ZJ TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 
           2           30           25          378          911         2167 
TCGA-58-A46L TCGA-58-A46N TCGA-60-2696 TCGA-60-2706 TCGA-60-2709 TCGA-60-2710 
        1723          910          109         1958         1505         1963 
TCGA-60-2711 TCGA-60-2715 TCGA-60-2716 TCGA-60-2721 TCGA-63-7020 TCGA-63-7021 
        1260         1075         1475          983         1957         1955 
TCGA-63-7022 TCGA-66-2727 TCGA-66-2737 TCGA-66-2754 TCGA-66-2758 TCGA-66-2759 
        1947         1967           61           61          639          762 
TCGA-66-2765 TCGA-66-2766 TCGA-66-2768 TCGA-66-2771 TCGA-66-2778 TCGA-66-2780 
          61           31           61          578          578         1956 
TCGA-66-2781 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2791 
         121          759           60          790         1217         1977 
TCGA-66-2794 TCGA-66-2795 TCGA-68-7755 TCGA-68-7757 TCGA-68-8250 TCGA-68-A59J 
        1645          122           83          211          244          104 
TCGA-77-6842 TCGA-77-6843 TCGA-77-6845 TCGA-77-7138 TCGA-77-7142 TCGA-77-8008 
        1950         1941         1952         1959         1286         1945 
TCGA-77-8144 TCGA-77-8145 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ 
         833         1943         1684         1092           10         1953 
TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF TCGA-85-6561 
        1942         1959         1280         1939          839          395 
TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7710 TCGA-85-7844 TCGA-85-8048 
          18           10           49         1965          911           26 
TCGA-85-8049 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8288 
          60          428          513           13           11           54 
TCGA-85-8351 TCGA-85-8352 TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 TCGA-85-A4CL 
          55           67           61           61           22           15 
TCGA-85-A4PA TCGA-85-A50M TCGA-85-A50Z TCGA-85-A512 TCGA-85-A53L TCGA-90-6837 
        1972           19         1973         1987           13          758 
TCGA-90-7766 TCGA-90-7964 TCGA-90-A4ED TCGA-90-A59Q TCGA-92-8063 TCGA-92-8064 
         289          428          244          269          122          160 
TCGA-92-8065 TCGA-94-7033 TCGA-96-7544 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 
          70           87         1213          183          256          413 
TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HE TCGA-NC-A5HI 
          36           83         1722         1135 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                1                 2 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             3644              5287 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              710               564 
[1] "1.0 - 3644.0 (710.0)" "2.0 - 5287.0 (564.0)"
[1] "hr=" "1.1"
D16V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  8Q GAIN MUTATED         1       29       69        0        23        45
  8Q GAIN WILD-TYPE       0       43       68        1        29        26
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  8Q GAIN MUTATED           33         10        6
  8Q GAIN WILD-TYPE         24         10        0
D16V3, multiclass
            clus
vv           8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  STAGE I                  1                 0
  STAGE IA                29                43
  STAGE IB                69                68
  STAGE II                 0                 1
  STAGE IIA               23                29
  STAGE IIB               45                26
  STAGE IIIA              33                24
  STAGE IIIB              10                10
  STAGE IV                 6                 0
[1] 9 2
[1] 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    41 135  29  12
  8Q GAIN WILD-TYPE  57 119  19   8
D16V4, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T1              41                57
  T2             135               119
  T3              29                19
  T4              12                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  8Q GAIN MUTATED   127  68  16   2
  8Q GAIN WILD-TYPE 134  45  19   3
D16V5, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  N0             127               134
  N1              68                45
  N2              16                19
  N3               2                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A  MX
  8Q GAIN MUTATED   188   5   1  22
  8Q GAIN WILD-TYPE 170   0   0  28
D16V6, multiclass
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  M0              188               170
  M1                5                 0
  M1A               1                 0
  MX               22                28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V7, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED    57 160
  8Q GAIN WILD-TYPE  50 153
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     57  160
  8Q GAIN WILD-TYPE   50  153
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE              57                50
  MALE               160               153
[1] 2 2
[1] FALSE
D16V8, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  8Q GAIN MUTATED                                       4
  8Q GAIN WILD-TYPE                                     8
                   vv
clus                LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  8Q GAIN MUTATED                                        3
  8Q GAIN WILD-TYPE                                      3
                   vv
clus                LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  8Q GAIN MUTATED                                         1
  8Q GAIN WILD-TYPE                                       0
                   vv
clus                LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  8Q GAIN MUTATED                                                           209
  8Q GAIN WILD-TYPE                                                         192
D16V9, multiclass
                                                             clus
vv                                                            8Q GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     4
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             209
                                                             clus
vv                                                            8Q GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       8
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               192
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V10, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED     8 209
  8Q GAIN WILD-TYPE   5 198
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      8  209
  8Q GAIN WILD-TYPE    5  198
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NO                8                 5
  YES             209               198
[1] 2 2
[1] FALSE
D16V11, continuous
                   vv
clus                 R0  R1  R2  RX
  8Q GAIN MUTATED   180   5   0   7
  8Q GAIN WILD-TYPE 162   3   4  11
D16V12, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  R0             180               162
  R1               5                 3
  R2               0                 4
  RX               7                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8Q GAIN MUTATED       5                        11   150
  8Q GAIN WILD-TYPE     4                         6   148
D16V13, multiclass
                           clus
vv                          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  ASIAN                                   5                 4
  BLACK OR AFRICAN AMERICAN              11                 6
  WHITE                                 150               148
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V14, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED     5 138
  8Q GAIN WILD-TYPE   3 129
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      5  138
  8Q GAIN WILD-TYPE    3  129
                        clus
vv                       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   5                 3
  NOT HISPANIC OR LATINO             138               129
[1] 2 2
[1] FALSE

Clustering(17) Variable = 9P GAIN MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                 0   1
  9P GAIN MUTATED    29  16
  9P GAIN WILD-TYPE 236 107
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               45               343 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               16               107 
$`9P GAIN MUTATED`
TCGA-18-3407 TCGA-18-3410 TCGA-18-3416 TCGA-22-4604 TCGA-22-5481 TCGA-33-4532 
         136          146          862          399         1952         2524 
TCGA-33-4533 TCGA-33-4566 TCGA-33-4583 TCGA-33-4586 TCGA-33-4589 TCGA-34-5239 
        1940         5287         1941          428         1948          707 
TCGA-34-5240 TCGA-37-3792 TCGA-37-4133 TCGA-39-5030 TCGA-39-5036 TCGA-43-6143 
         365           12          238           59         1084          376 
TCGA-43-7658 TCGA-43-A475 TCGA-46-6025 TCGA-51-4079 TCGA-52-7622 TCGA-60-2695 
        1970          296          324           12          541          642 
TCGA-60-2704 TCGA-60-2712 TCGA-60-2714 TCGA-60-2722 TCGA-66-2756 TCGA-68-7755 
        1943          274         1531          908           30           83 
TCGA-68-8250 TCGA-77-8007 TCGA-77-8133 TCGA-77-8136 TCGA-77-8150 TCGA-77-A5G3 
         244         1960         1941         1947         1961         1959 
TCGA-77-A5GA TCGA-77-A5GF TCGA-85-6561 TCGA-85-7698 TCGA-85-8070 TCGA-85-8072 
        1280          839          395           49          960          513 
TCGA-85-8277 TCGA-85-8353 TCGA-92-8064 
          11           54          160 

$`9P GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3408 TCGA-18-3409 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 
         370         2464         2417         1415          345          396 
TCGA-18-3415 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 
        1810          758           50         1331          187           85 
TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 
        2754           92          827         3636         1426         3016 
TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 
        2134         1852         1058          474          965         3724 
TCGA-21-1081 TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 
         284         3644          267          962         1268         1032 
TCGA-21-5787 TCGA-21-A5DI TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 
         329          979          608          223         1945          131 
TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 
        1952           53          429          822         1485          623 
TCGA-22-4593 TCGA-22-4594 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 
        1067         1470          734           17         1161         1057 
TCGA-22-4605 TCGA-22-4607 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 
        1946          587          358          965         1964         1933 
TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5482 
         445         1346           24         1651         1952          357 
TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 
         573          916         1912         1713          506           29 
TCGA-33-4538 TCGA-33-4547 TCGA-33-4582 TCGA-33-4587 TCGA-33-6738 TCGA-34-2596 
        2979         1311         1966         1970          822           80 
TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 
        1874          958          881         1000          951         1528 
TCGA-34-5232 TCGA-34-5234 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-8454 
        2062         1715          428          941          552          166 
TCGA-37-3783 TCGA-37-3789 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4135 
         120           13          200          247          227          207 
TCGA-37-4141 TCGA-37-5819 TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 
          12          103         1454         2253         1361         1947 
TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5031 
        1996         1964         1849           52          740          833 
TCGA-39-5034 TCGA-39-5035 TCGA-39-5037 TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 
        1107          474         1086          544         1964         1223 
TCGA-43-2578 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 
         684         1176          822         1007          349          849 
TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-7656 TCGA-43-7657 TCGA-43-8115 
         757          310         1936          212          236          407 
TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56U TCGA-43-A56V TCGA-46-6026 
         358         1971          353          432          366          423 
TCGA-51-4080 TCGA-51-4081 TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 
          12          911         1948          923         1958         1967 
TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 
         881            3          555           62           26           30 
TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 
          13           30           44           40           26            6 
TCGA-56-7731 TCGA-56-7822 TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 TCGA-56-8624 
        1961            1           41          178           55           36 
TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW 
          63           17           16           34           38            2 
TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS 
          46           30           25            4            4            8 
TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46L 
         378          911         2167         1058         2589         1723 
TCGA-58-A46M TCGA-58-A46N TCGA-60-2696 TCGA-60-2698 TCGA-60-2703 TCGA-60-2706 
        1072          910          109          311         1950         1958 
TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 TCGA-60-2713 
         661         1963         1505         1963         1260         1731 
TCGA-60-2715 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2723 
        1075         1475         1297           97          983         1092 
TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 
         717          816          358         1973         1957         1955 
TCGA-63-7022 TCGA-63-7023 TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 
        1947         1952         1967         1311           61          641 
TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2757 TCGA-66-2758 
          30           31           61           28           30          639 
TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 
         762           30           61           31           61           61 
TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 
        1947          700          578         1946           61          578 
TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 
        1956          121         1954          759           60          790 
TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 TCGA-66-2792 
        1217          699         1955          699         1977          913 
TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-68-7756 TCGA-68-7757 
        1952         1645          122         1492          202          211 
TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 
          96          121          104         1950         1941         1942 
TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 
        1952         1959         1968           15         1286         1954 
TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8008 TCGA-77-8009 
        1942         1952         1954          479         1945         1641 
TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 
        1953         1945         1941         1946         1951         1962 
TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 
         833         1943          293         1684         1092           10 
TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GB 
        1953         1942         1955         1963         1290         1939 
TCGA-77-A5GH TCGA-85-6560 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7699 
         713          364           34           18           10            1 
TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 
        1965           35          911           60           26           60 
TCGA-85-8052 TCGA-85-8071 TCGA-85-8276 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 
          16          428           13           13           54           60 
TCGA-85-8351 TCGA-85-8352 TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 
          55           67           61           61           22           21 
TCGA-85-8580 TCGA-85-8582 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4PA 
         445          424            3          475           15         1972 
TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 
        1960           25           19         1973         1967         1972 
TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7766 
        1987           24           13          111          758          289 
TCGA-90-7767 TCGA-90-7769 TCGA-90-7964 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q 
          89          358          428          244          331          269 
TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-92-8065 TCGA-94-7033 TCGA-94-7943 
          82          106          122           70           87          356 
TCGA-94-A4VJ TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK 
         430         1213         1344          189          211          273 
TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-J1-A4AH 
         183          256          413          224          308          222 
TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HE TCGA-NC-A5HG 
          35          449           36           83         1722         1548 
TCGA-NC-A5HI 
        1135 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               11                 1 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
             5287              3724 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
              541               661 
[1] "11.0 - 5287.0 (541.0)" "1.0 - 3724.0 (661.0)" 
[1] "hr=" "1.1"
D17V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  9P GAIN MUTATED         0        5       14        1         4        13
  9P GAIN WILD-TYPE       1       67      123        0        48        58
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  9P GAIN MUTATED            6          3        1
  9P GAIN WILD-TYPE         51         17        5
D17V3, multiclass
            clus
vv           9P GAIN MUTATED 9P GAIN WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                 5                67
  STAGE IB                14               123
  STAGE II                 1                 0
  STAGE IIA                4                48
  STAGE IIB               13                58
  STAGE IIIA               6                51
  STAGE IIIB               3                17
  STAGE IV                 1                 5
[1] 9 2
[1] 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  30   6   3
  9P GAIN WILD-TYPE  90 224  42  17
D17V4, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  T1               8                90
  T2              30               224
  T3               6                42
  T4               3                17
[1] 4 2
[1] 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    24  19   2   0
  9P GAIN WILD-TYPE 237  94  33   5
D17V5, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  N0              24               237
  N1              19                94
  N2               2                33
  N3               0                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A  MX
  9P GAIN MUTATED    43   1   0   2
  9P GAIN WILD-TYPE 315   4   1  48
D17V6, multiclass
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  M0               43               315
  M1                1                 4
  M1A               0                 1
  MX                2                48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V7, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    14  33
  9P GAIN WILD-TYPE  93 280
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     14   33
  9P GAIN WILD-TYPE   93  280
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE              14                93
  MALE                33               280
[1] 2 2
[1] FALSE
D17V8, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  9P GAIN MUTATED                                       3
  9P GAIN WILD-TYPE                                     9
                   vv
clus                LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  9P GAIN MUTATED                                        0
  9P GAIN WILD-TYPE                                      6
                   vv
clus                LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  9P GAIN MUTATED                                         0
  9P GAIN WILD-TYPE                                       1
                   vv
clus                LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  9P GAIN MUTATED                                                            44
  9P GAIN WILD-TYPE                                                         357
D17V9, multiclass
                                                             clus
vv                                                            9P GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     3
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    0
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              44
                                                             clus
vv                                                            9P GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       9
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               357
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V10, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     1  46
  9P GAIN WILD-TYPE  12 361
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      1   46
  9P GAIN WILD-TYPE   12  361
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  NO                1                12
  YES              46               361
[1] 2 2
[1] FALSE
D17V11, continuous
                   vv
clus                 R0  R1  R2  RX
  9P GAIN MUTATED    36   1   0   2
  9P GAIN WILD-TYPE 306   7   4  16
D17V12, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  R0              36               306
  R1               1                 7
  R2               0                 4
  RX               2                16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9P GAIN MUTATED       2                         3    31
  9P GAIN WILD-TYPE     7                        14   267
D17V13, multiclass
                           clus
vv                          9P GAIN MUTATED 9P GAIN WILD-TYPE
  ASIAN                                   2                 7
  BLACK OR AFRICAN AMERICAN               3                14
  WHITE                                  31               267
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V14, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     2  29
  9P GAIN WILD-TYPE   6 238
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      2   29
  9P GAIN WILD-TYPE    6  238
                        clus
vv                       9P GAIN MUTATED 9P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 6
  NOT HISPANIC OR LATINO              29               238
[1] 2 2
[1] FALSE

Clustering(18) Variable = 9Q GAIN MUTATION ANALYSIS
D18V1, survival
                   sevent
clus2                 0   1
  9Q GAIN MUTATED    49  24
  9Q GAIN WILD-TYPE 216  99
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               73               315 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               24                99 
$`9Q GAIN MUTATED`
TCGA-18-3407 TCGA-18-3410 TCGA-18-3412 TCGA-18-3416 TCGA-21-1072 TCGA-21-1076 
         136          146          345          862         3016         1852 
TCGA-22-0940 TCGA-22-0944 TCGA-22-4599 TCGA-22-4604 TCGA-22-4613 TCGA-22-5477 
         608          223         1161          399          358         1346 
TCGA-22-5483 TCGA-33-4533 TCGA-33-4566 TCGA-33-4583 TCGA-33-4586 TCGA-33-4589 
         573         1940         5287         1941          428         1948 
TCGA-34-2596 TCGA-34-5239 TCGA-37-3792 TCGA-37-4133 TCGA-39-5030 TCGA-39-5036 
          80          707           12          238           59         1084 
TCGA-43-3394 TCGA-43-5668 TCGA-43-6143 TCGA-43-7658 TCGA-43-A475 TCGA-46-6025 
         822          349          376         1970          296          324 
TCGA-51-4079 TCGA-52-7622 TCGA-52-7809 TCGA-56-7582 TCGA-56-A4BX TCGA-58-8391 
          12          541         1948           26           46         2167 
TCGA-58-A46M TCGA-60-2695 TCGA-60-2704 TCGA-60-2710 TCGA-60-2711 TCGA-60-2722 
        1072          642         1943         1963         1260          908 
TCGA-66-2744 TCGA-66-2756 TCGA-66-2757 TCGA-66-2770 TCGA-66-2792 TCGA-68-7755 
          30           30           30          700          913           83 
TCGA-77-7141 TCGA-77-7335 TCGA-77-7465 TCGA-77-8009 TCGA-77-8133 TCGA-77-8136 
          15         1954          479         1641         1941         1947 
TCGA-77-8144 TCGA-77-8150 TCGA-77-8153 TCGA-77-A5G3 TCGA-77-A5GA TCGA-77-A5GF 
         833         1961         1684         1959         1280          839 
TCGA-85-7696 TCGA-85-7698 TCGA-85-7844 TCGA-85-8070 TCGA-85-8072 TCGA-85-8277 
          18           49          911          960          513           11 
TCGA-85-8353 TCGA-85-8580 TCGA-85-A5B5 TCGA-90-7769 TCGA-96-A4JK TCGA-96-A4JL 
          54          445          111          358          273          183 
TCGA-L3-A524 
         449 

$`9Q GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3408 TCGA-18-3409 TCGA-18-3411 TCGA-18-3414 TCGA-18-3415 
         370         2464         2417         1415          396         1810 
TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 
         758           50         1331          187           85         2754 
TCGA-18-5592 TCGA-18-5595 TCGA-21-1070 TCGA-21-1071 TCGA-21-1075 TCGA-21-1077 
          92          827         3636         1426         2134         1058 
TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 TCGA-21-1083 
         474          965         3724          284         3644          267 
TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-21-A5DI TCGA-22-1000 
         962         1268         1032          329          979         1945 
TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-1017 
         131         1952           53          429          822         1485 
TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4595 TCGA-22-4596 TCGA-22-4601 
         623         1067         1470          734           17         1057 
TCGA-22-4605 TCGA-22-4607 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 
        1946          587          965         1964         1933          445 
TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 TCGA-22-5485 
          24         1651         1952         1952          357          916 
TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4538 
        1912         1713          506           29         2524         2979 
TCGA-33-4547 TCGA-33-4582 TCGA-33-4587 TCGA-33-6738 TCGA-34-2600 TCGA-34-2604 
        1311         1966         1970          822         1874          958 
TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 
         881         1000          951         1528         2062         1715 
TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-8454 TCGA-37-3783 
         365          428          941          552          166          120 
TCGA-37-3789 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4135 TCGA-37-4141 
          13          200          247          227          207           12 
TCGA-37-5819 TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 
         103         1454         2253         1361         1947         1996 
TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5031 TCGA-39-5034 
        1964         1849           52          740          833         1107 
TCGA-39-5035 TCGA-39-5037 TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 TCGA-43-2578 
         474         1086          544         1964         1223          684 
TCGA-43-2581 TCGA-43-3920 TCGA-43-5670 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 
        1176         1007          849          757          310         1936 
TCGA-43-7656 TCGA-43-7657 TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 
         212          236          407          358         1971          353 
TCGA-43-A56U TCGA-43-A56V TCGA-46-6026 TCGA-51-4080 TCGA-51-4081 TCGA-52-7810 
         432          366          423           12          911          923 
TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 
        1958         1967          881            3          555           62 
TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 
          26           30           13           30           44           40 
TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 
           6         1961            1           41          178           55 
TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D 
          36           63           17           16           34           38 
TCGA-56-A4BW TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS 
           2           30           25            4            4            8 
TCGA-58-8388 TCGA-58-8390 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46L TCGA-58-A46N 
         378          911         1058         2589         1723          910 
TCGA-60-2696 TCGA-60-2698 TCGA-60-2703 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 
         109          311         1950         1958          661         1963 
TCGA-60-2709 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2715 TCGA-60-2716 
        1505          274         1731         1531         1075         1475 
TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 
        1297           97          983         1092          717          816 
TCGA-60-2726 TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 
         358         1973         1957         1955         1947         1952 
TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2753 TCGA-66-2754 
        1967         1311           61          641           31           61 
TCGA-66-2755 TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 
          28          639          762           30           61           31 
TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 
          61           61         1947          578         1946           61 
TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 
         578         1956          121         1954          759           60 
TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 
         790         1217          699         1955          699         1977 
TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-68-7756 TCGA-68-7757 
        1952         1645          122         1492          202          211 
TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-77-6842 TCGA-77-6843 
         244           96          121          104         1950         1941 
TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7142 TCGA-77-7337 
        1942         1952         1959         1968         1286         1942 
TCGA-77-7338 TCGA-77-7463 TCGA-77-8007 TCGA-77-8008 TCGA-77-8128 TCGA-77-8130 
        1952         1954         1960         1945         1953         1945 
TCGA-77-8131 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8145 TCGA-77-8148 
        1941         1946         1951         1962         1943          293 
TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G6 TCGA-77-A5G7 
        1092           10         1953         1942         1955         1963 
TCGA-77-A5G8 TCGA-77-A5GB TCGA-77-A5GH TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 
        1290         1939          713          364          395           34 
TCGA-85-7697 TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 TCGA-85-7950 TCGA-85-8048 
          10            1         1965           35           60           26 
TCGA-85-8049 TCGA-85-8052 TCGA-85-8071 TCGA-85-8276 TCGA-85-8287 TCGA-85-8288 
          60           16          428           13           13           54 
TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 
          60           55           67           61           61           22 
TCGA-85-8481 TCGA-85-8582 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4PA 
          21          424            3          475           15         1972 
TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 
        1960           25           19         1973         1967         1972 
TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 
        1987           24           13          758          289           89 
TCGA-90-7964 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 
         428          244          331          269           82          106 
TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 TCGA-94-7943 TCGA-94-A4VJ 
         122          160           70           87          356          430 
TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-98-7454 TCGA-98-8021 
        1213         1344          189          211          256          413 
TCGA-98-8022 TCGA-98-8023 TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-LA-A446 TCGA-MF-A522 
         224          308          222           35           36           83 
TCGA-NC-A5HE TCGA-NC-A5HG TCGA-NC-A5HI 
        1722         1548         1135 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               11                 1 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             5287              3724 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
              573               684 
[1] "11.0 - 5287.0 (573.0)" "1.0 - 3724.0 (684.0)" 
[1] "hr=" "1.2"
D18V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  9Q GAIN MUTATED         0        8       27        1        12        16
  9Q GAIN WILD-TYPE       1       64      110        0        40        55
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  9Q GAIN MUTATED            8          4        1
  9Q GAIN WILD-TYPE         49         16        5
D18V3, multiclass
            clus
vv           9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                 8                64
  STAGE IB                27               110
  STAGE II                 1                 0
  STAGE IIA               12                40
  STAGE IIB               16                55
  STAGE IIIA               8                49
  STAGE IIIB               4                16
  STAGE IV                 1                 5
[1] 9 2
[1] 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    16  49   8   4
  9Q GAIN WILD-TYPE  82 205  40  16
D18V4, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  T1              16                82
  T2              49               205
  T3               8                40
  T4               4                16
[1] 4 2
[1] 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    43  29   4   0
  9Q GAIN WILD-TYPE 218  84  31   5
D18V5, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  N0              43               218
  N1              29                84
  N2               4                31
  N3               0                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A  MX
  9Q GAIN MUTATED    73   1   0   2
  9Q GAIN WILD-TYPE 285   4   1  48
D18V6, multiclass
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  M0               73               285
  M1                1                 4
  M1A               0                 1
  MX                2                48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V7, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    23  54
  9Q GAIN WILD-TYPE  84 259
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     23   54
  9Q GAIN WILD-TYPE   84  259
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE              23                84
  MALE                54               259
[1] 2 2
[1] FALSE
D18V8, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  9Q GAIN MUTATED                                       3
  9Q GAIN WILD-TYPE                                     9
                   vv
clus                LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  9Q GAIN MUTATED                                        0
  9Q GAIN WILD-TYPE                                      6
                   vv
clus                LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  9Q GAIN MUTATED                                         0
  9Q GAIN WILD-TYPE                                       1
                   vv
clus                LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  9Q GAIN MUTATED                                                            74
  9Q GAIN WILD-TYPE                                                         327
D18V9, multiclass
                                                             clus
vv                                                            9Q GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     3
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    0
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              74
                                                             clus
vv                                                            9Q GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       9
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               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"
D18V10, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     0  77
  9Q GAIN WILD-TYPE  13 330
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      0   77
  9Q GAIN WILD-TYPE   13  330
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  NO                0                13
  YES              77               330
[1] 2 2
[1] FALSE
D18V11, continuous
                   vv
clus                 R0  R1  R2  RX
  9Q GAIN MUTATED    67   1   0   1
  9Q GAIN WILD-TYPE 275   7   4  17
D18V12, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  R0              67               275
  R1               1                 7
  R2               0                 4
  RX               1                17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9Q GAIN MUTATED       3                         3    54
  9Q GAIN WILD-TYPE     6                        14   244
D18V13, multiclass
                           clus
vv                          9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  ASIAN                                   3                 6
  BLACK OR AFRICAN AMERICAN               3                14
  WHITE                                  54               244
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V14, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     2  47
  9Q GAIN WILD-TYPE   6 220
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      2   47
  9Q GAIN WILD-TYPE    6  220
                        clus
vv                       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 6
  NOT HISPANIC OR LATINO              47               220
[1] 2 2
[1] FALSE

Clustering(19) Variable = 10P GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                  0   1
  10P GAIN MUTATED    39  18
  10P GAIN WILD-TYPE 226 105
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                57                331 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                18                105 
$`10P GAIN MUTATED`
TCGA-18-3407 TCGA-18-3416 TCGA-18-3417 TCGA-21-1070 TCGA-21-1083 TCGA-21-5787 
         136          862          758         3636          267          329 
TCGA-22-0944 TCGA-22-1017 TCGA-22-5473 TCGA-33-4566 TCGA-34-2609 TCGA-34-5928 
         223         1485         1933         5287          951          552 
TCGA-37-4133 TCGA-37-4141 TCGA-43-3394 TCGA-43-5668 TCGA-43-5670 TCGA-46-6025 
         238           12          822          349          849          324 
TCGA-52-7811 TCGA-56-7222 TCGA-56-A4BX TCGA-56-A5DR TCGA-58-A46L TCGA-60-2698 
        1958           13           46            4         1723          311 
TCGA-60-2712 TCGA-60-2724 TCGA-60-2726 TCGA-63-6202 TCGA-66-2756 TCGA-66-2763 
         274          717          358         1973           30           30 
TCGA-66-2778 TCGA-66-2782 TCGA-66-2792 TCGA-77-7142 TCGA-77-7463 TCGA-77-8148 
         578         1954          913         1286         1954          293 
TCGA-77-8150 TCGA-77-A5G1 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-85-6560 TCGA-85-6561 
        1961         1942         1963         1290          364          395 
TCGA-85-7843 TCGA-85-8350 TCGA-85-8352 TCGA-85-8582 TCGA-85-A50M TCGA-85-A510 
          35           60           67          424           19         1967 
TCGA-85-A53L TCGA-90-7767 TCGA-90-A4ED TCGA-94-7943 TCGA-94-A4VJ TCGA-96-7545 
          13           89          244          356          430         1344 
TCGA-98-8022 TCGA-NC-A5HG TCGA-NC-A5HI 
         224         1548         1135 

$`10P GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 TCGA-18-3412 
         370         2464         2417          146         1415          345 
TCGA-18-3414 TCGA-18-3415 TCGA-18-3419 TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 
         396         1810           50         1331          187           85 
TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 
        2754           92          827         1426         3016         2134 
TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 
        1852         1058          474          965         3724          284 
TCGA-21-1082 TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 TCGA-21-A5DI TCGA-22-0940 
        3644          962         1268         1032          979          608 
TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 
        1945          131         1952           53          429          822 
TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 
         623         1067         1470          734           17         1161 
TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-4613 TCGA-22-5471 
        1057          399         1946          587          358          965 
TCGA-22-5472 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 
        1964          445         1346           24         1651         1952 
TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 
        1952          357          573          916         1912         1713 
TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 
         506           29         2524         1940         2979         1311 
TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-33-4589 TCGA-33-6738 
        1966         1941          428         1970         1948          822 
TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 TCGA-34-5231 
          80         1874          958          881         1000         1528 
TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 
        2062         1715          707          365          428          941 
TCGA-34-8454 TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 
         166          120           13           12          200          247 
TCGA-37-4132 TCGA-37-4135 TCGA-37-5819 TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 
         227          207          103         1454         2253         1361 
TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 
        1947         1996         1964         1849           52          740 
TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 
          59          833         1107          474         1084         1086 
TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 TCGA-43-2578 TCGA-43-2581 TCGA-43-3920 
         544         1964         1223          684         1176         1007 
TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-7656 TCGA-43-7657 
         376          757          310         1936          212          236 
TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 
        1970          407          358         1971          353          296 
TCGA-43-A56U TCGA-43-A56V TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 
         432          366          423           12           12          911 
TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 
         541         1948          923         1967          881            3 
TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 TCGA-56-7223 TCGA-56-7579 
         555           62           26           30           30           44 
TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-8503 
          40           26            6         1961            1           41 
TCGA-56-8504 TCGA-56-8622 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 
         178           55           36           63           17           16 
TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK 
          34           38            2           30           25            4 
TCGA-56-A5DS TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-8393 TCGA-58-A46J 
           8          378          911         2167         1058         2589 
TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 TCGA-60-2696 TCGA-60-2703 TCGA-60-2704 
        1072          910          642          109         1950         1943 
TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 
        1958          661         1963         1505         1963         1260 
TCGA-60-2713 TCGA-60-2714 TCGA-60-2715 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 
        1731         1531         1075         1475         1297           97 
TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 TCGA-60-2725 TCGA-63-7020 TCGA-63-7021 
         983          908         1092          816         1957         1955 
TCGA-63-7022 TCGA-63-7023 TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 
        1947         1952         1967         1311           61          641 
TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2757 TCGA-66-2758 
          30           31           61           28           30          639 
TCGA-66-2759 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 
         762           61           31           61           61         1947 
TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2780 TCGA-66-2781 
         700          578         1946           61         1956          121 
TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 
         759           60          790         1217          699         1955 
TCGA-66-2790 TCGA-66-2791 TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 
         699         1977         1952         1645          122         1492 
TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I 
          83          202          211          244           96          121 
TCGA-68-A59J TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 
         104         1950         1941         1942         1952         1959 
TCGA-77-7139 TCGA-77-7141 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7465 
        1968           15         1954         1942         1952          479 
TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 
        1960         1945         1641         1953         1945         1941 
TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8144 
        1941         1947         1946         1951         1962          833 
TCGA-77-8145 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G3 
        1943         1684         1092           10         1953         1959 
TCGA-77-A5G6 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6798 
        1955         1280         1939          839          713           34 
TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7844 
          18           10           49            1         1965          911 
TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 
          60           26           60           16          960          428 
TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 TCGA-85-8351 
         513           13           11           13           54           55 
TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 
          54           61           61           22           21          445 
TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR 
           3          475           15         1972         1960           25 
TCGA-85-A50Z TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 TCGA-85-A5B5 TCGA-90-6837 
        1973         1972         1987           24          111          758 
TCGA-90-7766 TCGA-90-7769 TCGA-90-7964 TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 
         289          358          428          331          269           82 
TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 TCGA-96-7544 
         106          122          160           70           87         1213 
TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 
         189          211          273          183          256          413 
TCGA-98-8023 TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-MF-A522 
         308          222           35          449           36           83 
TCGA-NC-A5HE 
        1722 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 4                  1 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              5287               3724 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
               424                699 
[1] "4.0 - 5287.0 (424.0)" "1.0 - 3724.0 (699.0)"
[1] "hr=" "1"  
D19V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  10P GAIN MUTATED         0       11       13        1         9        13
  10P GAIN WILD-TYPE       1       61      124        0        43        58
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  10P GAIN MUTATED           11          3        1
  10P GAIN WILD-TYPE         46         17        5
D19V3, multiclass
            clus
vv           10P GAIN MUTATED 10P GAIN WILD-TYPE
  STAGE I                   0                  1
  STAGE IA                 11                 61
  STAGE IB                 13                124
  STAGE II                  1                  0
  STAGE IIA                 9                 43
  STAGE IIB                13                 58
  STAGE IIIA               11                 46
  STAGE IIIB                3                 17
  STAGE IV                  1                  5
[1] 9 2
[1] 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    13  38  10   2
  10P GAIN WILD-TYPE  85 216  38  18
D19V4, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  T1               13                 85
  T2               38                216
  T3               10                 38
  T4                2                 18
[1] 4 2
[1] 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    35  20   5   1
  10P GAIN WILD-TYPE 226  93  30   4
D19V5, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  N0               35                226
  N1               20                 93
  N2                5                 30
  N3                1                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A  MX
  10P GAIN MUTATED    55   1   0   6
  10P GAIN WILD-TYPE 303   4   1  44
D19V6, multiclass
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  M0                55                303
  M1                 1                  4
  M1A                0                  1
  MX                 6                 44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V7, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    11  52
  10P GAIN WILD-TYPE  96 261
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     11   52
  10P GAIN WILD-TYPE   96  261
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE               11                 96
  MALE                 52                261
[1] 2 2
[1] FALSE
D19V8, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  10P GAIN MUTATED                                       2
  10P GAIN WILD-TYPE                                    10
                    vv
clus                 LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  10P GAIN MUTATED                                        0
  10P GAIN WILD-TYPE                                      6
                    vv
clus                 LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  10P GAIN MUTATED                                         0
  10P GAIN WILD-TYPE                                       1
                    vv
clus                 LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  10P GAIN MUTATED                                                            61
  10P GAIN WILD-TYPE                                                         340
D19V9, multiclass
                                                             clus
vv                                                            10P GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      2
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     0
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               61
                                                             clus
vv                                                            10P GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       10
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                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"
D19V10, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     2  61
  10P GAIN WILD-TYPE  11 346
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      2   61
  10P GAIN WILD-TYPE   11  346
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  NO                 2                 11
  YES               61                346
[1] 2 2
[1] FALSE
D19V11, continuous
                    vv
clus                  R0  R1  R2  RX
  10P GAIN MUTATED    52   0   1   1
  10P GAIN WILD-TYPE 290   8   3  17
D19V12, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  R0               52                290
  R1                0                  8
  R2                1                  3
  RX                1                 17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10P GAIN MUTATED       3                         4    42
  10P GAIN WILD-TYPE     6                        13   256
D19V13, multiclass
                           clus
vv                          10P GAIN MUTATED 10P GAIN WILD-TYPE
  ASIAN                                    3                  6
  BLACK OR AFRICAN AMERICAN                4                 13
  WHITE                                   42                256
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V14, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     1  41
  10P GAIN WILD-TYPE   7 226
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      1   41
  10P GAIN WILD-TYPE    7  226
                        clus
vv                       10P GAIN MUTATED 10P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  7
  NOT HISPANIC OR LATINO               41                226
[1] 2 2
[1] FALSE

Clustering(20) Variable = 10Q GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                  0   1
  10Q GAIN MUTATED    24  11
  10Q GAIN WILD-TYPE 241 112
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                35                353 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                11                112 
$`10Q GAIN MUTATED`
TCGA-18-3416 TCGA-21-1070 TCGA-21-1083 TCGA-21-5786 TCGA-21-5787 TCGA-22-5473 
         862         3636          267         1032          329         1933 
TCGA-33-4566 TCGA-33-4582 TCGA-34-2609 TCGA-34-5241 TCGA-34-5928 TCGA-37-4141 
        5287         1966          951          428          552           12 
TCGA-43-5670 TCGA-52-7811 TCGA-56-7222 TCGA-56-A5DR TCGA-60-2724 TCGA-60-2726 
         849         1958           13            4          717          358 
TCGA-63-6202 TCGA-77-7142 TCGA-77-8130 TCGA-77-8150 TCGA-77-A5G7 TCGA-85-6561 
        1973         1286         1945         1961         1963          395 
TCGA-85-7843 TCGA-85-8350 TCGA-85-8352 TCGA-85-A50M TCGA-85-A510 TCGA-85-A53L 
          35           60           67           19         1967           13 
TCGA-90-7767 TCGA-90-A4ED TCGA-94-7943 TCGA-94-A4VJ TCGA-NC-A5HG 
          89          244          356          430         1548 

$`10Q GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 
         370          136         2464         2417          146         1415 
TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 
         345          396         1810          758           50         1331 
TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1071 
         187           85         2754           92          827         1426 
TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 
        3016         2134         1852         1058          474          965 
TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 TCGA-21-5782 TCGA-21-5784 TCGA-21-A5DI 
        3724          284         3644          962         1268          979 
TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 
         608          223         1945          131         1952           53 
TCGA-22-1012 TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 
         429          822         1485          623         1067         1470 
TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 
         734           17         1161         1057          399         1946 
TCGA-22-4607 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5474 TCGA-22-5477 
         587          358          965         1964          445         1346 
TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 
          24         1651         1952         1952          357          573 
TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4532 
         916         1912         1713          506           29         2524 
TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 
        1940         2979         1311         1941          428         1970 
TCGA-33-4589 TCGA-33-6738 TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 
        1948          822           80         1874          958          881 
TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 
        1000         1528         2062         1715          707          365 
TCGA-34-5927 TCGA-34-8454 TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 
         941          166          120           13           12          200 
TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-5819 TCGA-39-5011 
         247          227          238          207          103         1454 
TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 
        2253         1361         1947         1996         1964         1849 
TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 
          52          740           59          833         1107          474 
TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 TCGA-43-2578 
        1084         1086          544         1964         1223          684 
TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 TCGA-43-6143 TCGA-43-6647 
        1176          822         1007          349          376          757 
TCGA-43-6770 TCGA-43-6771 TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 
         310         1936          212          236         1970          407 
TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V 
         358         1971          353          296          432          366 
TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 
         324          423           12           12          911          541 
TCGA-52-7809 TCGA-52-7810 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 
        1948          923         1967          881            3          555 
TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 
          62           26           30           30           44           40 
TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-8503 TCGA-56-8504 
          26            6         1961            1           41          178 
TCGA-56-8622 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 
          55           36           63           17           16           34 
TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK 
          38            2           46           30           25            4 
TCGA-56-A5DS TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-8393 TCGA-58-A46J 
           8          378          911         2167         1058         2589 
TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 TCGA-60-2696 TCGA-60-2698 
        1723         1072          910          642          109          311 
TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 
        1950         1943         1958          661         1963         1505 
TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2715 
        1963         1260          274         1731         1531         1075 
TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 
        1475         1297           97          983          908         1092 
TCGA-60-2725 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 TCGA-66-2727 
         816         1957         1955         1947         1952         1967 
TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 
        1311           61          641           30           31           61 
TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 
          28           30           30          639          762           30 
TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 
          61           31           61           61         1947          700 
TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 
         578         1946           61          578         1956          121 
TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 
        1954          759           60          790         1217          699 
TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 
        1955          699         1977          913         1952         1645 
TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 
         122         1492           83          202          211          244 
TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 
          96          121          104         1950         1941         1942 
TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 TCGA-77-7335 TCGA-77-7337 
        1952         1959         1968           15         1954         1942 
TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 
        1952         1954          479         1960         1945         1641 
TCGA-77-8128 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 
        1953         1941         1941         1947         1946         1951 
TCGA-77-8140 TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 TCGA-77-8153 TCGA-77-8154 
        1962          833         1943          293         1684         1092 
TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G8 
          10         1953         1942         1959         1955         1290 
TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6560 TCGA-85-6798 
        1280         1939          839          713          364           34 
TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7844 
          18           10           49            1         1965          911 
TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 
          60           26           60           16          960          428 
TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 TCGA-85-8351 
         513           13           11           13           54           55 
TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 
          54           61           61           22           21          445 
TCGA-85-8582 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A4QQ 
         424            3          475           15         1972         1960 
TCGA-85-A4QR TCGA-85-A50Z TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 TCGA-85-A5B5 
          25         1973         1972         1987           24          111 
TCGA-90-6837 TCGA-90-7766 TCGA-90-7769 TCGA-90-7964 TCGA-90-A4EE TCGA-90-A59Q 
         758          289          358          428          331          269 
TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 
          82          106          122          160           70           87 
TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL 
        1213         1344          189          211          273          183 
TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-J1-A4AH TCGA-L3-A4E7 
         256          413          224          308          222           35 
TCGA-L3-A524 TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HE TCGA-NC-A5HI 
         449           36           83         1722         1135 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 4                  1 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              5287               3724 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
               552                642 
[1] "4.0 - 5287.0 (552.0)" "1.0 - 3724.0 (642.0)"
[1] "hr=" "1.4"
D20V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  10Q GAIN MUTATED         0        8        8        0         6         7
  10Q GAIN WILD-TYPE       1       64      129        1        46        64
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  10Q GAIN MUTATED            6          0        0
  10Q GAIN WILD-TYPE         51         20        6
D20V3, multiclass
            clus
vv           10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  STAGE I                   0                  1
  STAGE IA                  8                 64
  STAGE IB                  8                129
  STAGE II                  0                  1
  STAGE IIA                 6                 46
  STAGE IIB                 7                 64
  STAGE IIIA                6                 51
  STAGE IIIB                0                 20
  STAGE IV                  0                  6
[1] 9 2
[1] 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     8  23   5   0
  10Q GAIN WILD-TYPE  90 231  43  20
D20V4, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  T1                8                 90
  T2               23                231
  T3                5                 43
  T4                0                 20
[1] 4 2
[1] 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    20  12   2   0
  10Q GAIN WILD-TYPE 241 101  33   5
D20V5, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  N0               20                241
  N1               12                101
  N2                2                 33
  N3                0                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A  MX
  10Q GAIN MUTATED    31   0   0   4
  10Q GAIN WILD-TYPE 327   5   1  46
D20V6, multiclass
     clus
vv    10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  M0                31                327
  M1                 0                  5
  M1A                0                  1
  MX                 4                 46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V7, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     7  29
  10Q GAIN WILD-TYPE 100 284
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      7   29
  10Q GAIN WILD-TYPE  100  284
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FEMALE                7                100
  MALE                 29                284
[1] 2 2
[1] FALSE
D20V8, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  10Q GAIN MUTATED                                       1
  10Q GAIN WILD-TYPE                                    11
                    vv
clus                 LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  10Q GAIN MUTATED                                        0
  10Q GAIN WILD-TYPE                                      6
                    vv
clus                 LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  10Q GAIN MUTATED                                         0
  10Q GAIN WILD-TYPE                                       1
                    vv
clus                 LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  10Q GAIN MUTATED                                                            35
  10Q GAIN WILD-TYPE                                                         366
D20V9, multiclass
                                                             clus
vv                                                            10Q GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     0
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               35
                                                             clus
vv                                                            10Q GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       11
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                366
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V10, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     2  34
  10Q GAIN WILD-TYPE  11 373
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      2   34
  10Q GAIN WILD-TYPE   11  373
     clus
vv    10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  NO                 2                 11
  YES               34                373
[1] 2 2
[1] FALSE
D20V11, continuous
                    vv
clus                  R0  R1  R2  RX
  10Q GAIN MUTATED    30   0   0   0
  10Q GAIN WILD-TYPE 312   8   4  18
D20V12, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  R0               30                312
  R1                0                  8
  R2                0                  4
  RX                0                 18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10Q GAIN MUTATED       2                         3    26
  10Q GAIN WILD-TYPE     7                        14   272
D20V13, multiclass
                           clus
vv                          10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  ASIAN                                    2                  7
  BLACK OR AFRICAN AMERICAN                3                 14
  WHITE                                   26                272
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V14, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     1  27
  10Q GAIN WILD-TYPE   7 240
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      1   27
  10Q GAIN WILD-TYPE    7  240
                        clus
vv                       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  7
  NOT HISPANIC OR LATINO               27                240
[1] 2 2
[1] FALSE

Clustering(21) Variable = 11P GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                  0   1
  11P GAIN MUTATED    38  24
  11P GAIN WILD-TYPE 227  99
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                62                326 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                24                 99 
$`11P GAIN MUTATED`
TCGA-18-3407 TCGA-18-3410 TCGA-21-1070 TCGA-21-1072 TCGA-21-1079 TCGA-22-1012 
         136          146         3636         3016          965          429 
TCGA-22-4591 TCGA-22-4594 TCGA-22-4595 TCGA-22-5491 TCGA-33-4582 TCGA-33-4583 
         623         1470          734         1713         1966         1941 
TCGA-34-5239 TCGA-39-5027 TCGA-39-5029 TCGA-39-5034 TCGA-39-5036 TCGA-43-2578 
         707         1849          740         1107         1084          684 
TCGA-43-5668 TCGA-43-5670 TCGA-43-6771 TCGA-43-A474 TCGA-46-6026 TCGA-52-7809 
         349          849         1936          353          423         1948 
TCGA-52-7810 TCGA-56-1622 TCGA-56-6545 TCGA-56-7730 TCGA-56-A49D TCGA-56-A4BX 
         923          881           62            6           38           46 
TCGA-60-2719 TCGA-60-2722 TCGA-63-7020 TCGA-66-2734 TCGA-66-2744 TCGA-66-2765 
        1297          908         1957         1311           30           61 
TCGA-66-2766 TCGA-66-2770 TCGA-66-2777 TCGA-66-2785 TCGA-66-2791 TCGA-68-7755 
          31          700           61           60         1977           83 
TCGA-77-6842 TCGA-77-6845 TCGA-77-7138 TCGA-77-7142 TCGA-77-7463 TCGA-77-8007 
        1950         1952         1959         1286         1954         1960 
TCGA-77-8139 TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G7 TCGA-77-A5GB TCGA-85-6560 
        1951         1942         1959         1963         1939          364 
TCGA-85-7950 TCGA-85-8276 TCGA-90-7767 TCGA-90-A4EE TCGA-92-8064 TCGA-94-7943 
          60           13           89          331          160          356 
TCGA-96-8169 TCGA-96-A4JK 
         189          273 

$`11P GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3408 TCGA-18-3409 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 
         370         2464         2417         1415          345          396 
TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4083 
        1810          862          758           50         1331          187 
TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1071 TCGA-21-1075 
          85         2754           92          827         1426         2134 
TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 
        1852         1058          474         3724          284         3644 
TCGA-21-1083 TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-21-A5DI 
         267          962         1268         1032          329          979 
TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 
         608          223         1945          131         1952           53 
TCGA-22-1016 TCGA-22-1017 TCGA-22-4593 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 
         822         1485         1067           17         1161         1057 
TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 
         399         1946          587          358          965         1964 
TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 
        1933          445         1346           24         1651         1952 
TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5492 
        1952          357          573          916         1912          506 
TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 
          29         2524         1940         2979         1311         5287 
TCGA-33-4586 TCGA-33-4587 TCGA-33-4589 TCGA-33-6738 TCGA-34-2596 TCGA-34-2600 
         428         1970         1948          822           80         1874 
TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 
         958          881         1000          951         1528         2062 
TCGA-34-5234 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-8454 
        1715          365          428          941          552          166 
TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 
         120           13           12          200          247          227 
TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5011 TCGA-39-5016 
         238          207           12          103         1454         2253 
TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5028 TCGA-39-5030 
        1361         1947         1996         1964           52           59 
TCGA-39-5031 TCGA-39-5035 TCGA-39-5037 TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 
         833          474         1086          544         1964         1223 
TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 
        1176          822         1007          376          757          310 
TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 
         212          236         1970          407          358         1971 
TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V TCGA-46-6025 TCGA-51-4079 TCGA-51-4080 
         296          432          366          324           12           12 
TCGA-51-4081 TCGA-52-7622 TCGA-52-7811 TCGA-52-7812 TCGA-56-5897 TCGA-56-5898 
         911          541         1958         1967            3          555 
TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 
          26           30           13           30           44           40 
TCGA-56-7582 TCGA-56-7731 TCGA-56-7822 TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 
          26         1961            1           41          178           55 
TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A4BW 
          36           63           17           16           34            2 
TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8388 
          30           25            4            4            8          378 
TCGA-58-8390 TCGA-58-8391 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46L TCGA-58-A46M 
         911         2167         1058         2589         1723         1072 
TCGA-58-A46N TCGA-60-2695 TCGA-60-2696 TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 
         910          642          109          311         1950         1943 
TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 
        1958          661         1963         1505         1963         1260 
TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2715 TCGA-60-2716 TCGA-60-2720 
         274         1731         1531         1075         1475           97 
TCGA-60-2721 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 
         983         1092          717          816          358         1973 
TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 TCGA-66-2727 TCGA-66-2737 TCGA-66-2742 
        1955         1947         1952         1967           61          641 
TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 
          31           61           28           30           30          639 
TCGA-66-2759 TCGA-66-2763 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 TCGA-66-2771 
         762           30           61           61         1947          578 
TCGA-66-2773 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 
        1946          578         1956          121         1954          759 
TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2792 
         790         1217          699         1955          699          913 
TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-68-7756 TCGA-68-7757 
        1952         1645          122         1492          202          211 
TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-77-6843 TCGA-77-6844 
         244           96          121          104         1941         1942 
TCGA-77-7139 TCGA-77-7141 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7465 
        1968           15         1954         1942         1952          479 
TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 
        1945         1641         1953         1945         1941         1941 
TCGA-77-8136 TCGA-77-8138 TCGA-77-8140 TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 
        1947         1946         1962          833         1943          293 
TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G6 
        1961         1684         1092           10         1953         1955 
TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6561 TCGA-85-6798 
        1290         1280          839          713          395           34 
TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 
          18           10           49            1         1965           35 
TCGA-85-7844 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 
         911           26           60           16          960          428 
TCGA-85-8072 TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 
         513           11           13           54           60           55 
TCGA-85-8352 TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 
          67           54           61           61           22           21 
TCGA-85-8580 TCGA-85-8582 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4PA 
         445          424            3          475           15         1972 
TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 
        1960           25           19         1973         1967         1972 
TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7766 
        1987           24           13          111          758          289 
TCGA-90-7769 TCGA-90-7964 TCGA-90-A4ED TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 
         358          428          244          269           82          106 
TCGA-92-8063 TCGA-92-8065 TCGA-94-7033 TCGA-94-A4VJ TCGA-96-7544 TCGA-96-7545 
         122           70           87          430         1213         1344 
TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 
         211          183          256          413          224          308 
TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HE 
         222           35          449           36           83         1722 
TCGA-NC-A5HG TCGA-NC-A5HI 
        1548         1135 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 6                  1 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              3636               5287 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             794.5              578.0 
[1] "6.0 - 3636.0 (794.5)" "1.0 - 5287.0 (578.0)"
[1] "hr=" "1.2"
D21V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  11P GAIN MUTATED         0        8       22        0        11        11
  11P GAIN WILD-TYPE       1       64      115        1        41        60
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  11P GAIN MUTATED           10          2        0
  11P GAIN WILD-TYPE         47         18        6
D21V3, multiclass
            clus
vv           11P GAIN MUTATED 11P GAIN WILD-TYPE
  STAGE I                   0                  1
  STAGE IA                  8                 64
  STAGE IB                 22                115
  STAGE II                  0                  1
  STAGE IIA                11                 41
  STAGE IIB                11                 60
  STAGE IIIA               10                 47
  STAGE IIIB                2                 18
  STAGE IV                  0                  6
[1] 9 2
[1] 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    14  37  12   1
  11P GAIN WILD-TYPE  84 217  36  19
D21V4, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  T1               14                 84
  T2               37                217
  T3               12                 36
  T4                1                 19
[1] 4 2
[1] 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    41  14   6   1
  11P GAIN WILD-TYPE 220  99  29   4
D21V5, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  N0               41                220
  N1               14                 99
  N2                6                 29
  N3                1                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A  MX
  11P GAIN MUTATED    56   0   0   7
  11P GAIN WILD-TYPE 302   5   1  43
D21V6, multiclass
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  M0                56                302
  M1                 0                  5
  M1A                0                  1
  MX                 7                 43
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V7, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    12  52
  11P GAIN WILD-TYPE  95 261
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     12   52
  11P GAIN WILD-TYPE   95  261
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE               12                 95
  MALE                 52                261
[1] 2 2
[1] FALSE
D21V8, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  11P GAIN MUTATED                                       1
  11P GAIN WILD-TYPE                                    11
                    vv
clus                 LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  11P GAIN MUTATED                                        1
  11P GAIN WILD-TYPE                                      5
                    vv
clus                 LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  11P GAIN MUTATED                                         0
  11P GAIN WILD-TYPE                                       1
                    vv
clus                 LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  11P GAIN MUTATED                                                            62
  11P GAIN WILD-TYPE                                                         339
D21V9, multiclass
                                                             clus
vv                                                            11P GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               62
                                                             clus
vv                                                            11P GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       11
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                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"
D21V10, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     2  62
  11P GAIN WILD-TYPE  11 345
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      2   62
  11P GAIN WILD-TYPE   11  345
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  NO                 2                 11
  YES               62                345
[1] 2 2
[1] FALSE
D21V11, continuous
                    vv
clus                  R0  R1  R2  RX
  11P GAIN MUTATED    50   1   1   4
  11P GAIN WILD-TYPE 292   7   3  14
D21V12, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  R0               50                292
  R1                1                  7
  R2                1                  3
  RX                4                 14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11P GAIN MUTATED       2                         1    43
  11P GAIN WILD-TYPE     7                        16   255
D21V13, multiclass
                           clus
vv                          11P GAIN MUTATED 11P GAIN WILD-TYPE
  ASIAN                                    2                  7
  BLACK OR AFRICAN AMERICAN                1                 16
  WHITE                                   43                255
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V14, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     1  34
  11P GAIN WILD-TYPE   7 233
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      1   34
  11P GAIN WILD-TYPE    7  233
                        clus
vv                       11P GAIN MUTATED 11P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  7
  NOT HISPANIC OR LATINO               34                233
[1] 2 2
[1] FALSE

Clustering(22) Variable = 11Q GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                  0   1
  11Q GAIN MUTATED    49  25
  11Q GAIN WILD-TYPE 216  98
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                74                314 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                25                 98 
$`11Q GAIN MUTATED`
TCGA-18-3410 TCGA-21-1070 TCGA-21-1072 TCGA-21-1079 TCGA-21-5786 TCGA-22-1012 
         146         3636         3016          965         1032          429 
TCGA-22-4591 TCGA-22-4594 TCGA-22-4595 TCGA-22-5491 TCGA-33-4582 TCGA-33-4583 
         623         1470          734         1713         1966         1941 
TCGA-34-5231 TCGA-34-5239 TCGA-37-4132 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 
        1528          707          227          207           12          103 
TCGA-39-5011 TCGA-39-5029 TCGA-39-5034 TCGA-39-5036 TCGA-43-2578 TCGA-43-5668 
        1454          740         1107         1084          684          349 
TCGA-43-5670 TCGA-43-6143 TCGA-43-6771 TCGA-52-7810 TCGA-56-1622 TCGA-56-5898 
         849          376         1936          923          881          555 
TCGA-56-6545 TCGA-56-7730 TCGA-56-A49D TCGA-56-A5DR TCGA-60-2719 TCGA-60-2720 
          62            6           38            4         1297           97 
TCGA-63-7020 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2759 TCGA-66-2763 
        1957         1311           61          641          762           30 
TCGA-66-2777 TCGA-66-2781 TCGA-66-2786 TCGA-66-2789 TCGA-66-2791 TCGA-68-7755 
          61          121          790         1955         1977           83 
TCGA-77-6842 TCGA-77-6845 TCGA-77-7138 TCGA-77-7141 TCGA-77-7142 TCGA-77-7337 
        1950         1952         1959           15         1286         1942 
TCGA-77-7463 TCGA-77-8007 TCGA-77-8139 TCGA-77-8154 TCGA-77-A5G1 TCGA-77-A5G7 
        1954         1960         1951         1092         1942         1963 
TCGA-77-A5GB TCGA-85-6560 TCGA-85-7843 TCGA-85-7950 TCGA-85-8276 TCGA-85-8353 
        1939          364           35           60           13           54 
TCGA-85-A510 TCGA-85-A53L TCGA-90-7767 TCGA-90-A4EE TCGA-92-8064 TCGA-94-7943 
        1967           13           89          331          160          356 
TCGA-94-A4VJ TCGA-96-A4JK 
         430          273 

$`11Q GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3411 TCGA-18-3412 
         370          136         2464         2417         1415          345 
TCGA-18-3414 TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 
         396         1810          862          758           50         1331 
TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1071 
         187           85         2754           92          827         1426 
TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1080 TCGA-21-1081 
        2134         1852         1058          474         3724          284 
TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 TCGA-21-5784 TCGA-21-5787 TCGA-21-A5DI 
        3644          267          962         1268          329          979 
TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 
         608          223         1945          131         1952           53 
TCGA-22-1016 TCGA-22-1017 TCGA-22-4593 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 
         822         1485         1067           17         1161         1057 
TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 
         399         1946          587          358          965         1964 
TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 
        1933          445         1346           24         1651         1952 
TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5492 
        1952          357          573          916         1912          506 
TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 
          29         2524         1940         2979         1311         5287 
TCGA-33-4586 TCGA-33-4587 TCGA-33-4589 TCGA-33-6738 TCGA-34-2596 TCGA-34-2600 
         428         1970         1948          822           80         1874 
TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 TCGA-34-5232 TCGA-34-5234 
         958          881         1000          951         2062         1715 
TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-8454 TCGA-37-3783 
         365          428          941          552          166          120 
TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4133 TCGA-39-5016 
          13           12          200          247          238         2253 
TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 
        1361         1947         1996         1964         1849           52 
TCGA-39-5030 TCGA-39-5031 TCGA-39-5035 TCGA-39-5037 TCGA-39-5039 TCGA-39-5040 
          59          833          474         1086          544         1964 
TCGA-43-2576 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-6647 TCGA-43-6770 
        1223         1176          822         1007          757          310 
TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 
         212          236         1970          407          358         1971 
TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V TCGA-46-6025 TCGA-46-6026 
         353          296          432          366          324          423 
TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 TCGA-52-7811 
          12           12          911          541         1948         1958 
TCGA-52-7812 TCGA-56-5897 TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 
        1967            3           26           30           13           30 
TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7731 TCGA-56-7822 TCGA-56-8503 
          44           40           26         1961            1           41 
TCGA-56-8504 TCGA-56-8622 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 
         178           55           36           63           17           16 
TCGA-56-8629 TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK 
          34            2           46           30           25            4 
TCGA-56-A5DS TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-8393 TCGA-58-A46J 
           8          378          911         2167         1058         2589 
TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 TCGA-60-2696 TCGA-60-2698 
        1723         1072          910          642          109          311 
TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 
        1950         1943         1958          661         1963         1505 
TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2715 
        1963         1260          274         1731         1531         1075 
TCGA-60-2716 TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 
        1475          983          908         1092          717          816 
TCGA-60-2726 TCGA-63-6202 TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 TCGA-66-2727 
         358         1973         1955         1947         1952         1967 
TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 
          30           31           61           28           30           30 
TCGA-66-2758 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 
         639           61           31           61           61         1947 
TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2778 TCGA-66-2780 TCGA-66-2782 
         700          578         1946          578         1956         1954 
TCGA-66-2783 TCGA-66-2785 TCGA-66-2787 TCGA-66-2788 TCGA-66-2790 TCGA-66-2792 
         759           60         1217          699          699          913 
TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-68-7756 TCGA-68-7757 
        1952         1645          122         1492          202          211 
TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-77-6843 TCGA-77-6844 
         244           96          121          104         1941         1942 
TCGA-77-7139 TCGA-77-7335 TCGA-77-7338 TCGA-77-7465 TCGA-77-8008 TCGA-77-8009 
        1968         1954         1952          479         1945         1641 
TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 
        1953         1945         1941         1941         1947         1946 
TCGA-77-8140 TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 
        1962          833         1943          293         1961         1684 
TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G8 TCGA-77-A5GA 
          10         1953         1959         1955         1290         1280 
TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 
         839          713          395           34           18           10 
TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7844 TCGA-85-8048 TCGA-85-8049 
          49            1         1965          911           26           60 
TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8277 TCGA-85-8287 
          16          960          428          513           11           13 
TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8354 TCGA-85-8355 
          54           60           55           67           61           61 
TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8664 TCGA-85-8666 
          22           21          445          424            3          475 
TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z 
          15         1972         1960           25           19         1973 
TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7766 
        1972         1987           24          111          758          289 
TCGA-90-7769 TCGA-90-7964 TCGA-90-A4ED TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 
         358          428          244          269           82          106 
TCGA-92-8063 TCGA-92-8065 TCGA-94-7033 TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 
         122           70           87         1213         1344          189 
TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 
         211          183          256          413          224          308 
TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HE 
         222           35          449           36           83         1722 
TCGA-NC-A5HG TCGA-NC-A5HI 
        1548         1135 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 4                  1 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              3636               5287 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             737.0              582.5 
[1] "4.0 - 3636.0 (737.0)" "1.0 - 5287.0 (582.5)"
[1] "hr=" "1.1"
D22V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  11Q GAIN MUTATED         0       15       21        0        11        12
  11Q GAIN WILD-TYPE       1       57      116        1        41        59
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  11Q GAIN MUTATED           12          4        3
  11Q GAIN WILD-TYPE         45         16        3
D22V3, multiclass
            clus
vv           11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  STAGE I                   0                  1
  STAGE IA                 15                 57
  STAGE IB                 21                116
  STAGE II                  0                  1
  STAGE IIA                11                 41
  STAGE IIB                12                 59
  STAGE IIIA               12                 45
  STAGE IIIB                4                 16
  STAGE IV                  3                  3
[1] 9 2
[1] 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    22  40  14   2
  11Q GAIN WILD-TYPE  76 214  34  18
D22V4, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T1               22                 76
  T2               40                214
  T3               14                 34
  T4                2                 18
[1] 4 2
[1] 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    50  17   7   2
  11Q GAIN WILD-TYPE 211  96  28   3
D22V5, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  N0               50                211
  N1               17                 96
  N2                7                 28
  N3                2                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A  MX
  11Q GAIN MUTATED    67   2   1   7
  11Q GAIN WILD-TYPE 291   3   0  43
D22V6, multiclass
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  M0                67                291
  M1                 2                  3
  M1A                1                  0
  MX                 7                 43
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V7, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    20  58
  11Q GAIN WILD-TYPE  87 255
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     20   58
  11Q GAIN WILD-TYPE   87  255
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE               20                 87
  MALE                 58                255
[1] 2 2
[1] FALSE
D22V8, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  11Q GAIN MUTATED                                       1
  11Q GAIN WILD-TYPE                                    11
                    vv
clus                 LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  11Q GAIN MUTATED                                        1
  11Q GAIN WILD-TYPE                                      5
                    vv
clus                 LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  11Q GAIN MUTATED                                         0
  11Q GAIN WILD-TYPE                                       1
                    vv
clus                 LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  11Q GAIN MUTATED                                                            76
  11Q GAIN WILD-TYPE                                                         325
D22V9, multiclass
                                                             clus
vv                                                            11Q GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               76
                                                             clus
vv                                                            11Q GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       11
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                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"
D22V10, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     1  77
  11Q GAIN WILD-TYPE  12 330
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      1   77
  11Q GAIN WILD-TYPE   12  330
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  NO                 1                 12
  YES               77                330
[1] 2 2
[1] FALSE
D22V11, continuous
                    vv
clus                  R0  R1  R2  RX
  11Q GAIN MUTATED    63   1   0   5
  11Q GAIN WILD-TYPE 279   7   4  13
D22V12, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  R0               63                279
  R1                1                  7
  R2                0                  4
  RX                5                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11Q GAIN MUTATED       2                         1    55
  11Q GAIN WILD-TYPE     7                        16   243
D22V13, multiclass
                           clus
vv                          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  ASIAN                                    2                  7
  BLACK OR AFRICAN AMERICAN                1                 16
  WHITE                                   55                243
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V14, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     1  44
  11Q GAIN WILD-TYPE   7 223
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      1   44
  11Q GAIN WILD-TYPE    7  223
                        clus
vv                       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  7
  NOT HISPANIC OR LATINO               44                223
[1] 2 2
[1] FALSE

Clustering(23) Variable = 12P GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                  0   1
  12P GAIN MUTATED   119  59
  12P GAIN WILD-TYPE 146  64
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               178                210 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                59                 64 
$`12P GAIN MUTATED`
TCGA-18-3410 TCGA-18-3412 TCGA-18-3417 TCGA-18-3421 TCGA-18-4083 TCGA-18-4721 
         146          345          758         1331          187         2754 
TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 TCGA-21-1077 TCGA-21-1079 TCGA-21-1083 
        3636         1426         3016         1058          965          267 
TCGA-21-5782 TCGA-21-5786 TCGA-21-5787 TCGA-21-A5DI TCGA-22-1012 TCGA-22-1017 
         962         1032          329          979          429         1485 
TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4595 TCGA-22-4599 TCGA-22-4601 
         623         1067         1470          734         1161         1057 
TCGA-22-4604 TCGA-22-5471 TCGA-22-5473 TCGA-22-5477 TCGA-22-5480 TCGA-22-5482 
         399          965         1933         1346         1952          357 
TCGA-22-5489 TCGA-22-5491 TCGA-33-4532 TCGA-33-4538 TCGA-33-4566 TCGA-33-4582 
        1912         1713         2524         2979         5287         1966 
TCGA-33-4583 TCGA-33-4586 TCGA-33-6738 TCGA-34-2596 TCGA-34-2605 TCGA-34-2609 
        1941          428          822           80          881          951 
TCGA-34-5231 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5928 TCGA-37-3792 
        1528          707          365          428          552           12 
TCGA-39-5019 TCGA-39-5021 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 
        1361         1947         1107          474         1084         1086 
TCGA-39-5040 TCGA-43-3394 TCGA-43-3920 TCGA-43-5670 TCGA-43-6770 TCGA-43-6771 
        1964          822         1007          849          310         1936 
TCGA-43-8115 TCGA-43-8116 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56V TCGA-46-6025 
         407          358          353          296          366          324 
TCGA-46-6026 TCGA-51-4079 TCGA-51-4081 TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 
         423           12          911         1948          923         1958 
TCGA-52-7812 TCGA-56-6545 TCGA-56-6546 TCGA-56-7222 TCGA-56-7223 TCGA-56-7582 
        1967           62           26           13           30           26 
TCGA-56-7730 TCGA-56-7822 TCGA-56-8504 TCGA-56-8629 TCGA-56-A4BW TCGA-56-A4BX 
           6            1          178           34            2           46 
TCGA-56-A5DR TCGA-60-2695 TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 
           4          642          311         1950         1943         1958 
TCGA-60-2708 TCGA-60-2711 TCGA-60-2712 TCGA-60-2719 TCGA-60-2723 TCGA-60-2724 
        1963         1260          274         1297         1092          717 
TCGA-60-2725 TCGA-60-2726 TCGA-63-7020 TCGA-63-7023 TCGA-66-2727 TCGA-66-2744 
         816          358         1957         1952         1967           30 
TCGA-66-2754 TCGA-66-2756 TCGA-66-2758 TCGA-66-2766 TCGA-66-2767 TCGA-66-2769 
          61           30          639           31           61         1947 
TCGA-66-2777 TCGA-66-2781 TCGA-66-2785 TCGA-66-2787 TCGA-66-2793 TCGA-66-2794 
          61          121           60         1217         1952         1645 
TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I 
        1492           83          202          244           96          121 
TCGA-68-A59J TCGA-77-6842 TCGA-77-7141 TCGA-77-7142 TCGA-77-7337 TCGA-77-7463 
         104         1950           15         1286         1942         1954 
TCGA-77-7465 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8133 TCGA-77-8138 
         479         1641         1953         1945         1941         1946 
TCGA-77-8148 TCGA-77-8156 TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 
         293           10         1942         1959         1955         1963 
TCGA-77-A5G8 TCGA-77-A5GF TCGA-85-6560 TCGA-85-7696 TCGA-85-7697 TCGA-85-7699 
        1290          839          364           18           10            1 
TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8276 
          60           26           60           16          960           13 
TCGA-85-8277 TCGA-85-8287 TCGA-85-8350 TCGA-85-8352 TCGA-85-8354 TCGA-85-8481 
          11           13           60           67           61           21 
TCGA-85-8664 TCGA-85-8666 TCGA-85-A4QR TCGA-85-A510 TCGA-85-A511 TCGA-85-A513 
           3          475           25         1967         1972           24 
TCGA-85-A53L TCGA-90-7767 TCGA-90-7769 TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 
          13           89          358          331          269           82 
TCGA-92-7341 TCGA-92-8064 TCGA-94-7943 TCGA-94-A4VJ TCGA-96-A4JK TCGA-J1-A4AH 
         106          160          356          430          273          222 
TCGA-L3-A524 TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HG 
         449           36           83         1548 

$`12P GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3411 TCGA-18-3414 
         370          136         2464         2417         1415          396 
TCGA-18-3415 TCGA-18-3416 TCGA-18-3419 TCGA-18-4086 TCGA-18-5592 TCGA-18-5595 
        1810          862           50           85           92          827 
TCGA-21-1075 TCGA-21-1076 TCGA-21-1078 TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 
        2134         1852          474         3724          284         3644 
TCGA-21-5784 TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 
        1268          608          223         1945          131         1952 
TCGA-22-1011 TCGA-22-1016 TCGA-22-4596 TCGA-22-4605 TCGA-22-4607 TCGA-22-4613 
          53          822           17         1946          587          358 
TCGA-22-5472 TCGA-22-5474 TCGA-22-5478 TCGA-22-5479 TCGA-22-5481 TCGA-22-5483 
        1964          445           24         1651         1952          573 
TCGA-22-5485 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4533 TCGA-33-4547 TCGA-33-4587 
         916          506           29         1940         1311         1970 
TCGA-33-4589 TCGA-34-2600 TCGA-34-2604 TCGA-34-2608 TCGA-34-5232 TCGA-34-5234 
        1948         1874          958         1000         2062         1715 
TCGA-34-5927 TCGA-34-8454 TCGA-37-3783 TCGA-37-3789 TCGA-37-4129 TCGA-37-4130 
         941          166          120           13          200          247 
TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5011 
         227          238          207           12          103         1454 
TCGA-39-5016 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 
        2253         1996         1964         1849           52          740 
TCGA-39-5030 TCGA-39-5031 TCGA-39-5039 TCGA-43-2576 TCGA-43-2578 TCGA-43-2581 
          59          833          544         1223          684         1176 
TCGA-43-5668 TCGA-43-6143 TCGA-43-6647 TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 
         349          376          757          212          236         1970 
TCGA-43-8118 TCGA-43-A56U TCGA-51-4080 TCGA-52-7622 TCGA-56-1622 TCGA-56-5897 
        1971          432           12          541          881            3 
TCGA-56-5898 TCGA-56-7221 TCGA-56-7579 TCGA-56-7580 TCGA-56-7731 TCGA-56-8503 
         555           30           44           40         1961           41 
TCGA-56-8622 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-A49D 
          55           36           63           17           16           38 
TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DS TCGA-58-8388 TCGA-58-8390 
          30           25            4            8          378          911 
TCGA-58-8391 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N 
        2167         1058         2589         1723         1072          910 
TCGA-60-2696 TCGA-60-2707 TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 TCGA-60-2714 
         109          661         1505         1963         1731         1531 
TCGA-60-2715 TCGA-60-2716 TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 TCGA-63-6202 
        1075         1475           97          983          908         1973 
TCGA-63-7021 TCGA-63-7022 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2753 
        1955         1947         1311           61          641           31 
TCGA-66-2755 TCGA-66-2757 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2768 
          28           30          762           30           61           61 
TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2778 TCGA-66-2780 TCGA-66-2782 
         700          578         1946          578         1956         1954 
TCGA-66-2783 TCGA-66-2786 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 
         759          790          699         1955          699         1977 
TCGA-66-2792 TCGA-66-2795 TCGA-68-7757 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 
         913          122          211         1941         1942         1952 
TCGA-77-7138 TCGA-77-7139 TCGA-77-7335 TCGA-77-7338 TCGA-77-8007 TCGA-77-8008 
        1959         1968         1954         1952         1960         1945 
TCGA-77-8131 TCGA-77-8136 TCGA-77-8139 TCGA-77-8140 TCGA-77-8144 TCGA-77-8145 
        1941         1947         1951         1962          833         1943 
TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5GA TCGA-77-A5GB 
        1961         1684         1092         1953         1280         1939 
TCGA-77-A5GH TCGA-85-6561 TCGA-85-6798 TCGA-85-7698 TCGA-85-7710 TCGA-85-7843 
         713          395           34           49         1965           35 
TCGA-85-7844 TCGA-85-8071 TCGA-85-8072 TCGA-85-8288 TCGA-85-8351 TCGA-85-8353 
         911          428          513           54           55           54 
TCGA-85-8355 TCGA-85-8479 TCGA-85-8580 TCGA-85-8582 TCGA-85-A4CL TCGA-85-A4PA 
          61           22          445          424           15         1972 
TCGA-85-A4QQ TCGA-85-A50M TCGA-85-A50Z TCGA-85-A512 TCGA-85-A5B5 TCGA-90-6837 
        1960           19         1973         1987          111          758 
TCGA-90-7766 TCGA-90-7964 TCGA-90-A4ED TCGA-92-8063 TCGA-92-8065 TCGA-94-7033 
         289          428          244          122           70           87 
TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 
        1213         1344          189          211          183          256 
TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-L3-A4E7 TCGA-NC-A5HE TCGA-NC-A5HI 
         413          224          308           35         1722         1135 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 1                  3 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              5287               3724 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             477.0              699.5 
[1] "1.0 - 5287.0 (477.0)" "3.0 - 3724.0 (699.5)"
[1] "hr=" "1.3"
D23V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  12P GAIN MUTATED         1       26       57        1        30        35
  12P GAIN WILD-TYPE       0       46       80        0        22        36
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  12P GAIN MUTATED           33          8        2
  12P GAIN WILD-TYPE         24         12        4
D23V3, multiclass
            clus
vv           12P GAIN MUTATED 12P GAIN WILD-TYPE
  STAGE I                   1                  0
  STAGE IA                 26                 46
  STAGE IB                 57                 80
  STAGE II                  1                  0
  STAGE IIA                30                 22
  STAGE IIB                35                 36
  STAGE IIIA               33                 24
  STAGE IIIB                8                 12
  STAGE IV                  2                  4
[1] 9 2
[1] 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    36 121  25  12
  12P GAIN WILD-TYPE  62 133  23   8
D23V4, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  T1               36                 62
  T2              121                133
  T3               25                 23
  T4               12                  8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  12P GAIN MUTATED   115  57  19   1
  12P GAIN WILD-TYPE 146  56  16   4
D23V5, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  N0              115                146
  N1               57                 56
  N2               19                 16
  N3                1                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A  MX
  12P GAIN MUTATED   165   1   1  24
  12P GAIN WILD-TYPE 193   4   0  26
D23V6, multiclass
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  M0               165                193
  M1                 1                  4
  M1A                1                  0
  MX                24                 26
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V7, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    36 158
  12P GAIN WILD-TYPE  71 155
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     36  158
  12P GAIN WILD-TYPE   71  155
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE               36                 71
  MALE                158                155
[1] 2 2
[1] FALSE
D23V8, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  12P GAIN MUTATED                                       5
  12P GAIN WILD-TYPE                                     7
                    vv
clus                 LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  12P GAIN MUTATED                                        2
  12P GAIN WILD-TYPE                                      4
                    vv
clus                 LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  12P GAIN MUTATED                                         0
  12P GAIN WILD-TYPE                                       1
                    vv
clus                 LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  12P GAIN MUTATED                                                           187
  12P GAIN WILD-TYPE                                                         214
D23V9, multiclass
                                                             clus
vv                                                            12P GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      5
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              187
                                                             clus
vv                                                            12P GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                        7
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                214
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V10, binary
                    cls
clus                   0   1
  12P GAIN MUTATED     7 187
  12P GAIN WILD-TYPE   6 220
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      7  187
  12P GAIN WILD-TYPE    6  220
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  NO                 7                  6
  YES              187                220
[1] 2 2
[1] FALSE
D23V11, continuous
                    vv
clus                  R0  R1  R2  RX
  12P GAIN MUTATED   154   4   2   8
  12P GAIN WILD-TYPE 188   4   2  10
D23V12, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  R0              154                188
  R1                4                  4
  R2                2                  2
  RX                8                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12P GAIN MUTATED       4                        11   143
  12P GAIN WILD-TYPE     5                         6   155
D23V13, multiclass
                           clus
vv                          12P GAIN MUTATED 12P GAIN WILD-TYPE
  ASIAN                                    4                  5
  BLACK OR AFRICAN AMERICAN               11                  6
  WHITE                                  143                155
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V14, binary
                    cls
clus                   0   1
  12P GAIN MUTATED     4 129
  12P GAIN WILD-TYPE   4 138
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      4  129
  12P GAIN WILD-TYPE    4  138
                        clus
vv                       12P GAIN MUTATED 12P GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                  4
  NOT HISPANIC OR LATINO              129                138
[1] 2 2
[1] FALSE

Clustering(24) Variable = 12Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                  0   1
  12Q GAIN MUTATED    77  42
  12Q GAIN WILD-TYPE 188  81
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               119                269 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                42                 81 
$`12Q GAIN MUTATED`
TCGA-18-3410 TCGA-18-3412 TCGA-18-3417 TCGA-18-3421 TCGA-18-4083 TCGA-18-4721 
         146          345          758         1331          187         2754 
TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 TCGA-21-1077 TCGA-21-1083 TCGA-21-5786 
        3636         1426         3016         1058          267         1032 
TCGA-21-5787 TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 
         329          822         1485          623         1067         1470 
TCGA-22-4601 TCGA-22-4604 TCGA-22-5471 TCGA-22-5473 TCGA-22-5480 TCGA-22-5482 
        1057          399          965         1933         1952          357 
TCGA-22-5491 TCGA-33-4532 TCGA-33-4538 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 
        1713         2524         2979         1966         1941          428 
TCGA-34-2596 TCGA-34-2605 TCGA-34-2609 TCGA-34-5231 TCGA-34-5239 TCGA-37-3792 
          80          881          951         1528          707           12 
TCGA-37-4130 TCGA-37-5819 TCGA-39-5011 TCGA-39-5019 TCGA-39-5035 TCGA-39-5036 
         247          103         1454         1361          474         1084 
TCGA-39-5037 TCGA-43-3394 TCGA-43-3920 TCGA-43-6771 TCGA-43-8116 TCGA-43-A475 
        1086          822         1007         1936          358          296 
TCGA-46-6025 TCGA-51-4079 TCGA-52-7809 TCGA-52-7812 TCGA-56-6546 TCGA-56-7582 
         324           12         1948         1967           26           26 
TCGA-56-7822 TCGA-56-A4BX TCGA-56-A5DR TCGA-60-2695 TCGA-60-2698 TCGA-60-2704 
           1           46            4          642          311         1943 
TCGA-60-2706 TCGA-60-2708 TCGA-60-2712 TCGA-60-2715 TCGA-60-2719 TCGA-60-2724 
        1958         1963          274         1075         1297          717 
TCGA-60-2725 TCGA-60-2726 TCGA-63-7023 TCGA-66-2754 TCGA-66-2756 TCGA-66-2766 
         816          358         1952           61           30           31 
TCGA-66-2767 TCGA-66-2781 TCGA-66-2787 TCGA-66-2793 TCGA-66-2794 TCGA-66-2800 
          61          121         1217         1952         1645         1492 
TCGA-68-7755 TCGA-68-7756 TCGA-68-8251 TCGA-77-6842 TCGA-77-7142 TCGA-77-7465 
          83          202           96         1950         1286          479 
TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8133 TCGA-77-8148 TCGA-77-8150 
        1641         1953         1945         1941          293         1961 
TCGA-77-8154 TCGA-77-A5G3 TCGA-77-A5G7 TCGA-77-A5GF TCGA-85-7950 TCGA-85-8052 
        1092         1959         1963          839           60           16 
TCGA-85-8070 TCGA-85-8276 TCGA-85-8277 TCGA-85-8350 TCGA-85-8353 TCGA-85-8354 
         960           13           11           60           54           61 
TCGA-85-8664 TCGA-85-A4QR TCGA-85-A510 TCGA-85-A513 TCGA-85-A5B5 TCGA-90-7767 
           3           25         1967           24          111           89 
TCGA-90-7769 TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-94-7943 
         358          331          269           82          106          356 
TCGA-98-8023 TCGA-J1-A4AH TCGA-L3-A524 TCGA-LA-A446 TCGA-NC-A5HG 
         308          222          449           36         1548 

$`12Q GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3411 TCGA-18-3414 
         370          136         2464         2417         1415          396 
TCGA-18-3415 TCGA-18-3416 TCGA-18-3419 TCGA-18-4086 TCGA-18-5592 TCGA-18-5595 
        1810          862           50           85           92          827 
TCGA-21-1075 TCGA-21-1076 TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 
        2134         1852          474          965         3724          284 
TCGA-21-1082 TCGA-21-5782 TCGA-21-5784 TCGA-21-A5DI TCGA-22-0940 TCGA-22-0944 
        3644          962         1268          979          608          223 
TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-4595 
        1945          131         1952           53          429          734 
TCGA-22-4596 TCGA-22-4599 TCGA-22-4605 TCGA-22-4607 TCGA-22-4613 TCGA-22-5472 
          17         1161         1946          587          358         1964 
TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5481 TCGA-22-5483 
         445         1346           24         1651         1952          573 
TCGA-22-5485 TCGA-22-5489 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4533 TCGA-33-4547 
         916         1912          506           29         1940         1311 
TCGA-33-4566 TCGA-33-4587 TCGA-33-4589 TCGA-33-6738 TCGA-34-2600 TCGA-34-2604 
        5287         1970         1948          822         1874          958 
TCGA-34-2608 TCGA-34-5232 TCGA-34-5234 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 
        1000         2062         1715          365          428          941 
TCGA-34-5928 TCGA-34-8454 TCGA-37-3783 TCGA-37-3789 TCGA-37-4129 TCGA-37-4132 
         552          166          120           13          200          227 
TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-39-5016 TCGA-39-5021 TCGA-39-5022 
         238          207           12         2253         1947         1996 
TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 
        1964         1849           52          740           59          833 
TCGA-39-5034 TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 TCGA-43-2578 TCGA-43-2581 
        1107          544         1964         1223          684         1176 
TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-7656 
         349          849          376          757          310          212 
TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56U 
         236         1970          407         1971          353          432 
TCGA-43-A56V TCGA-46-6026 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7810 
         366          423           12          911          541          923 
TCGA-52-7811 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-7221 
        1958          881            3          555           62           30 
TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-7730 TCGA-56-7731 
          13           30           44           40            6         1961 
TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 
          41          178           55           36           63           17 
TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BY TCGA-56-A4ZJ 
          16           34           38            2           30           25 
TCGA-56-A4ZK TCGA-56-A5DS TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-8393 
           4            8          378          911         2167         1058 
TCGA-58-A46J TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2696 TCGA-60-2703 
        2589         1723         1072          910          109         1950 
TCGA-60-2707 TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 TCGA-60-2713 TCGA-60-2714 
         661         1505         1963         1260         1731         1531 
TCGA-60-2716 TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 TCGA-63-6202 
        1475           97          983          908         1092         1973 
TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 
        1957         1955         1947         1967         1311           61 
TCGA-66-2742 TCGA-66-2744 TCGA-66-2753 TCGA-66-2755 TCGA-66-2757 TCGA-66-2758 
         641           30           31           28           30          639 
TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 
         762           30           61           61         1947          700 
TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2782 
         578         1946           61          578         1956         1954 
TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 
         759           60          790          699         1955          699 
TCGA-66-2791 TCGA-66-2792 TCGA-66-2795 TCGA-68-7757 TCGA-68-8250 TCGA-68-A59I 
        1977          913          122          211          244          121 
TCGA-68-A59J TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 
         104         1941         1942         1952         1959         1968 
TCGA-77-7141 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-8007 
          15         1954         1942         1952         1954         1960 
TCGA-77-8008 TCGA-77-8131 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 
        1945         1941         1947         1946         1951         1962 
TCGA-77-8144 TCGA-77-8145 TCGA-77-8153 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 
         833         1943         1684           10         1953         1942 
TCGA-77-A5G6 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GH TCGA-85-6560 
        1955         1290         1280         1939          713          364 
TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 
         395           34           18           10           49            1 
TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 TCGA-85-8048 TCGA-85-8049 TCGA-85-8071 
        1965           35          911           26           60          428 
TCGA-85-8072 TCGA-85-8287 TCGA-85-8288 TCGA-85-8351 TCGA-85-8352 TCGA-85-8355 
         513           13           54           55           67           61 
TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8666 TCGA-85-A4CL 
          22           21          445          424          475           15 
TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50M TCGA-85-A50Z TCGA-85-A511 TCGA-85-A512 
        1972         1960           19         1973         1972         1987 
TCGA-85-A53L TCGA-90-6837 TCGA-90-7766 TCGA-90-7964 TCGA-90-A4ED TCGA-92-8063 
          13          758          289          428          244          122 
TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 TCGA-94-A4VJ TCGA-96-7544 TCGA-96-7545 
         160           70           87          430         1213         1344 
TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 
         189          211          273          183          256          413 
TCGA-98-8022 TCGA-L3-A4E7 TCGA-MF-A522 TCGA-NC-A5HE TCGA-NC-A5HI 
         224           35           83         1722         1135 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 1                  1 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              3636               5287 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               707                639 
[1] "1.0 - 3636.0 (707.0)" "1.0 - 5287.0 (639.0)"
[1] "hr=" "1.3"
D24V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  12Q GAIN MUTATED         0       22       33        1        19        23
  12Q GAIN WILD-TYPE       1       50      104        0        33        48
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  12Q GAIN MUTATED           25          7        2
  12Q GAIN WILD-TYPE         32         13        4
D24V3, multiclass
            clus
vv           12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  STAGE I                   0                  1
  STAGE IA                 22                 50
  STAGE IB                 33                104
  STAGE II                  1                  0
  STAGE IIA                19                 33
  STAGE IIB                23                 48
  STAGE IIIA               25                 32
  STAGE IIIB                7                 13
  STAGE IV                  2                  4
[1] 9 2
[1] 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    29  77  16  10
  12Q GAIN WILD-TYPE  69 177  32  10
D24V4, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T1               29                 69
  T2               77                177
  T3               16                 32
  T4               10                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  12Q GAIN MUTATED    71  43  15   1
  12Q GAIN WILD-TYPE 190  70  20   4
D24V5, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  N0               71                190
  N1               43                 70
  N2               15                 20
  N3                1                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A  MX
  12Q GAIN MUTATED   115   1   1  14
  12Q GAIN WILD-TYPE 243   4   0  36
D24V6, multiclass
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  M0               115                243
  M1                 1                  4
  M1A                1                  0
  MX                14                 36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V7, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    21 111
  12Q GAIN WILD-TYPE  86 202
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     21  111
  12Q GAIN WILD-TYPE   86  202
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE               21                 86
  MALE                111                202
[1] 2 2
[1] FALSE
D24V8, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  12Q GAIN MUTATED                                       4
  12Q GAIN WILD-TYPE                                     8
                    vv
clus                 LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  12Q GAIN MUTATED                                        1
  12Q GAIN WILD-TYPE                                      5
                    vv
clus                 LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  12Q GAIN MUTATED                                         0
  12Q GAIN WILD-TYPE                                       1
                    vv
clus                 LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  12Q GAIN MUTATED                                                           127
  12Q GAIN WILD-TYPE                                                         274
D24V9, multiclass
                                                             clus
vv                                                            12Q GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      4
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              127
                                                             clus
vv                                                            12Q GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                        8
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                274
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V10, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED     4 128
  12Q GAIN WILD-TYPE   9 279
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      4  128
  12Q GAIN WILD-TYPE    9  279
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  NO                 4                  9
  YES              128                279
[1] 2 2
[1] FALSE
D24V11, continuous
                    vv
clus                  R0  R1  R2  RX
  12Q GAIN MUTATED   109   3   1   6
  12Q GAIN WILD-TYPE 233   5   3  12
D24V12, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  R0              109                233
  R1                3                  5
  R2                1                  3
  RX                6                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12Q GAIN MUTATED       2                         7    97
  12Q GAIN WILD-TYPE     7                        10   201
D24V13, multiclass
                           clus
vv                          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  ASIAN                                    2                  7
  BLACK OR AFRICAN AMERICAN                7                 10
  WHITE                                   97                201
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V14, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED     3  88
  12Q GAIN WILD-TYPE   5 179
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      3   88
  12Q GAIN WILD-TYPE    5  179
                        clus
vv                       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  5
  NOT HISPANIC OR LATINO               88                179
[1] 2 2
[1] FALSE

Clustering(25) Variable = 13Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                  0   1
  13Q GAIN MUTATED    21   8
  13Q GAIN WILD-TYPE 244 115
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                29                359 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 8                115 
$`13Q GAIN MUTATED`
TCGA-18-3407 TCGA-18-3412 TCGA-21-1079 TCGA-21-1081 TCGA-21-1082 TCGA-22-4599 
         136          345          965          284         3644         1161 
TCGA-33-4533 TCGA-37-4130 TCGA-39-5034 TCGA-39-5035 TCGA-43-2576 TCGA-43-7657 
        1940          247         1107          474         1223          236 
TCGA-43-A56V TCGA-51-4081 TCGA-52-7810 TCGA-56-5897 TCGA-56-5898 TCGA-56-7223 
         366          911          923            3          555           30 
TCGA-56-7822 TCGA-56-A4BX TCGA-60-2698 TCGA-66-2737 TCGA-66-2791 TCGA-85-7696 
           1           46          311           61         1977           18 
TCGA-85-7843 TCGA-85-A50M TCGA-90-A59Q TCGA-94-7943 TCGA-MF-A522 
          35           19          269          356           83 

$`13Q GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 TCGA-18-3414 
         370         2464         2417          146         1415          396 
TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4083 
        1810          862          758           50         1331          187 
TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1070 TCGA-21-1071 
          85         2754           92          827         3636         1426 
TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1080 
        3016         2134         1852         1058          474         3724 
TCGA-21-1083 TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-21-A5DI 
         267          962         1268         1032          329          979 
TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 
         608          223         1945          131         1952           53 
TCGA-22-1012 TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 
         429          822         1485          623         1067         1470 
TCGA-22-4595 TCGA-22-4596 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 
         734           17         1057          399         1946          587 
TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 
         358          965         1964         1933          445         1346 
TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 
          24         1651         1952         1952          357          573 
TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4532 
         916         1912         1713          506           29         2524 
TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 
        2979         1311         5287         1966         1941          428 
TCGA-33-4587 TCGA-33-4589 TCGA-33-6738 TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 
        1970         1948          822           80         1874          958 
TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 
         881         1000          951         1528         2062         1715 
TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-8454 
         707          365          428          941          552          166 
TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-37-4132 TCGA-37-4133 
         120           13           12          200          227          238 
TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 
         207           12          103         1454         2253         1361 
TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 
        1947         1996         1964         1849           52          740 
TCGA-39-5030 TCGA-39-5031 TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 TCGA-39-5040 
          59          833         1084         1086          544         1964 
TCGA-43-2578 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 
         684         1176          822         1007          349          849 
TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-7656 TCGA-43-7658 
         376          757          310         1936          212         1970 
TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U 
         407          358         1971          353          296          432 
TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-52-7622 TCGA-52-7809 
         324          423           12           12          541         1948 
TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 
        1958         1967          881           62           26           30 
TCGA-56-7222 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 
          13           44           40           26            6         1961 
TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 
          41          178           55           36           63           17 
TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BY TCGA-56-A4ZJ 
          16           34           38            2           30           25 
TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 
           4            4            8          378          911         2167 
TCGA-58-8393 TCGA-58-A46J TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 
        1058         2589         1723         1072          910          642 
TCGA-60-2696 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 
         109         1950         1943         1958          661         1963 
TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 
        1505         1963         1260          274         1731         1531 
TCGA-60-2715 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 
        1075         1475         1297           97          983          908 
TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 TCGA-63-7020 
        1092          717          816          358         1973         1957 
TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 TCGA-66-2727 TCGA-66-2734 TCGA-66-2742 
        1955         1947         1952         1967         1311          641 
TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 
          30           31           61           28           30           30 
TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 
         639          762           30           61           31           61 
TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 
          61         1947          700          578         1946           61 
TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 
         578         1956          121         1954          759           60 
TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2792 
         790         1217          699         1955          699          913 
TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 
        1952         1645          122         1492           83          202 
TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-77-6842 
         211          244           96          121          104         1950 
TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 
        1941         1942         1952         1959         1968           15 
TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 
        1286         1954         1942         1952         1954          479 
TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 
        1960         1945         1641         1953         1945         1941 
TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8144 
        1941         1947         1946         1951         1962          833 
TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 
        1943          293         1961         1684         1092           10 
TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 
        1953         1942         1959         1955         1963         1290 
TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6560 TCGA-85-6561 
        1280         1939          839          713          364          395 
TCGA-85-6798 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7844 
          34           10           49            1         1965          911 
TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 
          60           26           60           16          960          428 
TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 
         513           13           11           13           54           60 
TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 
          55           67           54           61           61           22 
TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL 
          21          445          424            3          475           15 
TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 
        1972         1960           25         1973         1967         1972 
TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7766 
        1987           24           13          111          758          289 
TCGA-90-7767 TCGA-90-7769 TCGA-90-7964 TCGA-90-A4ED TCGA-90-A4EE TCGA-92-7340 
          89          358          428          244          331           82 
TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 TCGA-94-A4VJ 
         106          122          160           70           87          430 
TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL 
        1213         1344          189          211          273          183 
TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-J1-A4AH TCGA-L3-A4E7 
         256          413          224          308          222           35 
TCGA-L3-A524 TCGA-LA-A446 TCGA-NC-A5HE TCGA-NC-A5HG TCGA-NC-A5HI 
         449           36         1722         1548         1135 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 1                  1 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              3644               5287 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
               311                700 
[1] "1.0 - 3644.0 (311.0)" "1.0 - 5287.0 (700.0)"
[1] "hr=" "1.4"
D25V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  13Q GAIN MUTATED         0        5        8        0         6         7
  13Q GAIN WILD-TYPE       1       67      129        1        46        64
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  13Q GAIN MUTATED            4          1        1
  13Q GAIN WILD-TYPE         53         19        5
D25V3, multiclass
            clus
vv           13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  STAGE I                   0                  1
  STAGE IA                  5                 67
  STAGE IB                  8                129
  STAGE II                  0                  1
  STAGE IIA                 6                 46
  STAGE IIB                 7                 64
  STAGE IIIA                4                 53
  STAGE IIIB                1                 19
  STAGE IV                  1                  5
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  13Q GAIN MUTATED     7  19   5   1
  13Q GAIN WILD-TYPE  91 235  43  19
D25V4, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  T1                7                 91
  T2               19                235
  T3                5                 43
  T4                1                 19
[1] 4 2
[1] 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    20   8   2   1
  13Q GAIN WILD-TYPE 241 105  33   4
D25V5, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  N0               20                241
  N1                8                105
  N2                2                 33
  N3                1                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A  MX
  13Q GAIN MUTATED    24   0   1   7
  13Q GAIN WILD-TYPE 334   5   0  43
D25V6, multiclass
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  M0                24                334
  M1                 0                  5
  M1A                1                  0
  MX                 7                 43
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V7, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     8  24
  13Q GAIN WILD-TYPE  99 289
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      8   24
  13Q GAIN WILD-TYPE   99  289
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE                8                 99
  MALE                 24                289
[1] 2 2
[1] FALSE
D25V8, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  13Q GAIN MUTATED                                       0
  13Q GAIN WILD-TYPE                                    12
                    vv
clus                 LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  13Q GAIN MUTATED                                        1
  13Q GAIN WILD-TYPE                                      5
                    vv
clus                 LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  13Q GAIN MUTATED                                         0
  13Q GAIN WILD-TYPE                                       1
                    vv
clus                 LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  13Q GAIN MUTATED                                                            31
  13Q GAIN WILD-TYPE                                                         370
D25V9, multiclass
                                                             clus
vv                                                            13Q GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               31
                                                             clus
vv                                                            13Q GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       12
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                370
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V10, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     1  31
  13Q GAIN WILD-TYPE  12 376
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      1   31
  13Q GAIN WILD-TYPE   12  376
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  NO                 1                 12
  YES               31                376
[1] 2 2
[1] FALSE
D25V11, continuous
                    vv
clus                  R0  R1  R2  RX
  13Q GAIN MUTATED    24   1   0   2
  13Q GAIN WILD-TYPE 318   7   4  16
D25V12, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  R0               24                318
  R1                1                  7
  R2                0                  4
  RX                2                 16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  13Q GAIN MUTATED       3                         3    24
  13Q GAIN WILD-TYPE     6                        14   274
D25V13, multiclass
                           clus
vv                          13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  ASIAN                                    3                  6
  BLACK OR AFRICAN AMERICAN                3                 14
  WHITE                                   24                274
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V14, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     0  27
  13Q GAIN WILD-TYPE   8 240
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      0   27
  13Q GAIN WILD-TYPE    8  240
                        clus
vv                       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  8
  NOT HISPANIC OR LATINO               27                240
[1] 2 2
[1] FALSE

Clustering(26) Variable = 14Q GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                  0   1
  14Q GAIN MUTATED    72  26
  14Q GAIN WILD-TYPE 193  97
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                98                290 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                26                 97 
$`14Q GAIN MUTATED`
TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 TCGA-18-3415 TCGA-18-3421 TCGA-18-5592 
        2464         1415          345         1810         1331           92 
TCGA-21-1076 TCGA-21-1079 TCGA-21-1082 TCGA-21-5786 TCGA-22-4591 TCGA-22-4593 
        1852          965         3644         1032          623         1067 
TCGA-22-4595 TCGA-22-5471 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4533 TCGA-33-4566 
         734          965           29         2524         1940         5287 
TCGA-33-4582 TCGA-33-4589 TCGA-37-3792 TCGA-37-5819 TCGA-39-5011 TCGA-39-5029 
        1966         1948           12          103         1454          740 
TCGA-39-5031 TCGA-39-5037 TCGA-43-2578 TCGA-43-6143 TCGA-43-6771 TCGA-43-8118 
         833         1086          684          376         1936         1971 
TCGA-43-A474 TCGA-43-A56V TCGA-46-6025 TCGA-51-4081 TCGA-52-7622 TCGA-52-7811 
         353          366          324          911          541         1958 
TCGA-56-1622 TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-56-7580 TCGA-56-7730 
         881          555           62           26           40            6 
TCGA-56-8504 TCGA-56-8624 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4ZK TCGA-58-8393 
         178           36           34           38            4         1058 
TCGA-58-A46M TCGA-58-A46N TCGA-60-2698 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 
        1072          910          311         1958          661         1963 
TCGA-60-2719 TCGA-60-2722 TCGA-60-2724 TCGA-63-7020 TCGA-63-7022 TCGA-66-2744 
        1297          908          717         1957         1947           30 
TCGA-66-2756 TCGA-66-2763 TCGA-66-2765 TCGA-66-2771 TCGA-66-2782 TCGA-66-2788 
          30           30           61          578         1954          699 
TCGA-66-2792 TCGA-66-2793 TCGA-66-2800 TCGA-68-7755 TCGA-77-6845 TCGA-77-7138 
         913         1952         1492           83         1952         1959 
TCGA-77-7142 TCGA-77-7337 TCGA-77-7463 TCGA-77-8007 TCGA-77-8130 TCGA-77-8136 
        1286         1942         1954         1960         1945         1947 
TCGA-77-8139 TCGA-77-8150 TCGA-77-8153 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G8 
        1951         1961         1684         1959         1955         1290 
TCGA-85-6561 TCGA-85-7698 TCGA-85-8353 TCGA-85-8355 TCGA-85-A4QQ TCGA-85-A50M 
         395           49           54           61         1960           19 
TCGA-85-A5B5 TCGA-92-7340 TCGA-92-7341 TCGA-96-A4JK TCGA-L3-A4E7 TCGA-L3-A524 
         111           82          106          273           35          449 
TCGA-NC-A5HG TCGA-NC-A5HI 
        1548         1135 

$`14Q GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3414 TCGA-18-3416 
         370          136         2417          146          396          862 
TCGA-18-3417 TCGA-18-3419 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5595 
         758           50          187           85         2754          827 
TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 TCGA-21-1077 TCGA-21-1078 
        3636         1426         3016         2134         1058          474 
TCGA-21-1080 TCGA-21-1081 TCGA-21-1083 TCGA-21-5782 TCGA-21-5784 TCGA-21-5787 
        3724          284          267          962         1268          329 
TCGA-21-A5DI TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 
         979          608          223         1945          131         1952 
TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-1017 TCGA-22-4594 TCGA-22-4596 
          53          429          822         1485         1470           17 
TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-4613 
        1161         1057          399         1946          587          358 
TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 
        1964         1933          445         1346           24         1651 
TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 
        1952         1952          357          573          916         1912 
TCGA-22-5491 TCGA-22-5492 TCGA-33-4538 TCGA-33-4547 TCGA-33-4583 TCGA-33-4586 
        1713          506         2979         1311         1941          428 
TCGA-33-4587 TCGA-33-6738 TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 
        1970          822           80         1874          958          881 
TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 
        1000          951         1528         2062         1715          707 
TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-8454 TCGA-37-3783 
         365          428          941          552          166          120 
TCGA-37-3789 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 
          13          200          247          227          238          207 
TCGA-37-4141 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 
          12         2253         1361         1947         1996         1964 
TCGA-39-5027 TCGA-39-5028 TCGA-39-5030 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 
        1849           52           59         1107          474         1084 
TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 
         544         1964         1223         1176          822         1007 
TCGA-43-5668 TCGA-43-5670 TCGA-43-6647 TCGA-43-6770 TCGA-43-7656 TCGA-43-7657 
         349          849          757          310          212          236 
TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 TCGA-43-A475 TCGA-43-A56U TCGA-46-6026 
        1970          407          358          296          432          423 
TCGA-51-4079 TCGA-51-4080 TCGA-52-7809 TCGA-52-7810 TCGA-52-7812 TCGA-56-5897 
          12           12         1948          923         1967            3 
TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7582 TCGA-56-7731 
          30           13           30           44           26         1961 
TCGA-56-7822 TCGA-56-8503 TCGA-56-8622 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 
           1           41           55           63           17           16 
TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A5DR TCGA-56-A5DS 
           2           46           30           25            4            8 
TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-A46J TCGA-58-A46L TCGA-60-2695 
         378          911         2167         2589         1723          642 
TCGA-60-2696 TCGA-60-2703 TCGA-60-2704 TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 
         109         1950         1943         1505         1963         1260 
TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2715 TCGA-60-2716 TCGA-60-2720 
         274         1731         1531         1075         1475           97 
TCGA-60-2721 TCGA-60-2723 TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 TCGA-63-7021 
         983         1092          816          358         1973         1955 
TCGA-63-7023 TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2753 
        1952         1967         1311           61          641           31 
TCGA-66-2754 TCGA-66-2755 TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 TCGA-66-2766 
          61           28           30          639          762           31 
TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 TCGA-66-2773 TCGA-66-2777 
          61           61         1947          700         1946           61 
TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 
         578         1956          121          759           60          790 
TCGA-66-2787 TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 TCGA-66-2794 TCGA-66-2795 
        1217         1955          699         1977         1645          122 
TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J 
         202          211          244           96          121          104 
TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-7139 TCGA-77-7141 TCGA-77-7335 
        1950         1941         1942         1968           15         1954 
TCGA-77-7338 TCGA-77-7465 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8131 
        1952          479         1945         1641         1953         1941 
TCGA-77-8133 TCGA-77-8138 TCGA-77-8140 TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 
        1941         1946         1962          833         1943          293 
TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G7 TCGA-77-A5GA 
        1092           10         1953         1942         1963         1280 
TCGA-77-A5GB TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6560 TCGA-85-6798 TCGA-85-7696 
        1939          839          713          364           34           18 
TCGA-85-7697 TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 
          10            1         1965           35          911           60 
TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 
          26           60           16          960          428          513 
TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 
          13           11           13           54           60           55 
TCGA-85-8352 TCGA-85-8354 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 
          67           61           22           21          445          424 
TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A4QR TCGA-85-A50Z 
           3          475           15         1972           25         1973 
TCGA-85-A510 TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L TCGA-90-6837 
        1967         1972         1987           24           13          758 
TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 TCGA-90-7964 TCGA-90-A4ED TCGA-90-A4EE 
         289           89          358          428          244          331 
TCGA-90-A59Q TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 TCGA-94-7943 
         269          122          160           70           87          356 
TCGA-94-A4VJ TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL 
         430         1213         1344          189          211          183 
TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-J1-A4AH TCGA-LA-A446 
         256          413          224          308          222           36 
TCGA-MF-A522 TCGA-NC-A5HE 
          83         1722 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 4                  1 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              5287               3724 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             910.5              492.5 
[1] "4.0 - 5287.0 (910.5)" "1.0 - 3724.0 (492.5)"
[1] "hr=" "1.6"
D26V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  14Q GAIN MUTATED         0       12       37        0        12        24
  14Q GAIN WILD-TYPE       1       60      100        1        40        47
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  14Q GAIN MUTATED           18          3        1
  14Q GAIN WILD-TYPE         39         17        5
D26V3, multiclass
            clus
vv           14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  STAGE I                   0                  1
  STAGE IA                 12                 60
  STAGE IB                 37                100
  STAGE II                  0                  1
  STAGE IIA                12                 40
  STAGE IIB                24                 47
  STAGE IIIA               18                 39
  STAGE IIIB                3                 17
  STAGE IV                  1                  5
[1] 9 2
[1] 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    17  68  18   4
  14Q GAIN WILD-TYPE  81 186  30  16
D26V4, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  T1               17                 81
  T2               68                186
  T3               18                 30
  T4                4                 16
[1] 4 2
[1] 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    69  25  12   0
  14Q GAIN WILD-TYPE 192  88  23   5
D26V5, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  N0               69                192
  N1               25                 88
  N2               12                 23
  N3                0                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A  MX
  14Q GAIN MUTATED    97   0   1   8
  14Q GAIN WILD-TYPE 261   5   0  42
D26V6, multiclass
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  M0                97                261
  M1                 0                  5
  M1A                1                  0
  MX                 8                 42
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V7, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    26  81
  14Q GAIN WILD-TYPE  81 232
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     26   81
  14Q GAIN WILD-TYPE   81  232
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE               26                 81
  MALE                 81                232
[1] 2 2
[1] FALSE
D26V8, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  14Q GAIN MUTATED                                       3
  14Q GAIN WILD-TYPE                                     9
                    vv
clus                 LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  14Q GAIN MUTATED                                        1
  14Q GAIN WILD-TYPE                                      5
                    vv
clus                 LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  14Q GAIN MUTATED                                         0
  14Q GAIN WILD-TYPE                                       1
                    vv
clus                 LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  14Q GAIN MUTATED                                                           103
  14Q GAIN WILD-TYPE                                                         298
D26V9, multiclass
                                                             clus
vv                                                            14Q GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      3
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              103
                                                             clus
vv                                                            14Q GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                        9
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                298
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V10, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     3 104
  14Q GAIN WILD-TYPE  10 303
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      3  104
  14Q GAIN WILD-TYPE   10  303
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  NO                 3                 10
  YES              104                303
[1] 2 2
[1] FALSE
D26V11, continuous
                    vv
clus                  R0  R1  R2  RX
  14Q GAIN MUTATED    90   2   1   6
  14Q GAIN WILD-TYPE 252   6   3  12
D26V12, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  R0               90                252
  R1                2                  6
  R2                1                  3
  RX                6                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  14Q GAIN MUTATED       3                         3    72
  14Q GAIN WILD-TYPE     6                        14   226
D26V13, multiclass
                           clus
vv                          14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  ASIAN                                    3                  6
  BLACK OR AFRICAN AMERICAN                3                 14
  WHITE                                   72                226
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V14, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     5  59
  14Q GAIN WILD-TYPE   3 208
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      5   59
  14Q GAIN WILD-TYPE    3  208
                        clus
vv                       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    5                  3
  NOT HISPANIC OR LATINO               59                208
[1] 2 2
[1] FALSE

Clustering(27) Variable = 15Q GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                  0   1
  15Q GAIN MUTATED    58  27
  15Q GAIN WILD-TYPE 207  96
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                85                303 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                27                 96 
$`15Q GAIN MUTATED`
TCGA-18-3410 TCGA-18-3414 TCGA-18-3417 TCGA-18-3421 TCGA-18-4083 TCGA-21-1077 
         146          396          758         1331          187         1058 
TCGA-21-1079 TCGA-21-1082 TCGA-21-5786 TCGA-22-4593 TCGA-22-4604 TCGA-22-4605 
         965         3644         1032         1067          399         1946 
TCGA-22-5472 TCGA-22-5474 TCGA-22-5482 TCGA-22-5483 TCGA-33-4538 TCGA-33-4566 
        1964          445          357          573         2979         5287 
TCGA-33-4583 TCGA-34-2596 TCGA-34-2605 TCGA-34-2609 TCGA-34-5231 TCGA-34-5240 
        1941           80          881          951         1528          365 
TCGA-37-3792 TCGA-39-5037 TCGA-43-3394 TCGA-43-6770 TCGA-43-A475 TCGA-56-7222 
          12         1086          822          310          296           13 
TCGA-56-7579 TCGA-56-7582 TCGA-56-A5DR TCGA-58-8391 TCGA-58-8393 TCGA-60-2695 
          44           26            4         2167         1058          642 
TCGA-60-2696 TCGA-60-2706 TCGA-60-2710 TCGA-60-2711 TCGA-60-2719 TCGA-60-2722 
         109         1958         1963         1260         1297          908 
TCGA-60-2724 TCGA-60-2725 TCGA-63-7020 TCGA-66-2734 TCGA-66-2754 TCGA-66-2767 
         717          816         1957         1311           61           61 
TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-68-7755 TCGA-77-7141 
        1947          700          578         1946           83           15 
TCGA-77-7463 TCGA-77-7465 TCGA-77-8133 TCGA-77-8136 TCGA-77-8150 TCGA-77-A5G1 
        1954          479         1941         1947         1961         1942 
TCGA-77-A5GF TCGA-85-6561 TCGA-85-6798 TCGA-85-7844 TCGA-85-7950 TCGA-85-8049 
         839          395           34          911           60           60 
TCGA-85-8052 TCGA-85-8070 TCGA-85-8276 TCGA-85-8277 TCGA-85-8351 TCGA-85-8352 
          16          960           13           11           55           67 
TCGA-85-8354 TCGA-85-8481 TCGA-85-8664 TCGA-85-A50Z TCGA-85-A510 TCGA-90-7769 
          61           21            3         1973         1967          358 
TCGA-90-A59Q TCGA-92-7341 TCGA-94-7943 TCGA-96-7545 TCGA-L3-A524 TCGA-LA-A446 
         269          106          356         1344          449           36 
TCGA-NC-A5HE 
        1722 

$`15Q GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3411 TCGA-18-3412 
         370          136         2464         2417         1415          345 
TCGA-18-3415 TCGA-18-3416 TCGA-18-3419 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 
        1810          862           50           85         2754           92 
TCGA-18-5595 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 
         827         3636         1426         3016         2134         1852 
TCGA-21-1078 TCGA-21-1080 TCGA-21-1081 TCGA-21-1083 TCGA-21-5782 TCGA-21-5784 
         474         3724          284          267          962         1268 
TCGA-21-5787 TCGA-21-A5DI TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 
         329          979          608          223         1945          131 
TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 
        1952           53          429          822         1485          623 
TCGA-22-4594 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 TCGA-22-4607 
        1470          734           17         1161         1057          587 
TCGA-22-4613 TCGA-22-5471 TCGA-22-5473 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 
         358          965         1933         1346           24         1651 
TCGA-22-5480 TCGA-22-5481 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 
        1952         1952          916         1912         1713          506 
TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4533 TCGA-33-4547 TCGA-33-4582 TCGA-33-4586 
          29         2524         1940         1311         1966          428 
TCGA-33-4587 TCGA-33-4589 TCGA-33-6738 TCGA-34-2600 TCGA-34-2604 TCGA-34-2608 
        1970         1948          822         1874          958         1000 
TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 
        2062         1715          707          428          941          552 
TCGA-34-8454 TCGA-37-3783 TCGA-37-3789 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 
         166          120           13          200          247          227 
TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5011 TCGA-39-5016 
         238          207           12          103         1454         2253 
TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 
        1361         1947         1996         1964         1849           52 
TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 
         740           59          833         1107          474         1084 
TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 TCGA-43-2578 TCGA-43-2581 TCGA-43-3920 
         544         1964         1223          684         1176         1007 
TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 TCGA-43-6771 TCGA-43-7656 
         349          849          376          757         1936          212 
TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 
         236         1970          407          358         1971          353 
TCGA-43-A56U TCGA-43-A56V TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 
         432          366          324          423           12           12 
TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 
         911          541         1948          923         1958         1967 
TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 
         881            3          555           62           26           30 
TCGA-56-7223 TCGA-56-7580 TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-8503 
          30           40            6         1961            1           41 
TCGA-56-8504 TCGA-56-8622 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 
         178           55           36           63           17           16 
TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ 
          34           38            2           46           30           25 
TCGA-56-A4ZK TCGA-56-A5DS TCGA-58-8388 TCGA-58-8390 TCGA-58-A46J TCGA-58-A46L 
           4            8          378          911         2589         1723 
TCGA-58-A46M TCGA-58-A46N TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2707 
        1072          910          311         1950         1943          661 
TCGA-60-2708 TCGA-60-2709 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2715 
        1963         1505          274         1731         1531         1075 
TCGA-60-2716 TCGA-60-2720 TCGA-60-2721 TCGA-60-2723 TCGA-60-2726 TCGA-63-6202 
        1475           97          983         1092          358         1973 
TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 TCGA-66-2727 TCGA-66-2737 TCGA-66-2742 
        1955         1947         1952         1967           61          641 
TCGA-66-2744 TCGA-66-2753 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 
          30           31           28           30           30          639 
TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2768 TCGA-66-2777 
         762           30           61           31           61           61 
TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 
         578         1956          121         1954          759           60 
TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 
         790         1217          699         1955          699         1977 
TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-68-7756 
         913         1952         1645          122         1492          202 
TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-77-6842 
         211          244           96          121          104         1950 
TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7142 
        1941         1942         1952         1959         1968         1286 
TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 
        1954         1942         1952         1960         1945         1641 
TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 
        1953         1945         1941         1946         1951         1962 
TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 
         833         1943          293         1684         1092           10 
TCGA-77-A5FZ TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA 
        1953         1959         1955         1963         1290         1280 
TCGA-77-A5GB TCGA-77-A5GH TCGA-85-6560 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 
        1939          713          364           18           10           49 
TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 TCGA-85-8048 TCGA-85-8071 TCGA-85-8072 
           1         1965           35           26          428          513 
TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8353 TCGA-85-8355 TCGA-85-8479 
          13           54           60           54           61           22 
TCGA-85-8580 TCGA-85-8582 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A4QQ 
         445          424          475           15         1972         1960 
TCGA-85-A4QR TCGA-85-A50M TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L 
          25           19         1972         1987           24           13 
TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 TCGA-90-7964 TCGA-90-A4ED 
         111          758          289           89          428          244 
TCGA-90-A4EE TCGA-92-7340 TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 
         331           82          122          160           70           87 
TCGA-94-A4VJ TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL 
         430         1213          189          211          273          183 
TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-J1-A4AH TCGA-L3-A4E7 
         256          413          224          308          222           35 
TCGA-MF-A522 TCGA-NC-A5HG TCGA-NC-A5HI 
          83         1548         1135 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 3                  1 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              5287               3724 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
               700                639 
[1] "3.0 - 5287.0 (700.0)" "1.0 - 3724.0 (639.0)"
[1] "hr=" "1"  
D27V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  15Q GAIN MUTATED         0        8       30        0        15        17
  15Q GAIN WILD-TYPE       1       64      107        1        37        54
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  15Q GAIN MUTATED           14          4        3
  15Q GAIN WILD-TYPE         43         16        3
D27V3, multiclass
            clus
vv           15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  STAGE I                   0                  1
  STAGE IA                  8                 64
  STAGE IB                 30                107
  STAGE II                  0                  1
  STAGE IIA                15                 37
  STAGE IIB                17                 54
  STAGE IIIA               14                 43
  STAGE IIIB                4                 16
  STAGE IV                  3                  3
[1] 9 2
[1] 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    15  60  13   4
  15Q GAIN WILD-TYPE  83 194  35  16
D27V4, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  T1               15                 83
  T2               60                194
  T3               13                 35
  T4                4                 16
[1] 4 2
[1] 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    49  35   5   1
  15Q GAIN WILD-TYPE 212  78  30   4
D27V5, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  N0               49                212
  N1               35                 78
  N2                5                 30
  N3                1                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A  MX
  15Q GAIN MUTATED    80   2   1   8
  15Q GAIN WILD-TYPE 278   3   0  42
D27V6, multiclass
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  M0                80                278
  M1                 2                  3
  M1A                1                  0
  MX                 8                 42
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V7, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    20  72
  15Q GAIN WILD-TYPE  87 241
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     20   72
  15Q GAIN WILD-TYPE   87  241
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE               20                 87
  MALE                 72                241
[1] 2 2
[1] FALSE
D27V8, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  15Q GAIN MUTATED                                       3
  15Q GAIN WILD-TYPE                                     9
                    vv
clus                 LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  15Q GAIN MUTATED                                        1
  15Q GAIN WILD-TYPE                                      5
                    vv
clus                 LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  15Q GAIN MUTATED                                         0
  15Q GAIN WILD-TYPE                                       1
                    vv
clus                 LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  15Q GAIN MUTATED                                                            88
  15Q GAIN WILD-TYPE                                                         313
D27V9, multiclass
                                                             clus
vv                                                            15Q GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      3
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               88
                                                             clus
vv                                                            15Q GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                        9
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                313
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V10, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     2  90
  15Q GAIN WILD-TYPE  11 317
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      2   90
  15Q GAIN WILD-TYPE   11  317
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  NO                 2                 11
  YES               90                317
[1] 2 2
[1] FALSE
D27V11, continuous
                    vv
clus                  R0  R1  R2  RX
  15Q GAIN MUTATED    79   2   0   4
  15Q GAIN WILD-TYPE 263   6   4  14
D27V12, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  R0               79                263
  R1                2                  6
  R2                0                  4
  RX                4                 14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  15Q GAIN MUTATED       1                         5    68
  15Q GAIN WILD-TYPE     8                        12   230
D27V13, multiclass
                           clus
vv                          15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  ASIAN                                    1                  8
  BLACK OR AFRICAN AMERICAN                5                 12
  WHITE                                   68                230
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V14, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     1  64
  15Q GAIN WILD-TYPE   7 203
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      1   64
  15Q GAIN WILD-TYPE    7  203
                        clus
vv                       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  7
  NOT HISPANIC OR LATINO               64                203
[1] 2 2
[1] FALSE

Clustering(28) Variable = 16P GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                  0   1
  16P GAIN MUTATED    42  23
  16P GAIN WILD-TYPE 223 100
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                65                323 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                23                100 
$`16P GAIN MUTATED`
TCGA-18-3412 TCGA-18-3416 TCGA-18-5595 TCGA-21-1071 TCGA-21-1072 TCGA-21-1081 
         345          862          827         1426         3016          284 
TCGA-21-1083 TCGA-21-5787 TCGA-22-1011 TCGA-22-1017 TCGA-22-4593 TCGA-33-4532 
         267          329           53         1485         1067         2524 
TCGA-33-4566 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-34-2604 TCGA-34-5240 
        5287         1941          428         1970          958          365 
TCGA-34-5241 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5034 TCGA-39-5036 
         428          207           12          103         1107         1084 
TCGA-43-2576 TCGA-43-2578 TCGA-43-5668 TCGA-43-A56V TCGA-52-7811 TCGA-56-1622 
        1223          684          349          366         1958          881 
TCGA-56-6545 TCGA-56-7222 TCGA-56-7223 TCGA-56-8504 TCGA-56-A4BW TCGA-60-2706 
          62           13           30          178            2         1958 
TCGA-60-2722 TCGA-60-2725 TCGA-60-2726 TCGA-63-7020 TCGA-66-2737 TCGA-66-2756 
         908          816          358         1957           61           30 
TCGA-66-2767 TCGA-66-2768 TCGA-66-2770 TCGA-66-2791 TCGA-66-2793 TCGA-77-7465 
          61           61          700         1977         1952          479 
TCGA-77-8009 TCGA-77-8139 TCGA-77-8150 TCGA-77-A5G1 TCGA-77-A5GA TCGA-85-6560 
        1641         1951         1961         1942         1280          364 
TCGA-85-7843 TCGA-85-8072 TCGA-85-8276 TCGA-85-8287 TCGA-85-8350 TCGA-85-A510 
          35          513           13           13           60         1967 
TCGA-90-A59Q TCGA-92-7341 TCGA-94-A4VJ TCGA-98-8022 TCGA-J1-A4AH 
         269          106          430          224          222 

$`16P GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 
         370          136         2464         2417          146         1415 
TCGA-18-3414 TCGA-18-3415 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4083 
         396         1810          758           50         1331          187 
TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 TCGA-21-1075 TCGA-21-1076 
          85         2754           92         3636         2134         1852 
TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 TCGA-21-1082 TCGA-21-5782 
        1058          474          965         3724         3644          962 
TCGA-21-5784 TCGA-21-5786 TCGA-21-A5DI TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 
        1268         1032          979          608          223         1945 
TCGA-22-1002 TCGA-22-1005 TCGA-22-1012 TCGA-22-1016 TCGA-22-4591 TCGA-22-4594 
         131         1952          429          822          623         1470 
TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 
         734           17         1161         1057          399         1946 
TCGA-22-4607 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 
         587          358          965         1964         1933          445 
TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 
        1346           24         1651         1952         1952          357 
TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 
         573          916         1912         1713          506           29 
TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 TCGA-33-4582 TCGA-33-4589 TCGA-33-6738 
        1940         2979         1311         1966         1948          822 
TCGA-34-2596 TCGA-34-2600 TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 
          80         1874          881         1000          951         1528 
TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 TCGA-34-5927 TCGA-34-5928 TCGA-34-8454 
        2062         1715          707          941          552          166 
TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 
         120           13           12          200          247          227 
TCGA-37-4133 TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 
         238         1454         2253         1361         1947         1996 
TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 
        1964         1849           52          740           59          833 
TCGA-39-5035 TCGA-39-5037 TCGA-39-5039 TCGA-39-5040 TCGA-43-2581 TCGA-43-3394 
         474         1086          544         1964         1176          822 
TCGA-43-3920 TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 
        1007          849          376          757          310         1936 
TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 
         212          236         1970          407          358         1971 
TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 
         353          296          432          324          423           12 
TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 TCGA-52-7812 
          12          911          541         1948          923         1967 
TCGA-56-5897 TCGA-56-5898 TCGA-56-6546 TCGA-56-7221 TCGA-56-7579 TCGA-56-7580 
           3          555           26           30           44           40 
TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-8503 TCGA-56-8622 
          26            6         1961            1           41           55 
TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D 
          36           63           17           16           34           38 
TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS 
          46           30           25            4            4            8 
TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46L 
         378          911         2167         1058         2589         1723 
TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 TCGA-60-2696 TCGA-60-2698 TCGA-60-2703 
        1072          910          642          109          311         1950 
TCGA-60-2704 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 
        1943          661         1963         1505         1963         1260 
TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2715 TCGA-60-2716 TCGA-60-2719 
         274         1731         1531         1075         1475         1297 
TCGA-60-2720 TCGA-60-2721 TCGA-60-2723 TCGA-60-2724 TCGA-63-6202 TCGA-63-7021 
          97          983         1092          717         1973         1955 
TCGA-63-7022 TCGA-63-7023 TCGA-66-2727 TCGA-66-2734 TCGA-66-2742 TCGA-66-2744 
        1947         1952         1967         1311          641           30 
TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 
          31           61           28           30          639          762 
TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2769 TCGA-66-2771 TCGA-66-2773 
          30           61           31         1947          578         1946 
TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 
          61          578         1956          121         1954          759 
TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 
          60          790         1217          699         1955          699 
TCGA-66-2792 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 
         913         1645          122         1492           83          202 
TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-77-6842 
         211          244           96          121          104         1950 
TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 
        1941         1942         1952         1959         1968           15 
TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-8007 
        1286         1954         1942         1952         1954         1960 
TCGA-77-8008 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 
        1945         1953         1945         1941         1941         1947 
TCGA-77-8138 TCGA-77-8140 TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 TCGA-77-8153 
        1946         1962          833         1943          293         1684 
TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 
        1092           10         1953         1959         1955         1963 
TCGA-77-A5G8 TCGA-77-A5GB TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6561 TCGA-85-6798 
        1290         1939          839          713          395           34 
TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7844 
          18           10           49            1         1965          911 
TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 
          60           26           60           16          960          428 
TCGA-85-8277 TCGA-85-8288 TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 TCGA-85-8354 
          11           54           55           67           54           61 
TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8664 
          61           22           21          445          424            3 
TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M 
         475           15         1972         1960           25           19 
TCGA-85-A50Z TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 
        1973         1972         1987           24           13          111 
TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 TCGA-90-7964 TCGA-90-A4ED 
         758          289           89          358          428          244 
TCGA-90-A4EE TCGA-92-7340 TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 
         331           82          122          160           70           87 
TCGA-94-7943 TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK 
         356         1213         1344          189          211          273 
TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8023 TCGA-L3-A4E7 TCGA-L3-A524 
         183          256          413          308           35          449 
TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HE TCGA-NC-A5HG TCGA-NC-A5HI 
          36           83         1722         1548         1135 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 2                  1 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              5287               3724 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
               430                699 
[1] "2.0 - 5287.0 (430.0)" "1.0 - 3724.0 (699.0)"
[1] "hr=" "1.1"
D28V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  16P GAIN MUTATED         0       12       20        1        11        12
  16P GAIN WILD-TYPE       1       60      117        0        41        59
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  16P GAIN MUTATED           10          5        0
  16P GAIN WILD-TYPE         47         15        6
D28V3, multiclass
            clus
vv           16P GAIN MUTATED 16P GAIN WILD-TYPE
  STAGE I                   0                  1
  STAGE IA                 12                 60
  STAGE IB                 20                117
  STAGE II                  1                  0
  STAGE IIA                11                 41
  STAGE IIB                12                 59
  STAGE IIIA               10                 47
  STAGE IIIB                5                 15
  STAGE IV                  0                  6
[1] 9 2
[1] 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    15  46   9   2
  16P GAIN WILD-TYPE  83 208  39  18
D28V4, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  T1               15                 83
  T2               46                208
  T3                9                 39
  T4                2                 18
[1] 4 2
[1] 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    43  21   6   2
  16P GAIN WILD-TYPE 218  92  29   3
D28V5, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  N0               43                218
  N1               21                 92
  N2                6                 29
  N3                2                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A  MX
  16P GAIN MUTATED    65   0   0   6
  16P GAIN WILD-TYPE 293   5   1  44
D28V6, multiclass
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  M0                65                293
  M1                 0                  5
  M1A                0                  1
  MX                 6                 44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V7, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    13  59
  16P GAIN WILD-TYPE  94 254
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     13   59
  16P GAIN WILD-TYPE   94  254
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE               13                 94
  MALE                 59                254
[1] 2 2
[1] FALSE
D28V8, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  16P GAIN MUTATED                                       1
  16P GAIN WILD-TYPE                                    11
                    vv
clus                 LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  16P GAIN MUTATED                                        1
  16P GAIN WILD-TYPE                                      5
                    vv
clus                 LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  16P GAIN MUTATED                                         1
  16P GAIN WILD-TYPE                                       0
                    vv
clus                 LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  16P GAIN MUTATED                                                            69
  16P GAIN WILD-TYPE                                                         332
D28V9, multiclass
                                                             clus
vv                                                            16P GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               69
                                                             clus
vv                                                            16P GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       11
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                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"
D28V10, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     2  70
  16P GAIN WILD-TYPE  11 337
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      2   70
  16P GAIN WILD-TYPE   11  337
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  NO                 2                 11
  YES               70                337
[1] 2 2
[1] FALSE
D28V11, continuous
                    vv
clus                  R0  R1  R2  RX
  16P GAIN MUTATED    60   1   0   2
  16P GAIN WILD-TYPE 282   7   4  16
D28V12, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  R0               60                282
  R1                1                  7
  R2                0                  4
  RX                2                 16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16P GAIN MUTATED       2                         3    52
  16P GAIN WILD-TYPE     7                        14   246
D28V13, multiclass
                           clus
vv                          16P GAIN MUTATED 16P GAIN WILD-TYPE
  ASIAN                                    2                  7
  BLACK OR AFRICAN AMERICAN                3                 14
  WHITE                                   52                246
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V14, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     1  52
  16P GAIN WILD-TYPE   7 215
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      1   52
  16P GAIN WILD-TYPE    7  215
                        clus
vv                       16P GAIN MUTATED 16P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  7
  NOT HISPANIC OR LATINO               52                215
[1] 2 2
[1] FALSE

Clustering(29) Variable = 16Q GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                  0   1
  16Q GAIN MUTATED    46  18
  16Q GAIN WILD-TYPE 219 105
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                64                324 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                18                105 
$`16Q GAIN MUTATED`
TCGA-18-3412 TCGA-18-3414 TCGA-18-3416 TCGA-18-5595 TCGA-21-1071 TCGA-21-1072 
         345          396          862          827         1426         3016 
TCGA-21-1079 TCGA-21-5786 TCGA-21-5787 TCGA-22-1011 TCGA-22-1017 TCGA-22-4593 
         965         1032          329           53         1485         1067 
TCGA-33-4532 TCGA-33-4566 TCGA-33-4583 TCGA-33-4587 TCGA-34-5241 TCGA-37-4133 
        2524         5287         1941         1970          428          238 
TCGA-37-4135 TCGA-37-4141 TCGA-39-5036 TCGA-39-5037 TCGA-43-2576 TCGA-43-5668 
         207           12         1084         1086         1223          349 
TCGA-43-6143 TCGA-43-A475 TCGA-43-A56V TCGA-52-7811 TCGA-56-1622 TCGA-56-6545 
         376          296          366         1958          881           62 
TCGA-56-7223 TCGA-56-8504 TCGA-56-A4BW TCGA-60-2706 TCGA-60-2708 TCGA-60-2722 
          30          178            2         1958         1963          908 
TCGA-60-2725 TCGA-60-2726 TCGA-63-7020 TCGA-66-2737 TCGA-66-2756 TCGA-66-2768 
         816          358         1957           61           30           61 
TCGA-66-2781 TCGA-66-2791 TCGA-77-7465 TCGA-77-8009 TCGA-77-A5G1 TCGA-77-A5GA 
         121         1977          479         1641         1942         1280 
TCGA-77-A5GF TCGA-85-6560 TCGA-85-7843 TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 
         839          364           35          513           13           11 
TCGA-85-8287 TCGA-85-8350 TCGA-85-8352 TCGA-85-A510 TCGA-85-A53L TCGA-90-A59Q 
          13           60           67         1967           13          269 
TCGA-92-7341 TCGA-98-8022 TCGA-J1-A4AH TCGA-LA-A446 
         106          224          222           36 

$`16Q GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 
         370          136         2464         2417          146         1415 
TCGA-18-3415 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 
        1810          758           50         1331          187           85 
TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 
        2754           92         3636         2134         1852         1058 
TCGA-21-1078 TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 
         474         3724          284         3644          267          962 
TCGA-21-5784 TCGA-21-A5DI TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 
        1268          979          608          223         1945          131 
TCGA-22-1005 TCGA-22-1012 TCGA-22-1016 TCGA-22-4591 TCGA-22-4594 TCGA-22-4595 
        1952          429          822          623         1470          734 
TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 
          17         1161         1057          399         1946          587 
TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 
         358          965         1964         1933          445         1346 
TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 
          24         1651         1952         1952          357          573 
TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4533 
         916         1912         1713          506           29         1940 
TCGA-33-4538 TCGA-33-4547 TCGA-33-4582 TCGA-33-4586 TCGA-33-4589 TCGA-33-6738 
        2979         1311         1966          428         1948          822 
TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 
          80         1874          958          881         1000          951 
TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 TCGA-34-5927 
        1528         2062         1715          707          365          941 
TCGA-34-5928 TCGA-34-8454 TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 
         552          166          120           13           12          200 
TCGA-37-4130 TCGA-37-4132 TCGA-37-5819 TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 
         247          227          103         1454         2253         1361 
TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 
        1947         1996         1964         1849           52          740 
TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5039 TCGA-39-5040 
          59          833         1107          474          544         1964 
TCGA-43-2578 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-5670 TCGA-43-6647 
         684         1176          822         1007          849          757 
TCGA-43-6770 TCGA-43-6771 TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 
         310         1936          212          236         1970          407 
TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56U TCGA-46-6025 TCGA-46-6026 
         358         1971          353          432          324          423 
TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 
          12           12          911          541         1948          923 
TCGA-52-7812 TCGA-56-5897 TCGA-56-5898 TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 
        1967            3          555           26           30           13 
TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 
          44           40           26            6         1961            1 
TCGA-56-8503 TCGA-56-8622 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 
          41           55           36           63           17           16 
TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK 
          34           38           46           30           25            4 
TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-8393 
           4            8          378          911         2167         1058 
TCGA-58-A46J TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 TCGA-60-2696 
        2589         1723         1072          910          642          109 
TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2707 TCGA-60-2709 TCGA-60-2710 
         311         1950         1943          661         1505         1963 
TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2715 TCGA-60-2716 
        1260          274         1731         1531         1075         1475 
TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2723 TCGA-60-2724 TCGA-63-6202 
        1297           97          983         1092          717         1973 
TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 TCGA-66-2727 TCGA-66-2734 TCGA-66-2742 
        1955         1947         1952         1967         1311          641 
TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2757 TCGA-66-2758 
          30           31           61           28           30          639 
TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2769 
         762           30           61           31           61         1947 
TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 
         700          578         1946           61          578         1956 
TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 
        1954          759           60          790         1217          699 
TCGA-66-2789 TCGA-66-2790 TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 
        1955          699          913         1952         1645          122 
TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 
        1492           83          202          211          244           96 
TCGA-68-A59I TCGA-68-A59J TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 
         121          104         1950         1941         1942         1952 
TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 
        1959         1968           15         1286         1954         1942 
TCGA-77-7338 TCGA-77-7463 TCGA-77-8007 TCGA-77-8008 TCGA-77-8128 TCGA-77-8130 
        1952         1954         1960         1945         1953         1945 
TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 
        1941         1941         1947         1946         1951         1962 
TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 
         833         1943          293         1961         1684         1092 
TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 
          10         1953         1959         1955         1963         1290 
TCGA-77-A5GB TCGA-77-A5GH TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 
        1939          713          395           34           18           10 
TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 
          49            1         1965          911           60           26 
TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8288 TCGA-85-8351 
          60           16          960          428           54           55 
TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 
          54           61           61           22           21          445 
TCGA-85-8582 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A4QQ 
         424            3          475           15         1972         1960 
TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 
          25           19         1973         1972         1987           24 
TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 TCGA-90-7964 
         111          758          289           89          358          428 
TCGA-90-A4ED TCGA-90-A4EE TCGA-92-7340 TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 
         244          331           82          122          160           70 
TCGA-94-7033 TCGA-94-7943 TCGA-94-A4VJ TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 
          87          356          430         1213         1344          189 
TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8023 
         211          273          183          256          413          308 
TCGA-L3-A4E7 TCGA-L3-A524 TCGA-MF-A522 TCGA-NC-A5HE TCGA-NC-A5HG TCGA-NC-A5HI 
          35          449           83         1722         1548         1135 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 2                  1 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              5287               3724 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
               386                699 
[1] "2.0 - 5287.0 (386.0)" "1.0 - 3724.0 (699.0)"
[1] "hr=" "1.1"
D29V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  16Q GAIN MUTATED         0       10       21        1        14        11
  16Q GAIN WILD-TYPE       1       62      116        0        38        60
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  16Q GAIN MUTATED           11          4        1
  16Q GAIN WILD-TYPE         46         16        5
D29V3, multiclass
            clus
vv           16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  STAGE I                   0                  1
  STAGE IA                 10                 62
  STAGE IB                 21                116
  STAGE II                  1                  0
  STAGE IIA                14                 38
  STAGE IIB                11                 60
  STAGE IIIA               11                 46
  STAGE IIIB                4                 16
  STAGE IV                  1                  5
[1] 9 2
[1] 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    14  46   9   4
  16Q GAIN WILD-TYPE  84 208  39  16
D29V4, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T1               14                 84
  T2               46                208
  T3                9                 39
  T4                4                 16
[1] 4 2
[1] 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    43  24   5   1
  16Q GAIN WILD-TYPE 218  89  30   4
D29V5, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  N0               43                218
  N1               24                 89
  N2                5                 30
  N3                1                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A  MX
  16Q GAIN MUTATED    65   1   0   7
  16Q GAIN WILD-TYPE 293   4   1  43
D29V6, multiclass
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  M0                65                293
  M1                 1                  4
  M1A                0                  1
  MX                 7                 43
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V7, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    10  63
  16Q GAIN WILD-TYPE  97 250
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     10   63
  16Q GAIN WILD-TYPE   97  250
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE               10                 97
  MALE                 63                250
[1] 2 2
[1] FALSE
D29V8, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  16Q GAIN MUTATED                                       2
  16Q GAIN WILD-TYPE                                    10
                    vv
clus                 LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  16Q GAIN MUTATED                                        1
  16Q GAIN WILD-TYPE                                      5
                    vv
clus                 LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  16Q GAIN MUTATED                                         1
  16Q GAIN WILD-TYPE                                       0
                    vv
clus                 LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  16Q GAIN MUTATED                                                            69
  16Q GAIN WILD-TYPE                                                         332
D29V9, multiclass
                                                             clus
vv                                                            16Q GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      2
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               69
                                                             clus
vv                                                            16Q GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       10
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                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"
D29V10, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     2  71
  16Q GAIN WILD-TYPE  11 336
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      2   71
  16Q GAIN WILD-TYPE   11  336
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  NO                 2                 11
  YES               71                336
[1] 2 2
[1] FALSE
D29V11, continuous
                    vv
clus                  R0  R1  R2  RX
  16Q GAIN MUTATED    62   3   0   3
  16Q GAIN WILD-TYPE 280   5   4  15
D29V12, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  R0               62                280
  R1                3                  5
  R2                0                  4
  RX                3                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16Q GAIN MUTATED       4                         3    53
  16Q GAIN WILD-TYPE     5                        14   245
D29V13, multiclass
                           clus
vv                          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  ASIAN                                    4                  5
  BLACK OR AFRICAN AMERICAN                3                 14
  WHITE                                   53                245
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V14, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     1  55
  16Q GAIN WILD-TYPE   7 212
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      1   55
  16Q GAIN WILD-TYPE    7  212
                        clus
vv                       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  7
  NOT HISPANIC OR LATINO               55                212
[1] 2 2
[1] FALSE

Clustering(30) Variable = 17P GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                  0   1
  17P GAIN MUTATED    38  15
  17P GAIN WILD-TYPE 227 108
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                53                335 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                15                108 
$`17P GAIN MUTATED`
TCGA-18-3412 TCGA-18-3417 TCGA-21-1071 TCGA-21-1072 TCGA-22-1017 TCGA-22-4593 
         345          758         1426         3016         1485         1067 
TCGA-22-4601 TCGA-22-4613 TCGA-22-5474 TCGA-33-4532 TCGA-33-4538 TCGA-33-4582 
        1057          358          445         2524         2979         1966 
TCGA-34-2596 TCGA-34-5240 TCGA-34-5241 TCGA-43-2578 TCGA-43-7657 TCGA-43-8118 
          80          365          428          684          236         1971 
TCGA-46-6025 TCGA-56-7222 TCGA-56-7582 TCGA-56-7730 TCGA-56-8504 TCGA-58-8391 
         324           13           26            6          178         2167 
TCGA-60-2726 TCGA-66-2756 TCGA-66-2770 TCGA-66-2787 TCGA-66-2792 TCGA-68-8250 
         358           30          700         1217          913          244 
TCGA-68-8251 TCGA-77-7142 TCGA-77-8156 TCGA-77-A5GA TCGA-77-A5GF TCGA-85-7843 
          96         1286           10         1280          839           35 
TCGA-85-7950 TCGA-85-8277 TCGA-85-8350 TCGA-85-8352 TCGA-85-8353 TCGA-85-8354 
          60           11           60           67           54           61 
TCGA-85-8664 TCGA-85-A510 TCGA-85-A5B5 TCGA-90-7769 TCGA-90-A4EE TCGA-92-7340 
           3         1967          111          358          331           82 
TCGA-94-7943 TCGA-96-8169 TCGA-J1-A4AH TCGA-L3-A524 TCGA-MF-A522 
         356          189          222          449           83 

$`17P GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 
         370          136         2464         2417          146         1415 
TCGA-18-3414 TCGA-18-3415 TCGA-18-3416 TCGA-18-3419 TCGA-18-3421 TCGA-18-4083 
         396         1810          862           50         1331          187 
TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1070 TCGA-21-1075 
          85         2754           92          827         3636         2134 
TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 
        1852         1058          474          965         3724          284 
TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 
        3644          267          962         1268         1032          329 
TCGA-21-A5DI TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 
         979          608          223         1945          131         1952 
TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-4591 TCGA-22-4594 TCGA-22-4595 
          53          429          822          623         1470          734 
TCGA-22-4596 TCGA-22-4599 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-5471 
          17         1161          399         1946          587          965 
TCGA-22-5472 TCGA-22-5473 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 
        1964         1933         1346           24         1651         1952 
TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 
        1952          357          573          916         1912         1713 
TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4533 TCGA-33-4547 TCGA-33-4566 TCGA-33-4583 
         506           29         1940         1311         5287         1941 
TCGA-33-4586 TCGA-33-4587 TCGA-33-4589 TCGA-33-6738 TCGA-34-2600 TCGA-34-2604 
         428         1970         1948          822         1874          958 
TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 
         881         1000          951         1528         2062         1715 
TCGA-34-5239 TCGA-34-5927 TCGA-34-5928 TCGA-34-8454 TCGA-37-3783 TCGA-37-3789 
         707          941          552          166          120           13 
TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 
          12          200          247          227          238          207 
TCGA-37-4141 TCGA-37-5819 TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 
          12          103         1454         2253         1361         1947 
TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 
        1996         1964         1849           52          740           59 
TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 
         833         1107          474         1084         1086          544 
TCGA-39-5040 TCGA-43-2576 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 
        1964         1223         1176          822         1007          349 
TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-7656 
         849          376          757          310         1936          212 
TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U 
        1970          407          358          353          296          432 
TCGA-43-A56V TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 
         366          423           12           12          911          541 
TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 
        1948          923         1958         1967          881            3 
TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 TCGA-56-7223 TCGA-56-7579 
         555           62           26           30           30           44 
TCGA-56-7580 TCGA-56-7731 TCGA-56-7822 TCGA-56-8503 TCGA-56-8622 TCGA-56-8624 
          40         1961            1           41           55           36 
TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW 
          63           17           16           34           38            2 
TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS 
          46           30           25            4            4            8 
TCGA-58-8388 TCGA-58-8390 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46L TCGA-58-A46M 
         378          911         1058         2589         1723         1072 
TCGA-58-A46N TCGA-60-2695 TCGA-60-2696 TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 
         910          642          109          311         1950         1943 
TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 
        1958          661         1963         1505         1963         1260 
TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2715 TCGA-60-2716 TCGA-60-2719 
         274         1731         1531         1075         1475         1297 
TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 
          97          983          908         1092          717          816 
TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 TCGA-66-2727 
        1973         1957         1955         1947         1952         1967 
TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 
        1311           61          641           30           31           61 
TCGA-66-2755 TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 
          28           30          639          762           30           61 
TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 TCGA-66-2771 TCGA-66-2773 
          31           61           61         1947          578         1946 
TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 
          61          578         1956          121         1954          759 
TCGA-66-2785 TCGA-66-2786 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 
          60          790          699         1955          699         1977 
TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 
        1952         1645          122         1492           83          202 
TCGA-68-7757 TCGA-68-A59I TCGA-68-A59J TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 
         211          121          104         1950         1941         1942 
TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 TCGA-77-7335 TCGA-77-7337 
        1952         1959         1968           15         1954         1942 
TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 
        1952         1954          479         1960         1945         1641 
TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 
        1953         1945         1941         1941         1947         1946 
TCGA-77-8139 TCGA-77-8140 TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 
        1951         1962          833         1943          293         1961 
TCGA-77-8153 TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 
        1684         1092         1953         1942         1959         1955 
TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GB TCGA-77-A5GH TCGA-85-6560 TCGA-85-6561 
        1963         1290         1939          713          364          395 
TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 
          34           18           10           49            1         1965 
TCGA-85-7844 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 
         911           26           60           16          960          428 
TCGA-85-8072 TCGA-85-8276 TCGA-85-8287 TCGA-85-8288 TCGA-85-8351 TCGA-85-8355 
         513           13           13           54           55           61 
TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8666 TCGA-85-A4CL 
          22           21          445          424          475           15 
TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A511 
        1972         1960           25           19         1973         1972 
TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 
        1987           24           13          758          289           89 
TCGA-90-7964 TCGA-90-A4ED TCGA-90-A59Q TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 
         428          244          269          106          122          160 
TCGA-92-8065 TCGA-94-7033 TCGA-94-A4VJ TCGA-96-7544 TCGA-96-7545 TCGA-96-8170 
          70           87          430         1213         1344          211 
TCGA-96-A4JK TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 
         273          183          256          413          224          308 
TCGA-L3-A4E7 TCGA-LA-A446 TCGA-NC-A5HE TCGA-NC-A5HG TCGA-NC-A5HI 
          35           36         1722         1548         1135 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 3                  1 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              3016               5287 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
               356                734 
[1] "3.0 - 3016.0 (356.0)" "1.0 - 5287.0 (734.0)"
[1] "hr=" "1.1"
D30V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  17P GAIN MUTATED         0       12       17        0        10         8
  17P GAIN WILD-TYPE       1       60      120        1        42        63
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  17P GAIN MUTATED            8          1        1
  17P GAIN WILD-TYPE         49         19        5
D30V3, multiclass
            clus
vv           17P GAIN MUTATED 17P GAIN WILD-TYPE
  STAGE I                   0                  1
  STAGE IA                 12                 60
  STAGE IB                 17                120
  STAGE II                  0                  1
  STAGE IIA                10                 42
  STAGE IIB                 8                 63
  STAGE IIIA                8                 49
  STAGE IIIB                1                 19
  STAGE IV                  1                  5
[1] 9 2
[1] 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    12  39   5   2
  17P GAIN WILD-TYPE  86 215  43  18
D30V4, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  T1               12                 86
  T2               39                215
  T3                5                 43
  T4                2                 18
[1] 4 2
[1] 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    37  16   4   0
  17P GAIN WILD-TYPE 224  97  31   5
D30V5, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  N0               37                224
  N1               16                 97
  N2                4                 31
  N3                0                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A  MX
  17P GAIN MUTATED    47   1   0   9
  17P GAIN WILD-TYPE 311   4   1  41
D30V6, multiclass
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  M0                47                311
  M1                 1                  4
  M1A                0                  1
  MX                 9                 41
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V7, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    13  45
  17P GAIN WILD-TYPE  94 268
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     13   45
  17P GAIN WILD-TYPE   94  268
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE               13                 94
  MALE                 45                268
[1] 2 2
[1] FALSE
D30V8, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  17P GAIN MUTATED                                       2
  17P GAIN WILD-TYPE                                    10
                    vv
clus                 LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  17P GAIN MUTATED                                        1
  17P GAIN WILD-TYPE                                      5
                    vv
clus                 LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  17P GAIN MUTATED                                         0
  17P GAIN WILD-TYPE                                       1
                    vv
clus                 LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  17P GAIN MUTATED                                                            55
  17P GAIN WILD-TYPE                                                         346
D30V9, multiclass
                                                             clus
vv                                                            17P GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      2
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               55
                                                             clus
vv                                                            17P GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       10
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                346
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V10, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     0  58
  17P GAIN WILD-TYPE  13 349
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      0   58
  17P GAIN WILD-TYPE   13  349
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  NO                 0                 13
  YES               58                349
[1] 2 2
[1] FALSE
D30V11, continuous
                    vv
clus                  R0  R1  R2  RX
  17P GAIN MUTATED    42   1   0   3
  17P GAIN WILD-TYPE 300   7   4  15
D30V12, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  R0               42                300
  R1                1                  7
  R2                0                  4
  RX                3                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17P GAIN MUTATED       1                         3    45
  17P GAIN WILD-TYPE     8                        14   253
D30V13, multiclass
                           clus
vv                          17P GAIN MUTATED 17P GAIN WILD-TYPE
  ASIAN                                    1                  8
  BLACK OR AFRICAN AMERICAN                3                 14
  WHITE                                   45                253
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V14, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     2  42
  17P GAIN WILD-TYPE   6 225
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      2   42
  17P GAIN WILD-TYPE    6  225
                        clus
vv                       17P GAIN MUTATED 17P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  6
  NOT HISPANIC OR LATINO               42                225
[1] 2 2
[1] FALSE

Clustering(31) Variable = 17Q GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                  0   1
  17Q GAIN MUTATED    83  45
  17Q GAIN WILD-TYPE 182  78
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               128                260 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                45                 78 
$`17Q GAIN MUTATED`
TCGA-18-3407 TCGA-18-3411 TCGA-18-3412 TCGA-18-3417 TCGA-21-1071 TCGA-21-1072 
         136         1415          345          758         1426         3016 
TCGA-21-1075 TCGA-21-1077 TCGA-21-1082 TCGA-21-1083 TCGA-21-5786 TCGA-21-5787 
        2134         1058         3644          267         1032          329 
TCGA-22-1012 TCGA-22-1017 TCGA-22-4593 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 
         429         1485         1067         1161         1057          399 
TCGA-22-4613 TCGA-22-5471 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5483 
         358          965         1933          445         1346          573 
TCGA-33-4532 TCGA-33-4538 TCGA-33-4582 TCGA-33-4586 TCGA-33-6738 TCGA-34-2596 
        2524         2979         1966          428          822           80 
TCGA-34-2604 TCGA-34-5231 TCGA-34-5240 TCGA-37-3792 TCGA-37-4133 TCGA-39-5016 
         958         1528          365           12          238         2253 
TCGA-39-5019 TCGA-39-5027 TCGA-39-5037 TCGA-43-2576 TCGA-43-2578 TCGA-43-5668 
        1361         1849         1086         1223          684          349 
TCGA-43-7657 TCGA-43-8118 TCGA-43-A475 TCGA-46-6025 TCGA-46-6026 TCGA-51-4080 
         236         1971          296          324          423           12 
TCGA-52-7812 TCGA-56-1622 TCGA-56-7222 TCGA-56-7223 TCGA-56-7582 TCGA-56-7730 
        1967          881           13           30           26            6 
TCGA-56-8504 TCGA-56-8629 TCGA-56-A4BX TCGA-58-8391 TCGA-58-A46J TCGA-58-A46M 
         178           34           46         2167         2589         1072 
TCGA-58-A46N TCGA-60-2703 TCGA-60-2706 TCGA-60-2707 TCGA-60-2715 TCGA-60-2722 
         910         1950         1958          661         1075          908 
TCGA-60-2726 TCGA-63-6202 TCGA-66-2742 TCGA-66-2756 TCGA-66-2758 TCGA-66-2763 
         358         1973          641           30          639           30 
TCGA-66-2767 TCGA-66-2770 TCGA-66-2773 TCGA-66-2777 TCGA-66-2781 TCGA-66-2787 
          61          700         1946           61          121         1217 
TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-68-7755 TCGA-68-8250 TCGA-68-8251 
        1977          913         1952           83          244           96 
TCGA-77-6842 TCGA-77-6845 TCGA-77-7138 TCGA-77-7141 TCGA-77-7142 TCGA-77-7465 
        1950         1952         1959           15         1286          479 
TCGA-77-8007 TCGA-77-8128 TCGA-77-8136 TCGA-77-8139 TCGA-77-8156 TCGA-77-A5G3 
        1960         1953         1947         1951           10         1959 
TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5GA TCGA-77-A5GF TCGA-85-6560 TCGA-85-7843 
        1955         1963         1280          839          364           35 
TCGA-85-7844 TCGA-85-8070 TCGA-85-8277 TCGA-85-8350 TCGA-85-8352 TCGA-85-8353 
         911          960           11           60           67           54 
TCGA-85-8354 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4QR TCGA-85-A510 
          61            3          475           15           25         1967 
TCGA-90-7767 TCGA-90-7769 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 
          89          358          244          331          269           82 
TCGA-92-7341 TCGA-96-7545 TCGA-96-8169 TCGA-96-A4JK TCGA-98-8023 TCGA-J1-A4AH 
         106         1344          189          273          308          222 
TCGA-L3-A524 TCGA-MF-A522 
         449           83 

$`17Q GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3414 TCGA-18-3415 
         370         2464         2417          146          396         1810 
TCGA-18-3416 TCGA-18-3419 TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 
         862           50         1331          187           85         2754 
TCGA-18-5592 TCGA-18-5595 TCGA-21-1070 TCGA-21-1076 TCGA-21-1078 TCGA-21-1079 
          92          827         3636         1852          474          965 
TCGA-21-1080 TCGA-21-1081 TCGA-21-5782 TCGA-21-5784 TCGA-21-A5DI TCGA-22-0940 
        3724          284          962         1268          979          608 
TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1016 
         223         1945          131         1952           53          822 
TCGA-22-4591 TCGA-22-4594 TCGA-22-4595 TCGA-22-4596 TCGA-22-4605 TCGA-22-4607 
         623         1470          734           17         1946          587 
TCGA-22-5472 TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 
        1964           24         1651         1952         1952          357 
TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4533 
         916         1912         1713          506           29         1940 
TCGA-33-4547 TCGA-33-4566 TCGA-33-4583 TCGA-33-4587 TCGA-33-4589 TCGA-34-2600 
        1311         5287         1941         1970         1948         1874 
TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 
         881         1000          951         2062         1715          707 
TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-8454 TCGA-37-3783 TCGA-37-3789 
         428          941          552          166          120           13 
TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 
         200          247          227          207           12          103 
TCGA-39-5011 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5028 TCGA-39-5029 
        1454         1947         1996         1964           52          740 
TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5039 
          59          833         1107          474         1084          544 
TCGA-39-5040 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-5670 TCGA-43-6143 
        1964         1176          822         1007          849          376 
TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-7656 TCGA-43-7658 TCGA-43-8115 
         757          310         1936          212         1970          407 
TCGA-43-8116 TCGA-43-A474 TCGA-43-A56U TCGA-43-A56V TCGA-51-4079 TCGA-51-4081 
         358          353          432          366           12          911 
TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 TCGA-56-5897 TCGA-56-5898 
         541         1948          923         1958            3          555 
TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 TCGA-56-7579 TCGA-56-7580 TCGA-56-7731 
          62           26           30           44           40         1961 
TCGA-56-7822 TCGA-56-8503 TCGA-56-8622 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 
           1           41           55           36           63           17 
TCGA-56-8628 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK 
          16           38            2           30           25            4 
TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8388 TCGA-58-8390 TCGA-58-8393 TCGA-58-A46L 
           4            8          378          911         1058         1723 
TCGA-60-2695 TCGA-60-2696 TCGA-60-2698 TCGA-60-2704 TCGA-60-2708 TCGA-60-2709 
         642          109          311         1943         1963         1505 
TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2716 
        1963         1260          274         1731         1531         1475 
TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 
        1297           97          983         1092          717          816 
TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 TCGA-66-2727 TCGA-66-2734 
        1957         1955         1947         1952         1967         1311 
TCGA-66-2737 TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2757 
          61           30           31           61           28           30 
TCGA-66-2759 TCGA-66-2765 TCGA-66-2766 TCGA-66-2768 TCGA-66-2769 TCGA-66-2771 
         762           61           31           61         1947          578 
TCGA-66-2778 TCGA-66-2780 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 
         578         1956         1954          759           60          790 
TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 
         699         1955          699         1645          122         1492 
TCGA-68-7756 TCGA-68-7757 TCGA-68-A59I TCGA-68-A59J TCGA-77-6843 TCGA-77-6844 
         202          211          121          104         1941         1942 
TCGA-77-7139 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-8008 
        1968         1954         1942         1952         1954         1945 
TCGA-77-8009 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8138 TCGA-77-8140 
        1641         1945         1941         1941         1946         1962 
TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 
         833         1943          293         1961         1684         1092 
TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G8 TCGA-77-A5GB TCGA-77-A5GH TCGA-85-6561 
        1953         1942         1290         1939          713          395 
TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 
          34           18           10           49            1         1965 
TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8071 TCGA-85-8072 
          60           26           60           16          428          513 
TCGA-85-8276 TCGA-85-8287 TCGA-85-8288 TCGA-85-8351 TCGA-85-8355 TCGA-85-8479 
          13           13           54           55           61           22 
TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50M 
          21          445          424         1972         1960           19 
TCGA-85-A50Z TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 
        1973         1972         1987           24           13          111 
TCGA-90-6837 TCGA-90-7766 TCGA-90-7964 TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 
         758          289          428          122          160           70 
TCGA-94-7033 TCGA-94-7943 TCGA-94-A4VJ TCGA-96-7544 TCGA-96-8170 TCGA-96-A4JL 
          87          356          430         1213          211          183 
TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-L3-A4E7 TCGA-LA-A446 TCGA-NC-A5HE 
         256          413          224           35           36         1722 
TCGA-NC-A5HG TCGA-NC-A5HI 
        1548         1135 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 3                  1 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              3644               5287 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             640.0              670.5 
[1] "3.0 - 3644.0 (640.0)" "1.0 - 5287.0 (670.5)"
[1] "hr=" "1.1"
D31V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  17Q GAIN MUTATED         0       18       41        0        24        24
  17Q GAIN WILD-TYPE       1       54       96        1        28        47
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  17Q GAIN MUTATED           17          6        3
  17Q GAIN WILD-TYPE         40         14        3
D31V3, multiclass
            clus
vv           17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  STAGE I                   0                  1
  STAGE IA                 18                 54
  STAGE IB                 41                 96
  STAGE II                  0                  1
  STAGE IIA                24                 28
  STAGE IIB                24                 47
  STAGE IIIA               17                 40
  STAGE IIIB                6                 14
  STAGE IV                  3                  3
[1] 9 2
[1] 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    24  92  13   5
  17Q GAIN WILD-TYPE  74 162  35  15
D31V4, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T1               24                 74
  T2               92                162
  T3               13                 35
  T4                5                 15
[1] 4 2
[1] 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    75  45  11   2
  17Q GAIN WILD-TYPE 186  68  24   3
D31V5, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  N0               75                186
  N1               45                 68
  N2               11                 24
  N3                2                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A  MX
  17Q GAIN MUTATED   112   3   0  17
  17Q GAIN WILD-TYPE 246   2   1  33
D31V6, multiclass
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  M0               112                246
  M1                 3                  2
  M1A                0                  1
  MX                17                 33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V7, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    22 112
  17Q GAIN WILD-TYPE  85 201
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     22  112
  17Q GAIN WILD-TYPE   85  201
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE               22                 85
  MALE                112                201
[1] 2 2
[1] FALSE
D31V8, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  17Q GAIN MUTATED                                       5
  17Q GAIN WILD-TYPE                                     7
                    vv
clus                 LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  17Q GAIN MUTATED                                        1
  17Q GAIN WILD-TYPE                                      5
                    vv
clus                 LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  17Q GAIN MUTATED                                         0
  17Q GAIN WILD-TYPE                                       1
                    vv
clus                 LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  17Q GAIN MUTATED                                                           128
  17Q GAIN WILD-TYPE                                                         273
D31V9, multiclass
                                                             clus
vv                                                            17Q GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      5
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              128
                                                             clus
vv                                                            17Q GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                        7
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                273
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V10, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     4 130
  17Q GAIN WILD-TYPE   9 277
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      4  130
  17Q GAIN WILD-TYPE    9  277
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  NO                 4                  9
  YES              130                277
[1] 2 2
[1] FALSE
D31V11, continuous
                    vv
clus                  R0  R1  R2  RX
  17Q GAIN MUTATED   107   3   2   4
  17Q GAIN WILD-TYPE 235   5   2  14
D31V12, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  R0              107                235
  R1                3                  5
  R2                2                  2
  RX                4                 14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17Q GAIN MUTATED       2                         3    98
  17Q GAIN WILD-TYPE     7                        14   200
D31V13, multiclass
                           clus
vv                          17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  ASIAN                                    2                  7
  BLACK OR AFRICAN AMERICAN                3                 14
  WHITE                                   98                200
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V14, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     4  84
  17Q GAIN WILD-TYPE   4 183
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      4   84
  17Q GAIN WILD-TYPE    4  183
                        clus
vv                       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                  4
  NOT HISPANIC OR LATINO               84                183
[1] 2 2
[1] FALSE

Clustering(32) Variable = 18P GAIN MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                  0   1
  18P GAIN MUTATED    87  36
  18P GAIN WILD-TYPE 178  87
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
               123                265 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                36                 87 
$`18P GAIN MUTATED`
TCGA-18-3407 TCGA-18-3411 TCGA-18-3412 TCGA-18-3416 TCGA-18-4083 TCGA-21-1075 
         136         1415          345          862          187         2134 
TCGA-21-1079 TCGA-21-1082 TCGA-21-5784 TCGA-21-5786 TCGA-22-0944 TCGA-22-4591 
         965         3644         1268         1032          223          623 
TCGA-22-4595 TCGA-22-4604 TCGA-22-4613 TCGA-22-5471 TCGA-22-5480 TCGA-22-5483 
         734          399          358          965         1952          573 
TCGA-22-5489 TCGA-22-5491 TCGA-33-4532 TCGA-33-4566 TCGA-33-4586 TCGA-34-2596 
        1912         1713         2524         5287          428           80 
TCGA-34-2604 TCGA-34-5231 TCGA-34-5239 TCGA-34-5240 TCGA-37-3792 TCGA-37-4141 
         958         1528          707          365           12           12 
TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5027 TCGA-39-5029 TCGA-39-5031 
        2253         1361         1947         1849          740          833 
TCGA-39-5037 TCGA-39-5040 TCGA-43-2576 TCGA-43-2578 TCGA-43-5670 TCGA-43-6143 
        1086         1964         1223          684          849          376 
TCGA-43-7657 TCGA-43-7658 TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 TCGA-46-6026 
         236         1970         1971          353          296          423 
TCGA-51-4081 TCGA-52-7811 TCGA-56-5898 TCGA-56-7223 TCGA-56-7580 TCGA-56-7730 
         911         1958          555           30           40            6 
TCGA-56-A49D TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8391 
          38           46           30            4            8         2167 
TCGA-58-A46N TCGA-60-2698 TCGA-60-2711 TCGA-60-2712 TCGA-60-2722 TCGA-60-2725 
         910          311         1260          274          908          816 
TCGA-60-2726 TCGA-63-7020 TCGA-63-7023 TCGA-66-2734 TCGA-66-2758 TCGA-66-2759 
         358         1957         1952         1311          639          762 
TCGA-66-2767 TCGA-66-2769 TCGA-66-2770 TCGA-66-2777 TCGA-66-2783 TCGA-66-2787 
          61         1947          700           61          759         1217 
TCGA-66-2793 TCGA-66-2794 TCGA-66-2800 TCGA-68-7755 TCGA-68-A59J TCGA-77-6845 
        1952         1645         1492           83          104         1952 
TCGA-77-7335 TCGA-77-7463 TCGA-77-7465 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 
        1954         1954          479         1641         1953         1945 
TCGA-77-8150 TCGA-77-8153 TCGA-77-8156 TCGA-77-A5G3 TCGA-77-A5GF TCGA-85-6561 
        1961         1684           10         1959          839          395 
TCGA-85-6798 TCGA-85-7843 TCGA-85-7844 TCGA-85-8049 TCGA-85-8070 TCGA-85-8071 
          34           35          911           60          960          428 
TCGA-85-8276 TCGA-85-8277 TCGA-85-8352 TCGA-85-8353 TCGA-85-8354 TCGA-85-8664 
          13           11           67           54           61            3 
TCGA-85-8666 TCGA-85-A50M TCGA-85-A510 TCGA-85-A5B5 TCGA-90-7769 TCGA-90-A4EE 
         475           19         1967          111          358          331 
TCGA-90-A59Q TCGA-92-8064 TCGA-94-A4VJ TCGA-96-7545 TCGA-98-8021 TCGA-J1-A4AH 
         269          160          430         1344          413          222 
TCGA-L3-A4E7 TCGA-L3-A524 TCGA-NC-A5HI 
          35          449         1135 

$`18P GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3414 TCGA-18-3415 
         370         2464         2417          146          396         1810 
TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 
         758           50         1331           85         2754           92 
TCGA-18-5595 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 TCGA-21-1076 TCGA-21-1077 
         827         3636         1426         3016         1852         1058 
TCGA-21-1078 TCGA-21-1080 TCGA-21-1081 TCGA-21-1083 TCGA-21-5782 TCGA-21-5787 
         474         3724          284          267          962          329 
TCGA-21-A5DI TCGA-22-0940 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 
         979          608         1945          131         1952           53 
TCGA-22-1012 TCGA-22-1016 TCGA-22-1017 TCGA-22-4593 TCGA-22-4594 TCGA-22-4596 
         429          822         1485         1067         1470           17 
TCGA-22-4599 TCGA-22-4601 TCGA-22-4605 TCGA-22-4607 TCGA-22-5472 TCGA-22-5473 
        1161         1057         1946          587         1964         1933 
TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5481 TCGA-22-5482 
         445         1346           24         1651         1952          357 
TCGA-22-5485 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 
         916          506           29         1940         2979         1311 
TCGA-33-4582 TCGA-33-4583 TCGA-33-4587 TCGA-33-4589 TCGA-33-6738 TCGA-34-2600 
        1966         1941         1970         1948          822         1874 
TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 TCGA-34-5232 TCGA-34-5234 TCGA-34-5241 
         881         1000          951         2062         1715          428 
TCGA-34-5927 TCGA-34-5928 TCGA-34-8454 TCGA-37-3783 TCGA-37-3789 TCGA-37-4129 
         941          552          166          120           13          200 
TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-5819 TCGA-39-5011 
         247          227          238          207          103         1454 
TCGA-39-5022 TCGA-39-5024 TCGA-39-5028 TCGA-39-5030 TCGA-39-5034 TCGA-39-5035 
        1996         1964           52           59         1107          474 
TCGA-39-5036 TCGA-39-5039 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 
        1084          544         1176          822         1007          349 
TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-7656 TCGA-43-8115 TCGA-43-8116 
         757          310         1936          212          407          358 
TCGA-43-A56U TCGA-43-A56V TCGA-46-6025 TCGA-51-4079 TCGA-51-4080 TCGA-52-7622 
         432          366          324           12           12          541 
TCGA-52-7809 TCGA-52-7810 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-6545 
        1948          923         1967          881            3           62 
TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 TCGA-56-7579 TCGA-56-7582 TCGA-56-7731 
          26           30           13           44           26         1961 
TCGA-56-7822 TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 TCGA-56-8624 TCGA-56-8625 
           1           41          178           55           36           63 
TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A4BW TCGA-56-A4ZJ TCGA-56-A4ZK 
          17           16           34            2           25            4 
TCGA-58-8388 TCGA-58-8390 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46L TCGA-58-A46M 
         378          911         1058         2589         1723         1072 
TCGA-60-2695 TCGA-60-2696 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 
         642          109         1950         1943         1958          661 
TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 TCGA-60-2714 TCGA-60-2715 
        1963         1505         1963         1731         1531         1075 
TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2723 TCGA-60-2724 
        1475         1297           97          983         1092          717 
TCGA-63-6202 TCGA-63-7021 TCGA-63-7022 TCGA-66-2727 TCGA-66-2737 TCGA-66-2742 
        1973         1955         1947         1967           61          641 
TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 
          30           31           61           28           30           30 
TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2768 TCGA-66-2771 TCGA-66-2773 
          30           61           31           61          578         1946 
TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2785 TCGA-66-2786 
         578         1956          121         1954           60          790 
TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 TCGA-66-2792 TCGA-66-2795 
         699         1955          699         1977          913          122 
TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-77-6842 
         202          211          244           96          121         1950 
TCGA-77-6843 TCGA-77-6844 TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 
        1941         1942         1959         1968           15         1286 
TCGA-77-7337 TCGA-77-7338 TCGA-77-8007 TCGA-77-8008 TCGA-77-8131 TCGA-77-8133 
        1942         1952         1960         1945         1941         1941 
TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8144 TCGA-77-8145 
        1947         1946         1951         1962          833         1943 
TCGA-77-8148 TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G6 TCGA-77-A5G7 
         293         1092         1953         1942         1955         1963 
TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GH TCGA-85-6560 TCGA-85-7696 
        1290         1280         1939          713          364           18 
TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7950 TCGA-85-8048 
          10           49            1         1965           60           26 
TCGA-85-8052 TCGA-85-8072 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 
          16          513           13           54           60           55 
TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-A4CL 
          61           22           21          445          424           15 
TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50Z TCGA-85-A511 TCGA-85-A512 
        1972         1960           25         1973         1972         1987 
TCGA-85-A513 TCGA-85-A53L TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 TCGA-90-7964 
          24           13          758          289           89          428 
TCGA-90-A4ED TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-92-8065 TCGA-94-7033 
         244           82          106          122           70           87 
TCGA-94-7943 TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL 
         356         1213          189          211          273          183 
TCGA-98-7454 TCGA-98-8022 TCGA-98-8023 TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HE 
         256          224          308           36           83         1722 
TCGA-NC-A5HG 
        1548 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 3                  1 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              5287               3724 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
               700                608 
[1] "3.0 - 5287.0 (700.0)" "1.0 - 3724.0 (608.0)"
[1] "hr=" "1.1"
D32V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  18P GAIN MUTATED         0       20       42        0        20        22
  18P GAIN WILD-TYPE       1       52       95        1        32        49
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  18P GAIN MUTATED           19          9        1
  18P GAIN WILD-TYPE         38         11        5
D32V3, multiclass
            clus
vv           18P GAIN MUTATED 18P GAIN WILD-TYPE
  STAGE I                   0                  1
  STAGE IA                 20                 52
  STAGE IB                 42                 95
  STAGE II                  0                  1
  STAGE IIA                20                 32
  STAGE IIB                22                 49
  STAGE IIIA               19                 38
  STAGE IIIB                9                 11
  STAGE IV                  1                  5
[1] 9 2
[1] 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    26  84  17   6
  18P GAIN WILD-TYPE  72 170  31  14
D32V4, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  T1               26                 72
  T2               84                170
  T3               17                 31
  T4                6                 14
[1] 4 2
[1] 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    76  39  14   2
  18P GAIN WILD-TYPE 185  74  21   3
D32V5, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  N0               76                185
  N1               39                 74
  N2               14                 21
  N3                2                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A  MX
  18P GAIN MUTATED   117   1   0  14
  18P GAIN WILD-TYPE 241   4   1  36
D32V6, multiclass
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  M0               117                241
  M1                 1                  4
  M1A                0                  1
  MX                14                 36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V7, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    30 103
  18P GAIN WILD-TYPE  77 210
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     30  103
  18P GAIN WILD-TYPE   77  210
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE               30                 77
  MALE                103                210
[1] 2 2
[1] FALSE
D32V8, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  18P GAIN MUTATED                                       4
  18P GAIN WILD-TYPE                                     8
                    vv
clus                 LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  18P GAIN MUTATED                                        1
  18P GAIN WILD-TYPE                                      5
                    vv
clus                 LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  18P GAIN MUTATED                                         0
  18P GAIN WILD-TYPE                                       1
                    vv
clus                 LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  18P GAIN MUTATED                                                           128
  18P GAIN WILD-TYPE                                                         273
D32V9, multiclass
                                                             clus
vv                                                            18P GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      4
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              128
                                                             clus
vv                                                            18P GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                        8
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                273
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V10, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     7 126
  18P GAIN WILD-TYPE   6 281
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      7  126
  18P GAIN WILD-TYPE    6  281
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  NO                 7                  6
  YES              126                281
[1] 2 2
[1] FALSE
D32V11, continuous
                    vv
clus                  R0  R1  R2  RX
  18P GAIN MUTATED   108   2   3   6
  18P GAIN WILD-TYPE 234   6   1  12
D32V12, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  R0              108                234
  R1                2                  6
  R2                3                  1
  RX                6                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18P GAIN MUTATED       4                         0   101
  18P GAIN WILD-TYPE     5                        17   197
D32V13, multiclass
                           clus
vv                          18P GAIN MUTATED 18P GAIN WILD-TYPE
  ASIAN                                    4                  5
  BLACK OR AFRICAN AMERICAN                0                 17
  WHITE                                  101                197
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V14, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     2  86
  18P GAIN WILD-TYPE   6 181
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      2   86
  18P GAIN WILD-TYPE    6  181
                        clus
vv                       18P GAIN MUTATED 18P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  6
  NOT HISPANIC OR LATINO               86                181
[1] 2 2
[1] FALSE

Clustering(33) Variable = 18Q GAIN MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                  0   1
  18Q GAIN MUTATED    60  31
  18Q GAIN WILD-TYPE 205  92
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                91                297 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                31                 92 
$`18Q GAIN MUTATED`
TCGA-18-3407 TCGA-18-3411 TCGA-18-4083 TCGA-21-1075 TCGA-21-1082 TCGA-21-5784 
         136         1415          187         2134         3644         1268 
TCGA-22-1012 TCGA-22-4595 TCGA-22-4604 TCGA-22-4613 TCGA-22-5471 TCGA-22-5478 
         429          734          399          358          965           24 
TCGA-22-5480 TCGA-22-5481 TCGA-22-5483 TCGA-22-5489 TCGA-22-5491 TCGA-33-4532 
        1952         1952          573         1912         1713         2524 
TCGA-33-4566 TCGA-33-4582 TCGA-33-4586 TCGA-34-2596 TCGA-34-2604 TCGA-34-2609 
        5287         1966          428           80          958          951 
TCGA-34-5239 TCGA-37-4141 TCGA-39-5019 TCGA-39-5021 TCGA-39-5029 TCGA-39-5031 
         707           12         1361         1947          740          833 
TCGA-39-5037 TCGA-39-5040 TCGA-43-2578 TCGA-43-3920 TCGA-43-6143 TCGA-43-7657 
        1086         1964          684         1007          376          236 
TCGA-43-7658 TCGA-43-8115 TCGA-43-A475 TCGA-46-6026 TCGA-51-4081 TCGA-52-7811 
        1970          407          296          423          911         1958 
TCGA-56-5898 TCGA-56-7580 TCGA-56-7730 TCGA-56-A49D TCGA-56-A4BX TCGA-58-A46N 
         555           40            6           38           46          910 
TCGA-60-2695 TCGA-60-2711 TCGA-60-2712 TCGA-60-2722 TCGA-60-2725 TCGA-63-7020 
         642         1260          274          908          816         1957 
TCGA-63-7023 TCGA-66-2758 TCGA-66-2759 TCGA-66-2769 TCGA-66-2770 TCGA-66-2777 
        1952          639          762         1947          700           61 
TCGA-66-2787 TCGA-66-2793 TCGA-66-2794 TCGA-66-2800 TCGA-68-7755 TCGA-77-7463 
        1217         1952         1645         1492           83         1954 
TCGA-77-7465 TCGA-77-8009 TCGA-77-8128 TCGA-77-8150 TCGA-77-8153 TCGA-77-8156 
         479         1641         1953         1961         1684           10 
TCGA-77-A5GF TCGA-85-6561 TCGA-85-6798 TCGA-85-7843 TCGA-85-7950 TCGA-85-8070 
         839          395           34           35           60          960 
TCGA-85-8071 TCGA-85-8277 TCGA-85-8664 TCGA-85-8666 TCGA-85-A50M TCGA-90-A4EE 
         428           11            3          475           19          331 
TCGA-90-A59Q TCGA-92-8064 TCGA-96-7545 TCGA-98-8021 TCGA-J1-A4AH TCGA-L3-A4E7 
         269          160         1344          413          222           35 
TCGA-MF-A522 
          83 

$`18Q GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3412 TCGA-18-3414 
         370         2464         2417          146          345          396 
TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4086 
        1810          862          758           50         1331           85 
TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 
        2754           92          827         3636         1426         3016 
TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 
        1852         1058          474          965         3724          284 
TCGA-21-1083 TCGA-21-5782 TCGA-21-5786 TCGA-21-5787 TCGA-21-A5DI TCGA-22-0940 
         267          962         1032          329          979          608 
TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1016 
         223         1945          131         1952           53          822 
TCGA-22-1017 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4596 TCGA-22-4599 
        1485          623         1067         1470           17         1161 
TCGA-22-4601 TCGA-22-4605 TCGA-22-4607 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 
        1057         1946          587         1964         1933          445 
TCGA-22-5477 TCGA-22-5479 TCGA-22-5482 TCGA-22-5485 TCGA-22-5492 TCGA-22-A5C4 
        1346         1651          357          916          506           29 
TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 TCGA-33-4583 TCGA-33-4587 TCGA-33-4589 
        1940         2979         1311         1941         1970         1948 
TCGA-33-6738 TCGA-34-2600 TCGA-34-2605 TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 
         822         1874          881         1000         1528         2062 
TCGA-34-5234 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-8454 
        1715          365          428          941          552          166 
TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 
         120           13           12          200          247          227 
TCGA-37-4133 TCGA-37-4135 TCGA-37-5819 TCGA-39-5011 TCGA-39-5016 TCGA-39-5022 
         238          207          103         1454         2253         1996 
TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5030 TCGA-39-5034 TCGA-39-5035 
        1964         1849           52           59         1107          474 
TCGA-39-5036 TCGA-39-5039 TCGA-43-2576 TCGA-43-2581 TCGA-43-3394 TCGA-43-5668 
        1084          544         1223         1176          822          349 
TCGA-43-5670 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-7656 TCGA-43-8116 
         849          757          310         1936          212          358 
TCGA-43-8118 TCGA-43-A474 TCGA-43-A56U TCGA-43-A56V TCGA-46-6025 TCGA-51-4079 
        1971          353          432          366          324           12 
TCGA-51-4080 TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 TCGA-52-7812 TCGA-56-1622 
          12          541         1948          923         1967          881 
TCGA-56-5897 TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 
           3           62           26           30           13           30 
TCGA-56-7579 TCGA-56-7582 TCGA-56-7731 TCGA-56-7822 TCGA-56-8503 TCGA-56-8504 
          44           26         1961            1           41          178 
TCGA-56-8622 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 
          55           36           63           17           16           34 
TCGA-56-A4BW TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS 
           2           30           25            4            4            8 
TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46L 
         378          911         2167         1058         2589         1723 
TCGA-58-A46M TCGA-60-2696 TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 
        1072          109          311         1950         1943         1958 
TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 TCGA-60-2714 
         661         1963         1505         1963         1731         1531 
TCGA-60-2715 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2723 
        1075         1475         1297           97          983         1092 
TCGA-60-2724 TCGA-60-2726 TCGA-63-6202 TCGA-63-7021 TCGA-63-7022 TCGA-66-2727 
         717          358         1973         1955         1947         1967 
TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 
        1311           61          641           30           31           61 
TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 
          28           30           30           30           61           31 
TCGA-66-2767 TCGA-66-2768 TCGA-66-2771 TCGA-66-2773 TCGA-66-2778 TCGA-66-2780 
          61           61          578         1946          578         1956 
TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2788 
         121         1954          759           60          790          699 
TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 TCGA-66-2792 TCGA-66-2795 TCGA-68-7756 
        1955          699         1977          913          122          202 
TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-77-6842 
         211          244           96          121          104         1950 
TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 
        1941         1942         1952         1959         1968           15 
TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-8007 TCGA-77-8008 
        1286         1954         1942         1952         1960         1945 
TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 
        1945         1941         1941         1947         1946         1951 
TCGA-77-8140 TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 TCGA-77-8154 TCGA-77-A5FZ 
        1962          833         1943          293         1092         1953 
TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA 
        1942         1959         1955         1963         1290         1280 
TCGA-77-A5GB TCGA-77-A5GH TCGA-85-6560 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 
        1939          713          364           18           10           49 
TCGA-85-7699 TCGA-85-7710 TCGA-85-7844 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 
           1         1965          911           26           60           16 
TCGA-85-8072 TCGA-85-8276 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 
         513           13           13           54           60           55 
TCGA-85-8352 TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 
          67           54           61           61           22           21 
TCGA-85-8580 TCGA-85-8582 TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR 
         445          424           15         1972         1960           25 
TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L 
        1973         1967         1972         1987           24           13 
TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 TCGA-90-7964 
         111          758          289           89          358          428 
TCGA-90-A4ED TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-92-8065 TCGA-94-7033 
         244           82          106          122           70           87 
TCGA-94-7943 TCGA-94-A4VJ TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK 
         356          430         1213          189          211          273 
TCGA-96-A4JL TCGA-98-7454 TCGA-98-8022 TCGA-98-8023 TCGA-L3-A524 TCGA-LA-A446 
         183          256          224          308          449           36 
TCGA-NC-A5HE TCGA-NC-A5HG TCGA-NC-A5HI 
        1722         1548         1135 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 3                  1 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              5287               3724 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
               707                587 
[1] "3.0 - 5287.0 (707.0)" "1.0 - 3724.0 (587.0)"
[1] "hr=" "1.1"
D33V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  18Q GAIN MUTATED         0       16       35        0        15        15
  18Q GAIN WILD-TYPE       1       56      102        1        37        56
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  18Q GAIN MUTATED           11          6        0
  18Q GAIN WILD-TYPE         46         14        6
D33V3, multiclass
            clus
vv           18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  STAGE I                   0                  1
  STAGE IA                 16                 56
  STAGE IB                 35                102
  STAGE II                  0                  1
  STAGE IIA                15                 37
  STAGE IIB                15                 56
  STAGE IIIA               11                 46
  STAGE IIIB                6                 14
  STAGE IV                  0                  6
[1] 9 2
[1] 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    21  65   7   5
  18Q GAIN WILD-TYPE  77 189  41  15
D33V4, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  T1               21                 77
  T2               65                189
  T3                7                 41
  T4                5                 15
[1] 4 2
[1] 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    59  28  10   0
  18Q GAIN WILD-TYPE 202  85  25   5
D33V5, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  N0               59                202
  N1               28                 85
  N2               10                 25
  N3                0                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A  MX
  18Q GAIN MUTATED    87   0   0  10
  18Q GAIN WILD-TYPE 271   5   1  40
D33V6, multiclass
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  M0                87                271
  M1                 0                  5
  M1A                0                  1
  MX                10                 40
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V7, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    22  76
  18Q GAIN WILD-TYPE  85 237
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     22   76
  18Q GAIN WILD-TYPE   85  237
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE               22                 85
  MALE                 76                237
[1] 2 2
[1] FALSE
D33V8, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  18Q GAIN MUTATED                                       3
  18Q GAIN WILD-TYPE                                     9
                    vv
clus                 LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  18Q GAIN MUTATED                                        0
  18Q GAIN WILD-TYPE                                      6
                    vv
clus                 LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  18Q GAIN MUTATED                                         0
  18Q GAIN WILD-TYPE                                       1
                    vv
clus                 LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  18Q GAIN MUTATED                                                            95
  18Q GAIN WILD-TYPE                                                         306
D33V9, multiclass
                                                             clus
vv                                                            18Q GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      3
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     0
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               95
                                                             clus
vv                                                            18Q GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                        9
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                306
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V10, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     6  92
  18Q GAIN WILD-TYPE   7 315
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      6   92
  18Q GAIN WILD-TYPE    7  315
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  NO                 6                  7
  YES               92                315
[1] 2 2
[1] FALSE
D33V11, continuous
                    vv
clus                  R0  R1  R2  RX
  18Q GAIN MUTATED    81   2   2   3
  18Q GAIN WILD-TYPE 261   6   2  15
D33V12, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  R0               81                261
  R1                2                  6
  R2                2                  2
  RX                3                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18Q GAIN MUTATED       2                         1    73
  18Q GAIN WILD-TYPE     7                        16   225
D33V13, multiclass
                           clus
vv                          18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  ASIAN                                    2                  7
  BLACK OR AFRICAN AMERICAN                1                 16
  WHITE                                   73                225
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V14, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     2  61
  18Q GAIN WILD-TYPE   6 206
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      2   61
  18Q GAIN WILD-TYPE    6  206
                        clus
vv                       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  6
  NOT HISPANIC OR LATINO               61                206
[1] 2 2
[1] FALSE

Clustering(34) Variable = 19P GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                  0   1
  19P GAIN MUTATED    58  32
  19P GAIN WILD-TYPE 207  91
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                90                298 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                32                 91 
$`19P GAIN MUTATED`
TCGA-18-3407 TCGA-18-3410 TCGA-18-3411 TCGA-18-3421 TCGA-21-5787 TCGA-22-1011 
         136          146         1415         1331          329           53 
TCGA-22-1012 TCGA-22-4593 TCGA-22-4595 TCGA-22-4604 TCGA-22-5471 TCGA-22-5474 
         429         1067          734          399          965          445 
TCGA-22-5477 TCGA-22-5481 TCGA-22-5483 TCGA-22-5489 TCGA-33-4533 TCGA-33-4538 
        1346         1952          573         1912         1940         2979 
TCGA-33-4566 TCGA-33-4586 TCGA-34-2596 TCGA-34-2600 TCGA-34-2605 TCGA-34-5231 
        5287          428           80         1874          881         1528 
TCGA-34-5239 TCGA-34-5240 TCGA-39-5016 TCGA-39-5019 TCGA-39-5031 TCGA-39-5034 
         707          365         2253         1361          833         1107 
TCGA-39-5035 TCGA-39-5040 TCGA-43-6143 TCGA-43-7657 TCGA-43-A475 TCGA-52-7809 
         474         1964          376          236          296         1948 
TCGA-56-6546 TCGA-56-7580 TCGA-56-7582 TCGA-58-8393 TCGA-58-A46M TCGA-58-A46N 
          26           40           26         1058         1072          910 
TCGA-60-2695 TCGA-60-2704 TCGA-60-2708 TCGA-60-2712 TCGA-60-2719 TCGA-63-7022 
         642         1943         1963          274         1297         1947 
TCGA-66-2763 TCGA-66-2770 TCGA-66-2777 TCGA-66-2787 TCGA-66-2794 TCGA-66-2800 
          30          700           61         1217         1645         1492 
TCGA-68-8251 TCGA-68-A59J TCGA-77-6843 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 
          96          104         1941         1968           15         1286 
TCGA-77-7465 TCGA-77-8008 TCGA-77-8009 TCGA-77-8148 TCGA-77-8150 TCGA-77-A5G1 
         479         1945         1641          293         1961         1942 
TCGA-77-A5G3 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GF TCGA-85-6561 TCGA-85-6798 
        1959         1963         1290          839          395           34 
TCGA-85-7696 TCGA-85-7843 TCGA-85-7950 TCGA-85-8277 TCGA-85-8353 TCGA-85-8354 
          18           35           60           11           54           61 
TCGA-85-8479 TCGA-85-A4QR TCGA-85-A5B5 TCGA-90-7769 TCGA-90-A4EE TCGA-90-A59Q 
          22           25          111          358          331          269 
TCGA-92-7340 TCGA-92-8064 TCGA-96-7545 TCGA-96-A4JK TCGA-J1-A4AH TCGA-LA-A446 
          82          160         1344          273          222           36 

$`19P GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3408 TCGA-18-3409 TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 
         370         2464         2417          345          396         1810 
TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 
         862          758           50          187           85         2754 
TCGA-18-5592 TCGA-18-5595 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 
          92          827         3636         1426         3016         2134 
TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 
        1852         1058          474          965         3724          284 
TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 TCGA-21-A5DI 
        3644          267          962         1268         1032          979 
TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1016 
         608          223         1945          131         1952          822 
TCGA-22-1017 TCGA-22-4591 TCGA-22-4594 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 
        1485          623         1470           17         1161         1057 
TCGA-22-4605 TCGA-22-4607 TCGA-22-4613 TCGA-22-5472 TCGA-22-5473 TCGA-22-5478 
        1946          587          358         1964         1933           24 
TCGA-22-5479 TCGA-22-5480 TCGA-22-5482 TCGA-22-5485 TCGA-22-5491 TCGA-22-5492 
        1651         1952          357          916         1713          506 
TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4547 TCGA-33-4582 TCGA-33-4583 TCGA-33-4587 
          29         2524         1311         1966         1941         1970 
TCGA-33-4589 TCGA-33-6738 TCGA-34-2604 TCGA-34-2608 TCGA-34-2609 TCGA-34-5232 
        1948          822          958         1000          951         2062 
TCGA-34-5234 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-8454 TCGA-37-3783 
        1715          428          941          552          166          120 
TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 
          13           12          200          247          227          238 
TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5011 TCGA-39-5021 TCGA-39-5022 
         207           12          103         1454         1947         1996 
TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5036 
        1964         1849           52          740           59         1084 
TCGA-39-5037 TCGA-39-5039 TCGA-43-2576 TCGA-43-2578 TCGA-43-2581 TCGA-43-3394 
        1086          544         1223          684         1176          822 
TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 
        1007          349          849          757          310         1936 
TCGA-43-7656 TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 
         212         1970          407          358         1971          353 
TCGA-43-A56U TCGA-43-A56V TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 
         432          366          324          423           12           12 
TCGA-51-4081 TCGA-52-7622 TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 
         911          541          923         1958         1967          881 
TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 
           3          555           62           30           13           30 
TCGA-56-7579 TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-8503 TCGA-56-8504 
          44            6         1961            1           41          178 
TCGA-56-8622 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 
          55           36           63           17           16           34 
TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK 
          38            2           46           30           25            4 
TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-A46J 
           4            8          378          911         2167         2589 
TCGA-58-A46L TCGA-60-2696 TCGA-60-2698 TCGA-60-2703 TCGA-60-2706 TCGA-60-2707 
        1723          109          311         1950         1958          661 
TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 TCGA-60-2713 TCGA-60-2714 TCGA-60-2715 
        1505         1963         1260         1731         1531         1075 
TCGA-60-2716 TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 
        1475           97          983          908         1092          717 
TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 TCGA-63-7023 
         816          358         1973         1957         1955         1952 
TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 TCGA-66-2753 
        1967         1311           61          641           30           31 
TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 
          61           28           30           30          639          762 
TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 TCGA-66-2771 
          61           31           61           61         1947          578 
TCGA-66-2773 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 
        1946          578         1956          121         1954          759 
TCGA-66-2785 TCGA-66-2786 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 
          60          790          699         1955          699         1977 
TCGA-66-2792 TCGA-66-2793 TCGA-66-2795 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 
         913         1952          122           83          202          211 
TCGA-68-8250 TCGA-68-A59I TCGA-77-6842 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 
         244          121         1950         1942         1952         1959 
TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-8007 TCGA-77-8128 
        1954         1942         1952         1954         1960         1953 
TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 
        1945         1941         1941         1947         1946         1951 
TCGA-77-8140 TCGA-77-8144 TCGA-77-8145 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 
        1962          833         1943         1684         1092           10 
TCGA-77-A5FZ TCGA-77-A5G6 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GH TCGA-85-6560 
        1953         1955         1280         1939          713          364 
TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7844 TCGA-85-8048 
          10           49            1         1965          911           26 
TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 
          60           16          960          428          513           13 
TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8355 
          13           54           60           55           67           61 
TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL 
          21          445          424            3          475           15 
TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 
        1972         1960           19         1973         1967         1972 
TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 
        1987           24           13          758          289           89 
TCGA-90-7964 TCGA-90-A4ED TCGA-92-7341 TCGA-92-8063 TCGA-92-8065 TCGA-94-7033 
         428          244          106          122           70           87 
TCGA-94-7943 TCGA-94-A4VJ TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL 
         356          430         1213          189          211          183 
TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-L3-A4E7 TCGA-L3-A524 
         256          413          224          308           35          449 
TCGA-MF-A522 TCGA-NC-A5HE TCGA-NC-A5HG TCGA-NC-A5HI 
          83         1722         1548         1135 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                11                  1 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              5287               3724 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             607.5              651.0 
[1] "11.0 - 5287.0 (607.5)" "1.0 - 3724.0 (651.0)" 
[1] "hr=" "1.3"
D34V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  19P GAIN MUTATED         0       14       32        1        14        16
  19P GAIN WILD-TYPE       1       58      105        0        38        55
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  19P GAIN MUTATED           15          5        0
  19P GAIN WILD-TYPE         42         15        6
D34V3, multiclass
            clus
vv           19P GAIN MUTATED 19P GAIN WILD-TYPE
  STAGE I                   0                  1
  STAGE IA                 14                 58
  STAGE IB                 32                105
  STAGE II                  1                  0
  STAGE IIA                14                 38
  STAGE IIB                16                 55
  STAGE IIIA               15                 42
  STAGE IIIB                5                 15
  STAGE IV                  0                  6
[1] 9 2
[1] 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    18  61  14   4
  19P GAIN WILD-TYPE  80 193  34  16
D34V4, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  T1               18                 80
  T2               61                193
  T3               14                 34
  T4                4                 16
[1] 4 2
[1] 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    56  32   8   0
  19P GAIN WILD-TYPE 205  81  27   5
D34V5, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  N0               56                205
  N1               32                 81
  N2                8                 27
  N3                0                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A  MX
  19P GAIN MUTATED    85   0   0  11
  19P GAIN WILD-TYPE 273   5   1  39
D34V6, multiclass
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  M0                85                273
  M1                 0                  5
  M1A                0                  1
  MX                11                 39
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V7, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    25  72
  19P GAIN WILD-TYPE  82 241
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     25   72
  19P GAIN WILD-TYPE   82  241
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE               25                 82
  MALE                 72                241
[1] 2 2
[1] FALSE
D34V8, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  19P GAIN MUTATED                                       6
  19P GAIN WILD-TYPE                                     6
                    vv
clus                 LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  19P GAIN MUTATED                                        1
  19P GAIN WILD-TYPE                                      5
                    vv
clus                 LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  19P GAIN MUTATED                                         0
  19P GAIN WILD-TYPE                                       1
                    vv
clus                 LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  19P GAIN MUTATED                                                            90
  19P GAIN WILD-TYPE                                                         311
D34V9, multiclass
                                                             clus
vv                                                            19P GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      6
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               90
                                                             clus
vv                                                            19P GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                        6
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                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"
D34V10, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     6  91
  19P GAIN WILD-TYPE   7 316
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      6   91
  19P GAIN WILD-TYPE    7  316
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  NO                 6                  7
  YES               91                316
[1] 2 2
[1] FALSE
D34V11, continuous
                    vv
clus                  R0  R1  R2  RX
  19P GAIN MUTATED    79   2   1   5
  19P GAIN WILD-TYPE 263   6   3  13
D34V12, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  R0               79                263
  R1                2                  6
  R2                1                  3
  RX                5                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19P GAIN MUTATED       2                         3    71
  19P GAIN WILD-TYPE     7                        14   227
D34V13, multiclass
                           clus
vv                          19P GAIN MUTATED 19P GAIN WILD-TYPE
  ASIAN                                    2                  7
  BLACK OR AFRICAN AMERICAN                3                 14
  WHITE                                   71                227
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V14, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     2  60
  19P GAIN WILD-TYPE   6 207
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      2   60
  19P GAIN WILD-TYPE    6  207
                        clus
vv                       19P GAIN MUTATED 19P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  6
  NOT HISPANIC OR LATINO               60                207
[1] 2 2
[1] FALSE

Clustering(35) Variable = 19Q GAIN MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                  0   1
  19Q GAIN MUTATED    80  47
  19Q GAIN WILD-TYPE 185  76
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
               127                261 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                47                 76 
$`19Q GAIN MUTATED`
TCGA-18-3407 TCGA-18-3410 TCGA-18-3411 TCGA-18-3417 TCGA-18-3421 TCGA-21-1070 
         136          146         1415          758         1331         3636 
TCGA-21-1071 TCGA-21-1081 TCGA-21-5786 TCGA-21-5787 TCGA-22-1011 TCGA-22-1012 
        1426          284         1032          329           53          429 
TCGA-22-4593 TCGA-22-4595 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-5477 
        1067          734         1161         1057          399         1346 
TCGA-22-5481 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-33-4533 TCGA-33-4538 
        1952          573          916         1912         1940         2979 
TCGA-33-4566 TCGA-33-4582 TCGA-33-6738 TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 
        5287         1966          822           80         1874          958 
TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 TCGA-34-5239 TCGA-34-5240 
         881         1000          951         1528          707          365 
TCGA-34-5928 TCGA-37-3792 TCGA-37-5819 TCGA-39-5016 TCGA-39-5019 TCGA-39-5029 
         552           12          103         2253         1361          740 
TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5039 TCGA-39-5040 TCGA-43-3920 
         833         1107          474          544         1964         1007 
TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 TCGA-43-7657 TCGA-43-A475 TCGA-43-A56V 
         349          849          376          236          296          366 
TCGA-52-7809 TCGA-56-6545 TCGA-56-6546 TCGA-56-7580 TCGA-56-7582 TCGA-56-8629 
        1948           62           26           40           26           34 
TCGA-56-A49D TCGA-56-A4BY TCGA-56-A5DR TCGA-58-8393 TCGA-58-A46M TCGA-58-A46N 
          38           30            4         1058         1072          910 
TCGA-60-2695 TCGA-60-2704 TCGA-60-2708 TCGA-60-2712 TCGA-60-2719 TCGA-60-2722 
         642         1943         1963          274         1297          908 
TCGA-60-2723 TCGA-63-7020 TCGA-63-7022 TCGA-66-2742 TCGA-66-2758 TCGA-66-2763 
        1092         1957         1947          641          639           30 
TCGA-66-2770 TCGA-66-2777 TCGA-66-2787 TCGA-66-2788 TCGA-66-2793 TCGA-66-2800 
         700           61         1217          699         1952         1492 
TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-77-6842 TCGA-77-6843 TCGA-77-7138 
          96          121          104         1950         1941         1959 
TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7465 TCGA-77-8008 TCGA-77-8009 
          15         1286         1954          479         1945         1641 
TCGA-77-8130 TCGA-77-8138 TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 TCGA-77-A5G1 
        1945         1946         1943          293         1961         1942 
TCGA-77-A5G3 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GF TCGA-85-7696 TCGA-85-7699 
        1959         1963         1290          839           18            1 
TCGA-85-8350 TCGA-85-8353 TCGA-85-8354 TCGA-85-A4QR TCGA-85-A50M TCGA-85-A510 
          60           54           61           25           19         1967 
TCGA-85-A53L TCGA-85-A5B5 TCGA-90-7769 TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 
          13          111          358          331          269           82 
TCGA-92-7341 TCGA-92-8064 TCGA-96-7545 TCGA-96-A4JK TCGA-98-8022 TCGA-J1-A4AH 
         106          160         1344          273          224          222 
TCGA-LA-A446 
          36 

$`19Q GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3408 TCGA-18-3409 TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 
         370         2464         2417          345          396         1810 
TCGA-18-3416 TCGA-18-3419 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 
         862           50          187           85         2754           92 
TCGA-18-5595 TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 
         827         3016         2134         1852         1058          474 
TCGA-21-1079 TCGA-21-1080 TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 TCGA-21-5784 
         965         3724         3644          267          962         1268 
TCGA-21-A5DI TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 
         979          608          223         1945          131         1952 
TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 TCGA-22-4594 TCGA-22-4596 TCGA-22-4605 
         822         1485          623         1470           17         1946 
TCGA-22-4607 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 
         587          358          965         1964         1933          445 
TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5482 TCGA-22-5491 TCGA-22-5492 
          24         1651         1952          357         1713          506 
TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4547 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 
          29         2524         1311         1941          428         1970 
TCGA-33-4589 TCGA-34-5232 TCGA-34-5234 TCGA-34-5241 TCGA-34-5927 TCGA-34-8454 
        1948         2062         1715          428          941          166 
TCGA-37-3783 TCGA-37-3789 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 
         120           13          200          247          227          238 
TCGA-37-4135 TCGA-37-4141 TCGA-39-5011 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 
         207           12         1454         1947         1996         1964 
TCGA-39-5027 TCGA-39-5028 TCGA-39-5030 TCGA-39-5036 TCGA-39-5037 TCGA-43-2576 
        1849           52           59         1084         1086         1223 
TCGA-43-2578 TCGA-43-2581 TCGA-43-3394 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 
         684         1176          822          757          310         1936 
TCGA-43-7656 TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 
         212         1970          407          358         1971          353 
TCGA-43-A56U TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 
         432          324          423           12           12          911 
TCGA-52-7622 TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 
         541          923         1958         1967          881            3 
TCGA-56-5898 TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7730 
         555           30           13           30           44            6 
TCGA-56-7731 TCGA-56-7822 TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 TCGA-56-8624 
        1961            1           41          178           55           36 
TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4ZJ 
          63           17           16            2           46           25 
TCGA-56-A4ZK TCGA-56-A5DS TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-A46J 
           4            8          378          911         2167         2589 
TCGA-58-A46L TCGA-60-2696 TCGA-60-2698 TCGA-60-2703 TCGA-60-2706 TCGA-60-2707 
        1723          109          311         1950         1958          661 
TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 TCGA-60-2713 TCGA-60-2714 TCGA-60-2715 
        1505         1963         1260         1731         1531         1075 
TCGA-60-2716 TCGA-60-2720 TCGA-60-2721 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 
        1475           97          983          717          816          358 
TCGA-63-6202 TCGA-63-7021 TCGA-63-7023 TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 
        1973         1955         1952         1967         1311           61 
TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 
          30           31           61           28           30           30 
TCGA-66-2759 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 
         762           61           31           61           61         1947 
TCGA-66-2771 TCGA-66-2773 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 
         578         1946          578         1956          121         1954 
TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 
         759           60          790         1955          699         1977 
TCGA-66-2792 TCGA-66-2794 TCGA-66-2795 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 
         913         1645          122           83          202          211 
TCGA-68-8250 TCGA-77-6844 TCGA-77-6845 TCGA-77-7139 TCGA-77-7337 TCGA-77-7338 
         244         1942         1952         1968         1942         1952 
TCGA-77-7463 TCGA-77-8007 TCGA-77-8128 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 
        1954         1960         1953         1941         1941         1947 
TCGA-77-8139 TCGA-77-8140 TCGA-77-8144 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 
        1951         1962          833         1684         1092           10 
TCGA-77-A5FZ TCGA-77-A5G6 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GH TCGA-85-6560 
        1953         1955         1280         1939          713          364 
TCGA-85-6561 TCGA-85-6798 TCGA-85-7697 TCGA-85-7698 TCGA-85-7710 TCGA-85-7843 
         395           34           10           49         1965           35 
TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 
         911           60           26           60           16          960 
TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 
         428          513           13           11           13           54 
TCGA-85-8351 TCGA-85-8352 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 
          55           67           61           22           21          445 
TCGA-85-8582 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A4QQ 
         424            3          475           15         1972         1960 
TCGA-85-A50Z TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 TCGA-90-6837 TCGA-90-7766 
        1973         1972         1987           24          758          289 
TCGA-90-7767 TCGA-90-7964 TCGA-90-A4ED TCGA-92-8063 TCGA-92-8065 TCGA-94-7033 
          89          428          244          122           70           87 
TCGA-94-7943 TCGA-94-A4VJ TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL 
         356          430         1213          189          211          183 
TCGA-98-7454 TCGA-98-8021 TCGA-98-8023 TCGA-L3-A4E7 TCGA-L3-A524 TCGA-MF-A522 
         256          413          308           35          449           83 
TCGA-NC-A5HE TCGA-NC-A5HG TCGA-NC-A5HI 
        1722         1548         1135 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 1                  1 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              5287               3724 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
               740                555 
[1] "1.0 - 5287.0 (740.0)" "1.0 - 3724.0 (555.0)"
[1] "hr=" "1.4"
D35V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  19Q GAIN MUTATED         0       19       43        1        19        22
  19Q GAIN WILD-TYPE       1       53       94        0        33        49
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  19Q GAIN MUTATED           24          6        2
  19Q GAIN WILD-TYPE         33         14        4
D35V3, multiclass
            clus
vv           19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  STAGE I                   0                  1
  STAGE IA                 19                 53
  STAGE IB                 43                 94
  STAGE II                  1                  0
  STAGE IIA                19                 33
  STAGE IIB                22                 49
  STAGE IIIA               24                 33
  STAGE IIIB                6                 14
  STAGE IV                  2                  4
[1] 9 2
[1] 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    26  88  14   8
  19Q GAIN WILD-TYPE  72 166  34  12
D35V4, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  T1               26                 72
  T2               88                166
  T3               14                 34
  T4                8                 12
[1] 4 2
[1] 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    81  41  14   0
  19Q GAIN WILD-TYPE 180  72  21   5
D35V5, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  N0               81                180
  N1               41                 72
  N2               14                 21
  N3                0                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A  MX
  19Q GAIN MUTATED   116   2   0  17
  19Q GAIN WILD-TYPE 242   3   1  33
D35V6, multiclass
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  M0               116                242
  M1                 2                  3
  M1A                0                  1
  MX                17                 33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V7, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    36 100
  19Q GAIN WILD-TYPE  71 213
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     36  100
  19Q GAIN WILD-TYPE   71  213
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE               36                 71
  MALE                100                213
[1] 2 2
[1] FALSE
D35V8, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  19Q GAIN MUTATED                                       7
  19Q GAIN WILD-TYPE                                     5
                    vv
clus                 LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  19Q GAIN MUTATED                                        0
  19Q GAIN WILD-TYPE                                      6
                    vv
clus                 LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  19Q GAIN MUTATED                                         0
  19Q GAIN WILD-TYPE                                       1
                    vv
clus                 LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  19Q GAIN MUTATED                                                           129
  19Q GAIN WILD-TYPE                                                         272
D35V9, multiclass
                                                             clus
vv                                                            19Q GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      7
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     0
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              129
                                                             clus
vv                                                            19Q GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                        5
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                272
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V10, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     3 133
  19Q GAIN WILD-TYPE  10 274
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      3  133
  19Q GAIN WILD-TYPE   10  274
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  NO                 3                 10
  YES              133                274
[1] 2 2
[1] FALSE
D35V11, continuous
                    vv
clus                  R0  R1  R2  RX
  19Q GAIN MUTATED   112   3   0   5
  19Q GAIN WILD-TYPE 230   5   4  13
D35V12, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  R0              112                230
  R1                3                  5
  R2                0                  4
  RX                5                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19Q GAIN MUTATED       4                         7    95
  19Q GAIN WILD-TYPE     5                        10   203
D35V13, multiclass
                           clus
vv                          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  ASIAN                                    4                  5
  BLACK OR AFRICAN AMERICAN                7                 10
  WHITE                                   95                203
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V14, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     3  82
  19Q GAIN WILD-TYPE   5 185
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      3   82
  19Q GAIN WILD-TYPE    5  185
                        clus
vv                       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  5
  NOT HISPANIC OR LATINO               82                185
[1] 2 2
[1] FALSE

Clustering(36) Variable = 20P GAIN MUTATION ANALYSIS
D36V1, survival
                    sevent
clus2                  0   1
  20P GAIN MUTATED   131  64
  20P GAIN WILD-TYPE 134  59
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               195                193 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                64                 59 
$`20P GAIN MUTATED`
TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 
         136         2417          146         1415          345          396 
TCGA-18-3417 TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 TCGA-21-1076 TCGA-21-1077 
         758           92         3636         1426         1852         1058 
TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 TCGA-21-1083 TCGA-21-5784 TCGA-21-5786 
        3724          284         3644          267         1268         1032 
TCGA-21-A5DI TCGA-22-1011 TCGA-22-1016 TCGA-22-4591 TCGA-22-4594 TCGA-22-4595 
         979           53          822          623         1470          734 
TCGA-22-4604 TCGA-22-4605 TCGA-22-5471 TCGA-22-5472 TCGA-22-5477 TCGA-22-5480 
         399         1946          965         1964         1346         1952 
TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5491 TCGA-22-A5C4 TCGA-33-4532 
         357          573          916         1713           29         2524 
TCGA-33-4538 TCGA-33-4582 TCGA-33-4587 TCGA-33-4589 TCGA-33-6738 TCGA-34-2596 
        2979         1966         1970         1948          822           80 
TCGA-34-2600 TCGA-34-2605 TCGA-34-2608 TCGA-34-5231 TCGA-34-5239 TCGA-34-5240 
        1874          881         1000         1528          707          365 
TCGA-34-5928 TCGA-37-3783 TCGA-37-4130 TCGA-37-4141 TCGA-37-5819 TCGA-39-5016 
         552          120          247           12          103         2253 
TCGA-39-5019 TCGA-39-5021 TCGA-39-5028 TCGA-39-5029 TCGA-39-5031 TCGA-39-5036 
        1361         1947           52          740          833         1084 
TCGA-39-5037 TCGA-39-5039 TCGA-43-2576 TCGA-43-2578 TCGA-43-3920 TCGA-43-5670 
        1086          544         1223          684         1007          849 
TCGA-43-6143 TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 TCGA-43-8118 TCGA-43-A474 
         376          212          236         1970         1971          353 
TCGA-43-A56V TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4081 TCGA-52-7622 
         366          324          423           12          911          541 
TCGA-52-7809 TCGA-52-7811 TCGA-56-1622 TCGA-56-5898 TCGA-56-6545 TCGA-56-7222 
        1948         1958          881          555           62           13 
TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7822 
          30           44           40           26            6            1 
TCGA-56-8504 TCGA-56-8622 TCGA-56-8624 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4ZJ 
         178           55           36           38            2           25 
TCGA-56-A4ZK TCGA-56-A5DR TCGA-58-8391 TCGA-58-8393 TCGA-60-2695 TCGA-60-2698 
           4            4         2167         1058          642          311 
TCGA-60-2703 TCGA-60-2704 TCGA-60-2707 TCGA-60-2708 TCGA-60-2711 TCGA-60-2715 
        1950         1943          661         1963         1260         1075 
TCGA-60-2719 TCGA-60-2720 TCGA-60-2722 TCGA-60-2723 TCGA-60-2726 TCGA-63-7020 
        1297           97          908         1092          358         1957 
TCGA-66-2737 TCGA-66-2742 TCGA-66-2756 TCGA-66-2759 TCGA-66-2763 TCGA-66-2769 
          61          641           30          762           30         1947 
TCGA-66-2770 TCGA-66-2773 TCGA-66-2777 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 
         700         1946           61         1956          121         1954 
TCGA-66-2783 TCGA-66-2787 TCGA-66-2788 TCGA-66-2792 TCGA-66-2793 TCGA-66-2800 
         759         1217          699          913         1952         1492 
TCGA-68-7756 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-77-6842 TCGA-77-6844 
         202          244           96          121         1950         1942 
TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7338 
        1952         1959         1968           15         1286         1952 
TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 TCGA-77-8130 TCGA-77-8133 TCGA-77-8136 
        1960         1945         1641         1945         1941         1947 
TCGA-77-8156 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB 
          10         1959         1955         1290         1280         1939 
TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6561 TCGA-85-7696 TCGA-85-7698 TCGA-85-7843 
         839          713          395           18           49           35 
TCGA-85-7844 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8276 TCGA-85-8277 
         911           60           16          960           13           11 
TCGA-85-8287 TCGA-85-8350 TCGA-85-8353 TCGA-85-8481 TCGA-85-8664 TCGA-85-8666 
          13           60           54           21            3          475 
TCGA-85-A4QQ TCGA-85-A50M TCGA-85-A510 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-7767 
        1960           19         1967           13          111           89 
TCGA-90-7769 TCGA-90-A4ED TCGA-90-A4EE TCGA-92-7341 TCGA-92-8064 TCGA-94-7943 
         358          244          331          106          160          356 
TCGA-96-7545 TCGA-96-A4JK TCGA-98-8021 TCGA-98-8022 TCGA-J1-A4AH TCGA-L3-A4E7 
        1344          273          413          224          222           35 
TCGA-L3-A524 TCGA-LA-A446 TCGA-NC-A5HI 
         449           36         1135 

$`20P GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3408 TCGA-18-3415 TCGA-18-3416 TCGA-18-3419 TCGA-18-3421 
         370         2464         1810          862           50         1331 
TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5595 TCGA-21-1072 TCGA-21-1075 
         187           85         2754          827         3016         2134 
TCGA-21-1078 TCGA-21-1079 TCGA-21-5782 TCGA-21-5787 TCGA-22-0940 TCGA-22-0944 
         474          965          962          329          608          223 
TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1012 TCGA-22-1017 TCGA-22-4593 
        1945          131         1952          429         1485         1067 
TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 TCGA-22-4607 TCGA-22-4613 TCGA-22-5473 
          17         1161         1057          587          358         1933 
TCGA-22-5474 TCGA-22-5478 TCGA-22-5479 TCGA-22-5481 TCGA-22-5489 TCGA-22-5492 
         445           24         1651         1952         1912          506 
TCGA-33-4533 TCGA-33-4547 TCGA-33-4566 TCGA-33-4583 TCGA-33-4586 TCGA-34-2604 
        1940         1311         5287         1941          428          958 
TCGA-34-2609 TCGA-34-5232 TCGA-34-5234 TCGA-34-5241 TCGA-34-5927 TCGA-34-8454 
         951         2062         1715          428          941          166 
TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 
          13           12          200          227          238          207 
TCGA-39-5011 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5030 TCGA-39-5034 
        1454         1996         1964         1849           59         1107 
TCGA-39-5035 TCGA-39-5040 TCGA-43-2581 TCGA-43-3394 TCGA-43-5668 TCGA-43-6647 
         474         1964         1176          822          349          757 
TCGA-43-6770 TCGA-43-6771 TCGA-43-8115 TCGA-43-8116 TCGA-43-A475 TCGA-43-A56U 
         310         1936          407          358          296          432 
TCGA-51-4080 TCGA-52-7810 TCGA-52-7812 TCGA-56-5897 TCGA-56-6546 TCGA-56-7221 
          12          923         1967            3           26           30 
TCGA-56-7731 TCGA-56-8503 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 
        1961           41           63           17           16           34 
TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A5DS TCGA-58-8388 TCGA-58-8390 TCGA-58-A46J 
          46           30            8          378          911         2589 
TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2696 TCGA-60-2706 TCGA-60-2709 
        1723         1072          910          109         1958         1505 
TCGA-60-2710 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2716 TCGA-60-2721 
        1963          274         1731         1531         1475          983 
TCGA-60-2724 TCGA-60-2725 TCGA-63-6202 TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 
         717          816         1973         1955         1947         1952 
TCGA-66-2727 TCGA-66-2734 TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 
        1967         1311           30           31           61           28 
TCGA-66-2757 TCGA-66-2758 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 
          30          639           61           31           61           61 
TCGA-66-2771 TCGA-66-2778 TCGA-66-2785 TCGA-66-2786 TCGA-66-2789 TCGA-66-2790 
         578          578           60          790         1955          699 
TCGA-66-2791 TCGA-66-2794 TCGA-66-2795 TCGA-68-7755 TCGA-68-7757 TCGA-68-A59J 
        1977         1645          122           83          211          104 
TCGA-77-6843 TCGA-77-7335 TCGA-77-7337 TCGA-77-7463 TCGA-77-7465 TCGA-77-8128 
        1941         1954         1942         1954          479         1953 
TCGA-77-8131 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8144 TCGA-77-8145 
        1941         1946         1951         1962          833         1943 
TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G1 
         293         1961         1684         1092         1953         1942 
TCGA-77-A5G7 TCGA-85-6560 TCGA-85-6798 TCGA-85-7697 TCGA-85-7699 TCGA-85-7710 
        1963          364           34           10            1         1965 
TCGA-85-7950 TCGA-85-8048 TCGA-85-8071 TCGA-85-8072 TCGA-85-8288 TCGA-85-8351 
          60           26          428          513           54           55 
TCGA-85-8352 TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 TCGA-85-8580 TCGA-85-8582 
          67           61           61           22          445          424 
TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A4QR TCGA-85-A50Z TCGA-85-A511 TCGA-85-A512 
          15         1972           25         1973         1972         1987 
TCGA-85-A513 TCGA-90-6837 TCGA-90-7766 TCGA-90-7964 TCGA-90-A59Q TCGA-92-7340 
          24          758          289          428          269           82 
TCGA-92-8063 TCGA-92-8065 TCGA-94-7033 TCGA-94-A4VJ TCGA-96-7544 TCGA-96-8169 
         122           70           87          430         1213          189 
TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8023 TCGA-MF-A522 TCGA-NC-A5HE 
         211          183          256          308           83         1722 
TCGA-NC-A5HG 
        1548 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 1                  1 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              3724               5287 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               699                578 
[1] "1.0 - 3724.0 (699.0)" "1.0 - 5287.0 (578.0)"
[1] "hr=" "1.2"
D36V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  20P GAIN MUTATED         1       33       73        1        22        40
  20P GAIN WILD-TYPE       0       39       64        0        30        31
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  20P GAIN MUTATED           32          7        5
  20P GAIN WILD-TYPE         25         13        1
D36V3, multiclass
            clus
vv           20P GAIN MUTATED 20P GAIN WILD-TYPE
  STAGE I                   1                  0
  STAGE IA                 33                 39
  STAGE IB                 73                 64
  STAGE II                  1                  0
  STAGE IIA                22                 30
  STAGE IIB                40                 31
  STAGE IIIA               32                 25
  STAGE IIIB                7                 13
  STAGE IV                  5                  1
[1] 9 2
[1] 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    45 134  27  10
  20P GAIN WILD-TYPE  53 120  21  10
D36V4, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  T1               45                 53
  T2              134                120
  T3               27                 21
  T4               10                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  20P GAIN MUTATED   134  59  18   1
  20P GAIN WILD-TYPE 127  54  17   4
D36V5, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  N0              134                127
  N1               59                 54
  N2               18                 17
  N3                1                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A  MX
  20P GAIN MUTATED   186   4   1  22
  20P GAIN WILD-TYPE 172   1   0  28
D36V6, multiclass
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  M0               186                172
  M1                 4                  1
  M1A                1                  0
  MX                22                 28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V7, binary
                    cls
clus                   0   1
  20P GAIN MUTATED    45 171
  20P GAIN WILD-TYPE  62 142
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     45  171
  20P GAIN WILD-TYPE   62  142
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE               45                 62
  MALE                171                142
[1] 2 2
[1] FALSE
D36V8, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  20P GAIN MUTATED                                       7
  20P GAIN WILD-TYPE                                     5
                    vv
clus                 LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  20P GAIN MUTATED                                        2
  20P GAIN WILD-TYPE                                      4
                    vv
clus                 LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  20P GAIN MUTATED                                         1
  20P GAIN WILD-TYPE                                       0
                    vv
clus                 LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  20P GAIN MUTATED                                                           206
  20P GAIN WILD-TYPE                                                         195
D36V9, multiclass
                                                             clus
vv                                                            20P GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      7
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              206
                                                             clus
vv                                                            20P GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                        5
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                195
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V10, binary
                    cls
clus                   0   1
  20P GAIN MUTATED     9 207
  20P GAIN WILD-TYPE   4 200
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      9  207
  20P GAIN WILD-TYPE    4  200
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  NO                 9                  4
  YES              207                200
[1] 2 2
[1] FALSE
D36V11, continuous
                    vv
clus                  R0  R1  R2  RX
  20P GAIN MUTATED   178   3   3   8
  20P GAIN WILD-TYPE 164   5   1  10
D36V12, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  R0              178                164
  R1                3                  5
  R2                3                  1
  RX                8                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20P GAIN MUTATED       6                         8   154
  20P GAIN WILD-TYPE     3                         9   144
D36V13, multiclass
                           clus
vv                          20P GAIN MUTATED 20P GAIN WILD-TYPE
  ASIAN                                    6                  3
  BLACK OR AFRICAN AMERICAN                8                  9
  WHITE                                  154                144
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V14, binary
                    cls
clus                   0   1
  20P GAIN MUTATED     7 135
  20P GAIN WILD-TYPE   1 132
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      7  135
  20P GAIN WILD-TYPE    1  132
                        clus
vv                       20P GAIN MUTATED 20P GAIN WILD-TYPE
  HISPANIC OR LATINO                    7                  1
  NOT HISPANIC OR LATINO              135                132
[1] 2 2
[1] FALSE

Clustering(37) Variable = 20Q GAIN MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                  0   1
  20Q GAIN MUTATED   127  66
  20Q GAIN WILD-TYPE 138  57
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               193                195 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                66                 57 
$`20Q GAIN MUTATED`
TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3412 TCGA-18-3414 TCGA-18-3417 
         136         2417          146          345          396          758 
TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 TCGA-21-1076 TCGA-21-1077 TCGA-21-1079 
          92         3636         1426         1852         1058          965 
TCGA-21-1081 TCGA-21-1082 TCGA-21-1083 TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 
         284         3644          267         1268         1032          329 
TCGA-21-A5DI TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-4591 TCGA-22-4593 
         979           53          429          822          623         1067 
TCGA-22-4594 TCGA-22-4595 TCGA-22-4605 TCGA-22-5472 TCGA-22-5480 TCGA-22-5483 
        1470          734         1946         1964         1952          573 
TCGA-22-5485 TCGA-22-5491 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4538 TCGA-33-4582 
         916         1713           29         2524         2979         1966 
TCGA-33-4587 TCGA-33-4589 TCGA-33-6738 TCGA-34-2596 TCGA-34-2604 TCGA-34-2605 
        1970         1948          822           80          958          881 
TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 TCGA-34-5239 TCGA-34-5240 TCGA-34-5928 
        1000          951         1528          707          365          552 
TCGA-37-3783 TCGA-37-3792 TCGA-37-4130 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 
         120           12          247          207           12          103 
TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5028 TCGA-39-5029 TCGA-39-5031 
        1454         2253         1361           52          740          833 
TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 TCGA-43-2576 TCGA-43-2578 TCGA-43-3920 
        1084         1086          544         1223          684         1007 
TCGA-43-5670 TCGA-43-6143 TCGA-43-6771 TCGA-43-7656 TCGA-43-7658 TCGA-43-8118 
         849          376         1936          212         1970         1971 
TCGA-43-A56V TCGA-46-6026 TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 TCGA-56-1622 
         366          423         1948          923         1958          881 
TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 
         555           62           26           13           30           44 
TCGA-56-7582 TCGA-56-7822 TCGA-56-8504 TCGA-56-8624 TCGA-56-8626 TCGA-56-A4BW 
          26            1          178           36           17            2 
TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR TCGA-58-8393 TCGA-60-2695 TCGA-60-2703 
          25            4            4         1058          642         1950 
TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2711 TCGA-60-2714 
        1943         1958          661         1963         1260         1531 
TCGA-60-2715 TCGA-60-2719 TCGA-60-2720 TCGA-60-2722 TCGA-60-2726 TCGA-63-7020 
        1075         1297           97          908          358         1957 
TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 TCGA-66-2756 TCGA-66-2757 TCGA-66-2759 
          61          641           30           30           30          762 
TCGA-66-2763 TCGA-66-2769 TCGA-66-2770 TCGA-66-2777 TCGA-66-2780 TCGA-66-2781 
          30         1947          700           61         1956          121 
TCGA-66-2782 TCGA-66-2785 TCGA-66-2787 TCGA-66-2788 TCGA-66-2793 TCGA-66-2800 
        1954           60         1217          699         1952         1492 
TCGA-68-7756 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-77-6845 TCGA-77-7138 
         202          244           96          121         1952         1959 
TCGA-77-7139 TCGA-77-7141 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 
        1968           15         1942         1952         1954          479 
TCGA-77-8007 TCGA-77-8008 TCGA-77-8130 TCGA-77-8133 TCGA-77-8136 TCGA-77-8145 
        1960         1945         1945         1941         1947         1943 
TCGA-77-8148 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5GA TCGA-77-A5GB 
         293         1959         1955         1963         1280         1939 
TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6560 TCGA-85-6561 TCGA-85-7696 TCGA-85-7843 
         839          713          364          395           18           35 
TCGA-85-7844 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8276 TCGA-85-8277 
         911           60           16          960           13           11 
TCGA-85-8287 TCGA-85-8350 TCGA-85-8351 TCGA-85-8353 TCGA-85-8354 TCGA-85-8481 
          13           60           55           54           61           21 
TCGA-85-8582 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M 
         424            3          475         1960           25           19 
TCGA-85-A510 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-7767 TCGA-90-7769 TCGA-90-A4ED 
        1967           13          111           89          358          244 
TCGA-90-A4EE TCGA-92-7341 TCGA-92-8064 TCGA-94-7943 TCGA-94-A4VJ TCGA-96-7545 
         331          106          160          356          430         1344 
TCGA-98-8022 TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HG 
         224          222           35           36           83         1548 
TCGA-NC-A5HI 
        1135 

$`20Q GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3408 TCGA-18-3411 TCGA-18-3415 TCGA-18-3416 TCGA-18-3419 
         370         2464         1415         1810          862           50 
TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5595 TCGA-21-1072 
        1331          187           85         2754          827         3016 
TCGA-21-1075 TCGA-21-1078 TCGA-21-1080 TCGA-21-5782 TCGA-22-0940 TCGA-22-0944 
        2134          474         3724          962          608          223 
TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1017 TCGA-22-4596 TCGA-22-4599 
        1945          131         1952         1485           17         1161 
TCGA-22-4601 TCGA-22-4604 TCGA-22-4607 TCGA-22-4613 TCGA-22-5471 TCGA-22-5473 
        1057          399          587          358          965         1933 
TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5481 TCGA-22-5482 
         445         1346           24         1651         1952          357 
TCGA-22-5489 TCGA-22-5492 TCGA-33-4533 TCGA-33-4547 TCGA-33-4566 TCGA-33-4583 
        1912          506         1940         1311         5287         1941 
TCGA-33-4586 TCGA-34-2600 TCGA-34-5232 TCGA-34-5234 TCGA-34-5241 TCGA-34-5927 
         428         1874         2062         1715          428          941 
TCGA-34-8454 TCGA-37-3789 TCGA-37-4129 TCGA-37-4132 TCGA-37-4133 TCGA-39-5021 
         166           13          200          227          238         1947 
TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5030 TCGA-39-5034 TCGA-39-5035 
        1996         1964         1849           59         1107          474 
TCGA-39-5040 TCGA-43-2581 TCGA-43-3394 TCGA-43-5668 TCGA-43-6647 TCGA-43-6770 
        1964         1176          822          349          757          310 
TCGA-43-7657 TCGA-43-8115 TCGA-43-8116 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U 
         236          407          358          353          296          432 
TCGA-46-6025 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7812 
         324           12           12          911          541         1967 
TCGA-56-5897 TCGA-56-7221 TCGA-56-7580 TCGA-56-7730 TCGA-56-7731 TCGA-56-8503 
           3           30           40            6         1961           41 
TCGA-56-8622 TCGA-56-8625 TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BX 
          55           63           16           34           38           46 
TCGA-56-A4BY TCGA-56-A5DS TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-A46J 
          30            8          378          911         2167         2589 
TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2696 TCGA-60-2698 TCGA-60-2709 
        1723         1072          910          109          311         1505 
TCGA-60-2710 TCGA-60-2712 TCGA-60-2713 TCGA-60-2716 TCGA-60-2721 TCGA-60-2723 
        1963          274         1731         1475          983         1092 
TCGA-60-2724 TCGA-60-2725 TCGA-63-6202 TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 
         717          816         1973         1955         1947         1952 
TCGA-66-2727 TCGA-66-2734 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2758 
        1967         1311           31           61           28          639 
TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2771 TCGA-66-2773 
          61           31           61           61          578         1946 
TCGA-66-2778 TCGA-66-2783 TCGA-66-2786 TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 
         578          759          790         1955          699         1977 
TCGA-66-2792 TCGA-66-2794 TCGA-66-2795 TCGA-68-7755 TCGA-68-7757 TCGA-68-A59J 
         913         1645          122           83          211          104 
TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-7142 TCGA-77-7335 TCGA-77-8009 
        1950         1941         1942         1286         1954         1641 
TCGA-77-8128 TCGA-77-8131 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8144 
        1953         1941         1946         1951         1962          833 
TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 
        1961         1684         1092           10         1953         1942 
TCGA-77-A5G8 TCGA-85-6798 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 
        1290           34           10           49            1         1965 
TCGA-85-7950 TCGA-85-8048 TCGA-85-8071 TCGA-85-8072 TCGA-85-8288 TCGA-85-8352 
          60           26          428          513           54           67 
TCGA-85-8355 TCGA-85-8479 TCGA-85-8580 TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A50Z 
          61           22          445           15         1972         1973 
TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 TCGA-90-6837 TCGA-90-7766 TCGA-90-7964 
        1972         1987           24          758          289          428 
TCGA-90-A59Q TCGA-92-7340 TCGA-92-8063 TCGA-92-8065 TCGA-94-7033 TCGA-96-7544 
         269           82          122           70           87         1213 
TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 
         189          211          273          183          256          413 
TCGA-98-8023 TCGA-L3-A524 TCGA-NC-A5HE 
         308          449         1722 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 1                  1 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              3644               5287 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               661                608 
[1] "1.0 - 3644.0 (661.0)" "1.0 - 5287.0 (608.0)"
[1] "hr=" "1.3"
D37V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  20Q GAIN MUTATED         1       34       68        0        23        35
  20Q GAIN WILD-TYPE       0       38       69        1        29        36
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  20Q GAIN MUTATED           32          8        5
  20Q GAIN WILD-TYPE         25         12        1
D37V3, multiclass
            clus
vv           20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  STAGE I                   1                  0
  STAGE IA                 34                 38
  STAGE IB                 68                 69
  STAGE II                  0                  1
  STAGE IIA                23                 29
  STAGE IIB                35                 36
  STAGE IIIA               32                 25
  STAGE IIIB                8                 12
  STAGE IV                  5                  1
[1] 9 2
[1] 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    46 124  27  11
  20Q GAIN WILD-TYPE  52 130  21   9
D37V4, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T1               46                 52
  T2              124                130
  T3               27                 21
  T4               11                  9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  20Q GAIN MUTATED   130  57  17   0
  20Q GAIN WILD-TYPE 131  56  18   5
D37V5, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  N0              130                131
  N1               57                 56
  N2               17                 18
  N3                0                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A  MX
  20Q GAIN MUTATED   178   4   1  23
  20Q GAIN WILD-TYPE 180   1   0  27
D37V6, multiclass
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  M0               178                180
  M1                 4                  1
  M1A                1                  0
  MX                23                 27
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V7, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED    41 167
  20Q GAIN WILD-TYPE  66 146
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     41  167
  20Q GAIN WILD-TYPE   66  146
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE               41                 66
  MALE                167                146
[1] 2 2
[1] FALSE
D37V8, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  20Q GAIN MUTATED                                       8
  20Q GAIN WILD-TYPE                                     4
                    vv
clus                 LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  20Q GAIN MUTATED                                        2
  20Q GAIN WILD-TYPE                                      4
                    vv
clus                 LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  20Q GAIN MUTATED                                         1
  20Q GAIN WILD-TYPE                                       0
                    vv
clus                 LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  20Q GAIN MUTATED                                                           197
  20Q GAIN WILD-TYPE                                                         204
D37V9, multiclass
                                                             clus
vv                                                            20Q GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      8
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              197
                                                             clus
vv                                                            20Q GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                        4
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                204
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V10, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED     8 200
  20Q GAIN WILD-TYPE   5 207
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      8  200
  20Q GAIN WILD-TYPE    5  207
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  NO                 8                  5
  YES              200                207
[1] 2 2
[1] FALSE
D37V11, continuous
                    vv
clus                  R0  R1  R2  RX
  20Q GAIN MUTATED   170   4   1   8
  20Q GAIN WILD-TYPE 172   4   3  10
D37V12, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  R0              170                172
  R1                4                  4
  R2                1                  3
  RX                8                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20Q GAIN MUTATED       6                         9   147
  20Q GAIN WILD-TYPE     3                         8   151
D37V13, multiclass
                           clus
vv                          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  ASIAN                                    6                  3
  BLACK OR AFRICAN AMERICAN                9                  8
  WHITE                                  147                151
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V14, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED     6 134
  20Q GAIN WILD-TYPE   2 133
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      6  134
  20Q GAIN WILD-TYPE    2  133
                        clus
vv                       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    6                  2
  NOT HISPANIC OR LATINO              134                133
[1] 2 2
[1] FALSE

Clustering(38) Variable = 21Q GAIN MUTATION ANALYSIS
D38V1, survival
                    sevent
clus2                  0   1
  21Q GAIN MUTATED    30  14
  21Q GAIN WILD-TYPE 235 109
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                44                344 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                14                109 
$`21Q GAIN MUTATED`
TCGA-18-3410 TCGA-21-1077 TCGA-21-1081 TCGA-21-1082 TCGA-21-A5DI TCGA-22-1011 
         146         1058          284         3644          979           53 
TCGA-22-4595 TCGA-22-A5C4 TCGA-33-4566 TCGA-33-4583 TCGA-33-4587 TCGA-34-2596 
         734           29         5287         1941         1970           80 
TCGA-34-2605 TCGA-34-5240 TCGA-34-5928 TCGA-39-5028 TCGA-43-6143 TCGA-43-6647 
         881          365          552           52          376          757 
TCGA-43-A475 TCGA-56-7221 TCGA-56-8504 TCGA-56-A4BY TCGA-60-2706 TCGA-60-2714 
         296           30          178           30         1958         1531 
TCGA-60-2724 TCGA-66-2756 TCGA-66-2767 TCGA-66-2770 TCGA-66-2783 TCGA-77-6844 
         717           30           61          700          759         1942 
TCGA-77-7139 TCGA-77-8130 TCGA-77-8139 TCGA-77-A5G7 TCGA-77-A5GA TCGA-85-6560 
        1968         1945         1951         1963         1280          364 
TCGA-85-7844 TCGA-85-7950 TCGA-85-8277 TCGA-85-8353 TCGA-92-7340 TCGA-96-7545 
         911           60           11           54           82         1344 
TCGA-NC-A5HG TCGA-NC-A5HI 
        1548         1135 

$`21Q GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3411 TCGA-18-3412 
         370          136         2464         2417         1415          345 
TCGA-18-3414 TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 
         396         1810          862          758           50         1331 
TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1070 
         187           85         2754           92          827         3636 
TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1078 TCGA-21-1079 
        1426         3016         2134         1852          474          965 
TCGA-21-1080 TCGA-21-1083 TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 
        3724          267          962         1268         1032          329 
TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1012 
         608          223         1945          131         1952          429 
TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4596 
         822         1485          623         1067         1470           17 
TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-4613 
        1161         1057          399         1946          587          358 
TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 
         965         1964         1933          445         1346           24 
TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 
        1651         1952         1952          357          573          916 
TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-33-4532 TCGA-33-4533 TCGA-33-4538 
        1912         1713          506         2524         1940         2979 
TCGA-33-4547 TCGA-33-4582 TCGA-33-4586 TCGA-33-4589 TCGA-33-6738 TCGA-34-2600 
        1311         1966          428         1948          822         1874 
TCGA-34-2604 TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 
         958         1000          951         1528         2062         1715 
TCGA-34-5239 TCGA-34-5241 TCGA-34-5927 TCGA-34-8454 TCGA-37-3783 TCGA-37-3789 
         707          428          941          166          120           13 
TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 
          12          200          247          227          238          207 
TCGA-37-4141 TCGA-37-5819 TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 
          12          103         1454         2253         1361         1947 
TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 
        1996         1964         1849          740           59          833 
TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 TCGA-39-5040 
        1107          474         1084         1086          544         1964 
TCGA-43-2576 TCGA-43-2578 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 
        1223          684         1176          822         1007          349 
TCGA-43-5670 TCGA-43-6770 TCGA-43-6771 TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 
         849          310         1936          212          236         1970 
TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56U TCGA-43-A56V 
         407          358         1971          353          432          366 
TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 
         324          423           12           12          911          541 
TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 
        1948          923         1958         1967          881            3 
TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 
         555           62           26           13           30           44 
TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-8503 
          40           26            6         1961            1           41 
TCGA-56-8622 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 
          55           36           63           17           16           34 
TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR 
          38            2           46           25            4            4 
TCGA-56-A5DS TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-8393 TCGA-58-A46J 
           8          378          911         2167         1058         2589 
TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 TCGA-60-2696 TCGA-60-2698 
        1723         1072          910          642          109          311 
TCGA-60-2703 TCGA-60-2704 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 
        1950         1943          661         1963         1505         1963 
TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2715 TCGA-60-2716 TCGA-60-2719 
        1260          274         1731         1075         1475         1297 
TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 TCGA-60-2725 TCGA-60-2726 
          97          983          908         1092          816          358 
TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 TCGA-66-2727 
        1973         1957         1955         1947         1952         1967 
TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 
        1311           61          641           30           31           61 
TCGA-66-2755 TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 
          28           30          639          762           30           61 
TCGA-66-2766 TCGA-66-2768 TCGA-66-2769 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 
          31           61         1947          578         1946           61 
TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2785 TCGA-66-2786 
         578         1956          121         1954           60          790 
TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 TCGA-66-2792 
        1217          699         1955          699         1977          913 
TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 
        1952         1645          122         1492           83          202 
TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-77-6842 
         211          244           96          121          104         1950 
TCGA-77-6843 TCGA-77-6845 TCGA-77-7138 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 
        1941         1952         1959           15         1286         1954 
TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 
        1942         1952         1954          479         1960         1945 
TCGA-77-8009 TCGA-77-8128 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 
        1641         1953         1941         1941         1947         1946 
TCGA-77-8140 TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 
        1962          833         1943          293         1961         1684 
TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 
        1092           10         1953         1942         1959         1955 
TCGA-77-A5G8 TCGA-77-A5GB TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6561 TCGA-85-6798 
        1290         1939          839          713          395           34 
TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 
          18           10           49            1         1965           35 
TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 
          26           60           16          960          428          513 
TCGA-85-8276 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 
          13           13           54           60           55           67 
TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 
          61           61           22           21          445          424 
TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR 
           3          475           15         1972         1960           25 
TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 
          19         1973         1967         1972         1987           24 
TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 
          13          111          758          289           89          358 
TCGA-90-7964 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7341 TCGA-92-8063 
         428          244          331          269          106          122 
TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 TCGA-94-7943 TCGA-94-A4VJ TCGA-96-7544 
         160           70           87          356          430         1213 
TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 
         189          211          273          183          256          413 
TCGA-98-8022 TCGA-98-8023 TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 
         224          308          222           35          449           36 
TCGA-MF-A522 TCGA-NC-A5HE 
          83         1722 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                11                  1 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              5287               3724 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             725.5              631.0 
[1] "11.0 - 5287.0 (725.5)" "1.0 - 3724.0 (631.0)" 
[1] "hr=" "1.1"
D38V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  21Q GAIN MUTATED         1        4       13        0         3        12
  21Q GAIN WILD-TYPE       0       68      124        1        49        59
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  21Q GAIN MUTATED           10          4        0
  21Q GAIN WILD-TYPE         47         16        6
D38V3, multiclass
            clus
vv           21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  STAGE I                   1                  0
  STAGE IA                  4                 68
  STAGE IB                 13                124
  STAGE II                  0                  1
  STAGE IIA                 3                 49
  STAGE IIB                12                 59
  STAGE IIIA               10                 47
  STAGE IIIB                4                 16
  STAGE IV                  0                  6
[1] 9 2
[1] 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     6  29  10   3
  21Q GAIN WILD-TYPE  92 225  38  17
D38V4, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  T1                6                 92
  T2               29                225
  T3               10                 38
  T4                3                 17
[1] 4 2
[1] 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    25  18   3   2
  21Q GAIN WILD-TYPE 236  95  32   3
D38V5, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  N0               25                236
  N1               18                 95
  N2                3                 32
  N3                2                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A  MX
  21Q GAIN MUTATED    40   0   0   6
  21Q GAIN WILD-TYPE 318   5   1  44
D38V6, multiclass
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  M0                40                318
  M1                 0                  5
  M1A                0                  1
  MX                 6                 44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V7, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     8  40
  21Q GAIN WILD-TYPE  99 273
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      8   40
  21Q GAIN WILD-TYPE   99  273
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE                8                 99
  MALE                 40                273
[1] 2 2
[1] FALSE
D38V8, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  21Q GAIN MUTATED                                       3
  21Q GAIN WILD-TYPE                                     9
                    vv
clus                 LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  21Q GAIN MUTATED                                        0
  21Q GAIN WILD-TYPE                                      6
                    vv
clus                 LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  21Q GAIN MUTATED                                         1
  21Q GAIN WILD-TYPE                                       0
                    vv
clus                 LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  21Q GAIN MUTATED                                                            44
  21Q GAIN WILD-TYPE                                                         357
D38V9, multiclass
                                                             clus
vv                                                            21Q GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      3
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     0
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               44
                                                             clus
vv                                                            21Q GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                        9
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                357
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V10, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     3  45
  21Q GAIN WILD-TYPE  10 362
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      3   45
  21Q GAIN WILD-TYPE   10  362
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  NO                 3                 10
  YES               45                362
[1] 2 2
[1] FALSE
D38V11, continuous
                    vv
clus                  R0  R1  R2  RX
  21Q GAIN MUTATED    35   2   1   5
  21Q GAIN WILD-TYPE 307   6   3  13
D38V12, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  R0               35                307
  R1                2                  6
  R2                1                  3
  RX                5                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  21Q GAIN MUTATED       1                         0    36
  21Q GAIN WILD-TYPE     8                        17   262
D38V13, multiclass
                           clus
vv                          21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  ASIAN                                    1                  8
  BLACK OR AFRICAN AMERICAN                0                 17
  WHITE                                   36                262
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V14, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     0  31
  21Q GAIN WILD-TYPE   8 236
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      0   31
  21Q GAIN WILD-TYPE    8  236
                        clus
vv                       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  8
  NOT HISPANIC OR LATINO               31                236
[1] 2 2
[1] FALSE

Clustering(39) Variable = 22Q GAIN MUTATION ANALYSIS
D39V1, survival
                    sevent
clus2                  0   1
  22Q GAIN MUTATED   119  56
  22Q GAIN WILD-TYPE 146  67
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
               175                213 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                56                 67 
$`22Q GAIN MUTATED`
TCGA-18-3408 TCGA-18-3409 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 TCGA-21-1072 
        2464         2417         1415          345          396         3016 
TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1079 TCGA-21-1082 TCGA-21-1083 
        2134         1852         1058          965         3644          267 
TCGA-21-5784 TCGA-21-5786 TCGA-22-1002 TCGA-22-1011 TCGA-22-1012 TCGA-22-4591 
        1268         1032          131           53          429          623 
TCGA-22-4593 TCGA-22-4595 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 TCGA-22-5477 
        1067          734         1057          399         1946         1346 
TCGA-22-5479 TCGA-22-5481 TCGA-22-5482 TCGA-22-5491 TCGA-22-5492 TCGA-33-4532 
        1651         1952          357         1713          506         2524 
TCGA-33-4586 TCGA-33-4589 TCGA-33-6738 TCGA-34-2596 TCGA-34-2600 TCGA-34-2605 
         428         1948          822           80         1874          881 
TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 
        1000          951         1528          707          365          428 
TCGA-37-4130 TCGA-37-4133 TCGA-37-4141 TCGA-39-5019 TCGA-39-5021 TCGA-39-5034 
         247          238           12         1361         1947         1107 
TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 
        1084         1086          544          822         1007          349 
TCGA-43-5670 TCGA-43-6647 TCGA-43-6770 TCGA-43-7657 TCGA-43-8118 TCGA-43-A474 
         849          757          310          236         1971          353 
TCGA-43-A475 TCGA-43-A56V TCGA-46-6025 TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 
         296          366          324         1948          923         1958 
TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-7221 TCGA-56-7579 
         881            3          555           62           30           44 
TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-8503 
          40           26            6         1961            1           41 
TCGA-56-8504 TCGA-56-8622 TCGA-56-8626 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW 
         178           55           17           34           38            2 
TCGA-56-A4BX TCGA-56-A4ZJ TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8390 TCGA-58-A46M 
          46           25            4            8          911         1072 
TCGA-58-A46N TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 
         910         1950         1943         1958          661         1963 
TCGA-60-2711 TCGA-60-2714 TCGA-60-2719 TCGA-60-2720 TCGA-60-2722 TCGA-60-2723 
        1260         1531         1297           97          908         1092 
TCGA-60-2725 TCGA-60-2726 TCGA-63-7020 TCGA-63-7023 TCGA-66-2734 TCGA-66-2737 
         816          358         1957         1952         1311           61 
TCGA-66-2742 TCGA-66-2755 TCGA-66-2758 TCGA-66-2763 TCGA-66-2769 TCGA-66-2773 
         641           28          639           30         1947         1946 
TCGA-66-2777 TCGA-66-2781 TCGA-66-2783 TCGA-66-2785 TCGA-66-2788 TCGA-66-2792 
          61          121          759           60          699          913 
TCGA-66-2794 TCGA-66-2800 TCGA-68-A59J TCGA-77-6842 TCGA-77-6845 TCGA-77-7139 
        1645         1492          104         1950         1952         1968 
TCGA-77-7141 TCGA-77-7338 TCGA-77-7463 TCGA-77-8007 TCGA-77-8008 TCGA-77-8128 
          15         1952         1954         1960         1945         1953 
TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8140 TCGA-77-8145 TCGA-77-8153 
        1945         1941         1941         1962         1943         1684 
TCGA-77-8156 TCGA-77-A5G1 TCGA-77-A5G7 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF 
          10         1942         1963         1280         1939          839 
TCGA-77-A5GH TCGA-85-6561 TCGA-85-7696 TCGA-85-7698 TCGA-85-8052 TCGA-85-8070 
         713          395           18           49           16          960 
TCGA-85-8276 TCGA-85-8277 TCGA-85-8350 TCGA-85-8354 TCGA-85-8481 TCGA-85-8580 
          13           11           60           61           21          445 
TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A5B5 TCGA-90-7767 TCGA-90-7769 
        1960           25           19          111           89          358 
TCGA-92-7341 TCGA-94-7033 TCGA-94-7943 TCGA-94-A4VJ TCGA-96-7545 TCGA-96-8169 
         106           87          356          430         1344          189 
TCGA-96-8170 TCGA-96-A4JK TCGA-98-8022 TCGA-J1-A4AH TCGA-LA-A446 TCGA-NC-A5HG 
         211          273          224          222           36         1548 
TCGA-NC-A5HI 
        1135 

$`22Q GAIN WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3410 TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 
         370          136          146         1810          862          758 
TCGA-18-3419 TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 
          50         1331          187           85         2754           92 
TCGA-18-5595 TCGA-21-1070 TCGA-21-1071 TCGA-21-1078 TCGA-21-1080 TCGA-21-1081 
         827         3636         1426          474         3724          284 
TCGA-21-5782 TCGA-21-5787 TCGA-21-A5DI TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 
         962          329          979          608          223         1945 
TCGA-22-1005 TCGA-22-1016 TCGA-22-1017 TCGA-22-4594 TCGA-22-4596 TCGA-22-4599 
        1952          822         1485         1470           17         1161 
TCGA-22-4607 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 
         587          358          965         1964         1933          445 
TCGA-22-5478 TCGA-22-5480 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-A5C4 
          24         1952          573          916         1912           29 
TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 
        1940         2979         1311         5287         1966         1941 
TCGA-33-4587 TCGA-34-2604 TCGA-34-5232 TCGA-34-5234 TCGA-34-5927 TCGA-34-5928 
        1970          958         2062         1715          941          552 
TCGA-34-8454 TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-37-4132 
         166          120           13           12          200          227 
TCGA-37-4135 TCGA-37-5819 TCGA-39-5011 TCGA-39-5016 TCGA-39-5022 TCGA-39-5024 
         207          103         1454         2253         1996         1964 
TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5035 
        1849           52          740           59          833          474 
TCGA-39-5040 TCGA-43-2576 TCGA-43-2578 TCGA-43-2581 TCGA-43-6143 TCGA-43-6771 
        1964         1223          684         1176          376         1936 
TCGA-43-7656 TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 TCGA-43-A56U TCGA-46-6026 
         212         1970          407          358          432          423 
TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7812 TCGA-56-6546 
          12           12          911          541         1967           26 
TCGA-56-7222 TCGA-56-7223 TCGA-56-8624 TCGA-56-8625 TCGA-56-8628 TCGA-56-A4BY 
          13           30           36           63           16           30 
TCGA-56-A4ZK TCGA-58-8388 TCGA-58-8391 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46L 
           4          378         2167         1058         2589         1723 
TCGA-60-2695 TCGA-60-2696 TCGA-60-2698 TCGA-60-2709 TCGA-60-2710 TCGA-60-2712 
         642          109          311         1505         1963          274 
TCGA-60-2713 TCGA-60-2715 TCGA-60-2716 TCGA-60-2721 TCGA-60-2724 TCGA-63-6202 
        1731         1075         1475          983          717         1973 
TCGA-63-7021 TCGA-63-7022 TCGA-66-2727 TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 
        1955         1947         1967           30           31           61 
TCGA-66-2756 TCGA-66-2757 TCGA-66-2759 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 
          30           30          762           61           31           61 
TCGA-66-2768 TCGA-66-2770 TCGA-66-2771 TCGA-66-2778 TCGA-66-2780 TCGA-66-2782 
          61          700          578          578         1956         1954 
TCGA-66-2786 TCGA-66-2787 TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 TCGA-66-2793 
         790         1217         1955          699         1977         1952 
TCGA-66-2795 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 
         122           83          202          211          244           96 
TCGA-68-A59I TCGA-77-6843 TCGA-77-6844 TCGA-77-7138 TCGA-77-7142 TCGA-77-7335 
         121         1941         1942         1959         1286         1954 
TCGA-77-7337 TCGA-77-7465 TCGA-77-8009 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 
        1942          479         1641         1947         1946         1951 
TCGA-77-8144 TCGA-77-8148 TCGA-77-8150 TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G3 
         833          293         1961         1092         1953         1959 
TCGA-77-A5G6 TCGA-77-A5G8 TCGA-85-6560 TCGA-85-6798 TCGA-85-7697 TCGA-85-7699 
        1955         1290          364           34           10            1 
TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 
        1965           35          911           60           26           60 
TCGA-85-8071 TCGA-85-8072 TCGA-85-8287 TCGA-85-8288 TCGA-85-8351 TCGA-85-8352 
         428          513           13           54           55           67 
TCGA-85-8353 TCGA-85-8355 TCGA-85-8479 TCGA-85-8582 TCGA-85-8664 TCGA-85-8666 
          54           61           22          424            3          475 
TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A512 
          15         1972         1973         1967         1972         1987 
TCGA-85-A513 TCGA-85-A53L TCGA-90-6837 TCGA-90-7766 TCGA-90-7964 TCGA-90-A4ED 
          24           13          758          289          428          244 
TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 
         331          269           82          122          160           70 
TCGA-96-7544 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8023 TCGA-L3-A4E7 
        1213          183          256          413          308           35 
TCGA-L3-A524 TCGA-MF-A522 TCGA-NC-A5HE 
         449           83         1722 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 1                  1 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              3644               5287 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
               734                573 
[1] "1.0 - 3644.0 (734.0)" "1.0 - 5287.0 (573.0)"
[1] "hr=" "1.2"
D39V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  22Q GAIN MUTATED         0       26       71        0        23        37
  22Q GAIN WILD-TYPE       1       46       66        1        29        34
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  22Q GAIN MUTATED           20          8        4
  22Q GAIN WILD-TYPE         37         12        2
D39V3, multiclass
            clus
vv           22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  STAGE I                   0                  1
  STAGE IA                 26                 46
  STAGE IB                 71                 66
  STAGE II                  0                  1
  STAGE IIA                23                 29
  STAGE IIB                37                 34
  STAGE IIIA               20                 37
  STAGE IIIB                8                 12
  STAGE IV                  4                  2
[1] 9 2
[1] 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    38 124  19  10
  22Q GAIN WILD-TYPE  60 130  29  10
D39V4, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  T1               38                 60
  T2              124                130
  T3               19                 29
  T4               10                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  22Q GAIN MUTATED   124  48  13   1
  22Q GAIN WILD-TYPE 137  65  22   4
D39V5, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  N0              124                137
  N1               48                 65
  N2               13                 22
  N3                1                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A  MX
  22Q GAIN MUTATED   163   3   1  22
  22Q GAIN WILD-TYPE 195   2   0  28
D39V6, multiclass
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  M0               163                195
  M1                 3                  2
  M1A                1                  0
  MX                22                 28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V7, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    46 145
  22Q GAIN WILD-TYPE  61 168
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     46  145
  22Q GAIN WILD-TYPE   61  168
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE               46                 61
  MALE                145                168
[1] 2 2
[1] FALSE
D39V8, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  22Q GAIN MUTATED                                       5
  22Q GAIN WILD-TYPE                                     7
                    vv
clus                 LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  22Q GAIN MUTATED                                        1
  22Q GAIN WILD-TYPE                                      5
                    vv
clus                 LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  22Q GAIN MUTATED                                         0
  22Q GAIN WILD-TYPE                                       1
                    vv
clus                 LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  22Q GAIN MUTATED                                                           185
  22Q GAIN WILD-TYPE                                                         216
D39V9, multiclass
                                                             clus
vv                                                            22Q GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      5
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              185
                                                             clus
vv                                                            22Q GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                        7
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                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"
D39V10, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED     5 186
  22Q GAIN WILD-TYPE   8 221
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      5  186
  22Q GAIN WILD-TYPE    8  221
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  NO                 5                  8
  YES              186                221
[1] 2 2
[1] FALSE
D39V11, continuous
                    vv
clus                  R0  R1  R2  RX
  22Q GAIN MUTATED   160   4   1   3
  22Q GAIN WILD-TYPE 182   4   3  15
D39V12, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  R0              160                182
  R1                4                  4
  R2                1                  3
  RX                3                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  22Q GAIN MUTATED       2                         6   139
  22Q GAIN WILD-TYPE     7                        11   159
D39V13, multiclass
                           clus
vv                          22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  ASIAN                                    2                  7
  BLACK OR AFRICAN AMERICAN                6                 11
  WHITE                                  139                159
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V14, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED     3 120
  22Q GAIN WILD-TYPE   5 147
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      3  120
  22Q GAIN WILD-TYPE    5  147
                        clus
vv                       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  5
  NOT HISPANIC OR LATINO              120                147
[1] 2 2
[1] FALSE

Clustering(40) Variable = XQ GAIN MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                 0   1
  XQ GAIN MUTATED    46  17
  XQ GAIN WILD-TYPE 219 106
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               63               325 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               17               106 
$`XQ GAIN MUTATED`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3417 TCGA-18-3421 TCGA-18-4083 TCGA-21-1081 
         370          136          758         1331          187          284 
TCGA-21-5786 TCGA-22-1012 TCGA-22-4593 TCGA-22-4595 TCGA-22-5483 TCGA-33-4532 
        1032          429         1067          734          573         2524 
TCGA-33-4566 TCGA-34-2596 TCGA-34-5240 TCGA-34-5927 TCGA-34-5928 TCGA-34-8454 
        5287           80          365          941          552          166 
TCGA-37-5819 TCGA-39-5019 TCGA-43-3920 TCGA-43-5670 TCGA-43-7657 TCGA-43-A475 
         103         1361         1007          849          236          296 
TCGA-51-4079 TCGA-56-7223 TCGA-56-7730 TCGA-56-8504 TCGA-56-8624 TCGA-56-8629 
          12           30            6          178           36           34 
TCGA-56-A4BW TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 TCGA-60-2703 TCGA-60-2711 
           2         1072          910          642         1950         1260 
TCGA-60-2719 TCGA-60-2724 TCGA-66-2756 TCGA-66-2758 TCGA-66-2766 TCGA-66-2769 
        1297          717           30          639           31         1947 
TCGA-66-2781 TCGA-66-2792 TCGA-66-2793 TCGA-77-6842 TCGA-77-7138 TCGA-77-7335 
         121          913         1952         1950         1959         1954 
TCGA-77-8009 TCGA-77-8156 TCGA-77-A5GA TCGA-77-A5GF TCGA-85-6561 TCGA-85-7710 
        1641           10         1280          839          395         1965 
TCGA-85-8070 TCGA-85-8072 TCGA-85-8350 TCGA-85-8354 TCGA-85-A50M TCGA-92-7341 
         960          513           60           61           19          106 
TCGA-94-A4VJ TCGA-96-A4JK TCGA-J1-A4AH 
         430          273          222 

$`XQ GAIN WILD-TYPE`
TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 
        2464         2417          146         1415          345          396 
TCGA-18-3415 TCGA-18-3416 TCGA-18-3419 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 
        1810          862           50           85         2754           92 
TCGA-18-5595 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 
         827         3636         1426         3016         2134         1852 
TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 TCGA-21-1082 TCGA-21-1083 
        1058          474          965         3724         3644          267 
TCGA-21-5782 TCGA-21-5784 TCGA-21-5787 TCGA-21-A5DI TCGA-22-0940 TCGA-22-0944 
         962         1268          329          979          608          223 
TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1016 TCGA-22-1017 
        1945          131         1952           53          822         1485 
TCGA-22-4591 TCGA-22-4594 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 
         623         1470           17         1161         1057          399 
TCGA-22-4605 TCGA-22-4607 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 
        1946          587          358          965         1964         1933 
TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 
         445         1346           24         1651         1952         1952 
TCGA-22-5482 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 
         357          916         1912         1713          506           29 
TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 
        1940         2979         1311         1966         1941          428 
TCGA-33-4587 TCGA-33-4589 TCGA-33-6738 TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 
        1970         1948          822         1874          958          881 
TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 
        1000          951         1528         2062         1715          707 
TCGA-34-5241 TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 
         428          120           13           12          200          247 
TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-39-5011 TCGA-39-5016 
         227          238          207           12         1454         2253 
TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 
        1947         1996         1964         1849           52          740 
TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 
          59          833         1107          474         1084         1086 
TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 TCGA-43-2578 TCGA-43-2581 TCGA-43-3394 
         544         1964         1223          684         1176          822 
TCGA-43-5668 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-7656 
         349          376          757          310         1936          212 
TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56U 
        1970          407          358         1971          353          432 
TCGA-43-A56V TCGA-46-6025 TCGA-46-6026 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 
         366          324          423           12          911          541 
TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 
        1948          923         1958         1967          881            3 
TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 TCGA-56-7579 
         555           62           26           30           13           44 
TCGA-56-7580 TCGA-56-7582 TCGA-56-7731 TCGA-56-7822 TCGA-56-8503 TCGA-56-8622 
          40           26         1961            1           41           55 
TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-A49D TCGA-56-A4BX TCGA-56-A4BY 
          63           17           16           38           46           30 
TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8388 TCGA-58-8390 
          25            4            4            8          378          911 
TCGA-58-8391 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46L TCGA-60-2696 TCGA-60-2698 
        2167         1058         2589         1723          109          311 
TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 
        1943         1958          661         1963         1505         1963 
TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2715 TCGA-60-2716 TCGA-60-2720 
         274         1731         1531         1075         1475           97 
TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 
         983          908         1092          816          358         1973 
TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 TCGA-66-2727 TCGA-66-2734 
        1957         1955         1947         1952         1967         1311 
TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 
          61          641           30           31           61           28 
TCGA-66-2757 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2767 TCGA-66-2768 
          30          762           30           61           61           61 
TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 
         700          578         1946           61          578         1956 
TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 
        1954          759           60          790         1217          699 
TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 
        1955          699         1977         1645          122         1492 
TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I 
          83          202          211          244           96          121 
TCGA-68-A59J TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7139 TCGA-77-7141 
         104         1941         1942         1952         1968           15 
TCGA-77-7142 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 
        1286         1942         1952         1954          479         1960 
TCGA-77-8008 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 
        1945         1953         1945         1941         1941         1947 
TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 
        1946         1951         1962          833         1943          293 
TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 
        1961         1684         1092         1953         1942         1959 
TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GB TCGA-77-A5GH TCGA-85-6560 
        1955         1963         1290         1939          713          364 
TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 TCGA-85-7843 
          34           18           10           49            1           35 
TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8071 
         911           60           26           60           16          428 
TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 TCGA-85-8351 TCGA-85-8352 
          13           11           13           54           55           67 
TCGA-85-8353 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 
          54           61           22           21          445          424 
TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR 
           3          475           15         1972         1960           25 
TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L 
        1973         1967         1972         1987           24           13 
TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 TCGA-90-7964 
         111          758          289           89          358          428 
TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-8063 TCGA-92-8064 
         244          331          269           82          122          160 
TCGA-92-8065 TCGA-94-7033 TCGA-94-7943 TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 
          70           87          356         1213         1344          189 
TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 
         211          183          256          413          224          308 
TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HE TCGA-NC-A5HG 
          35          449           36           83         1722         1548 
TCGA-NC-A5HI 
        1135 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                2                 1 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             5287              3724 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
              552               699 
[1] "2.0 - 5287.0 (552.0)" "1.0 - 3724.0 (699.0)"
[1] "hr=" "1.1"
D40V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  XQ GAIN MUTATED         0        7       24        0        11        13
  XQ GAIN WILD-TYPE       1       65      113        1        41        58
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  XQ GAIN MUTATED            6          4        2
  XQ GAIN WILD-TYPE         51         16        4
D40V3, multiclass
            clus
vv           XQ GAIN MUTATED XQ GAIN WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                 7                65
  STAGE IB                24               113
  STAGE II                 0                 1
  STAGE IIA               11                41
  STAGE IIB               13                58
  STAGE IIIA               6                51
  STAGE IIIB               4                16
  STAGE IV                 2                 4
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  XQ GAIN MUTATED     9  46   8   4
  XQ GAIN WILD-TYPE  89 208  40  16
D40V4, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  T1               9                89
  T2              46               208
  T3               8                40
  T4               4                16
[1] 4 2
[1] 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    41  20   4   0
  XQ GAIN WILD-TYPE 220  93  31   5
D40V5, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  N0              41               220
  N1              20                93
  N2               4                31
  N3               0                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A  MX
  XQ GAIN MUTATED    56   2   0   7
  XQ GAIN WILD-TYPE 302   3   1  43
D40V6, multiclass
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  M0               56               302
  M1                2                 3
  M1A               0                 1
  MX                7                43
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V7, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    15  52
  XQ GAIN WILD-TYPE  92 261
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     15   52
  XQ GAIN WILD-TYPE   92  261
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE              15                92
  MALE                52               261
[1] 2 2
[1] FALSE
D40V8, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  XQ GAIN MUTATED                                       3
  XQ GAIN WILD-TYPE                                     9
                   vv
clus                LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  XQ GAIN MUTATED                                        1
  XQ GAIN WILD-TYPE                                      5
                   vv
clus                LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  XQ GAIN MUTATED                                         0
  XQ GAIN WILD-TYPE                                       1
                   vv
clus                LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  XQ GAIN MUTATED                                                            63
  XQ GAIN WILD-TYPE                                                         338
D40V9, multiclass
                                                             clus
vv                                                            XQ GAIN MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     3
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              63
                                                             clus
vv                                                            XQ GAIN WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       9
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               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"
D40V10, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     2  65
  XQ GAIN WILD-TYPE  11 342
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      2   65
  XQ GAIN WILD-TYPE   11  342
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  NO                2                11
  YES              65               342
[1] 2 2
[1] FALSE
D40V11, continuous
                   vv
clus                 R0  R1  R2  RX
  XQ GAIN MUTATED    55   2   0   1
  XQ GAIN WILD-TYPE 287   6   4  17
D40V12, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  R0              55               287
  R1               2                 6
  R2               0                 4
  RX               1                17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XQ GAIN MUTATED       3                         2    48
  XQ GAIN WILD-TYPE     6                        15   250
D40V13, multiclass
                           clus
vv                          XQ GAIN MUTATED XQ GAIN WILD-TYPE
  ASIAN                                   3                 6
  BLACK OR AFRICAN AMERICAN               2                15
  WHITE                                  48               250
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V14, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     0  46
  XQ GAIN WILD-TYPE   8 221
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      0   46
  XQ GAIN WILD-TYPE    8  221
                        clus
vv                       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 8
  NOT HISPANIC OR LATINO              46               221
[1] 2 2
[1] FALSE

Clustering(41) Variable = 1P LOSS MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                 0   1
  1P LOSS MUTATED    79  35
  1P LOSS WILD-TYPE 186  88
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
              114               274 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               35                88 
$`1P LOSS MUTATED`
TCGA-18-3406 TCGA-18-3408 TCGA-18-3415 TCGA-18-5592 TCGA-21-1071 TCGA-21-1072 
         370         2464         1810           92         1426         3016 
TCGA-21-1075 TCGA-21-1077 TCGA-21-5786 TCGA-22-0940 TCGA-22-0944 TCGA-22-1017 
        2134         1058         1032          608          223         1485 
TCGA-22-4593 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4604 TCGA-22-5471 
        1067          734           17         1161          399          965 
TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5479 TCGA-33-4538 TCGA-33-4583 
        1933          445         1346         1651         2979         1941 
TCGA-33-4586 TCGA-34-2596 TCGA-34-2600 TCGA-34-2605 TCGA-37-4129 TCGA-37-5819 
         428           80         1874          881          200          103 
TCGA-39-5016 TCGA-39-5027 TCGA-39-5029 TCGA-39-5034 TCGA-43-2581 TCGA-43-3394 
        2253         1849          740         1107         1176          822 
TCGA-43-7657 TCGA-43-A474 TCGA-43-A56V TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 
         236          353          366          423           12           12 
TCGA-51-4081 TCGA-52-7622 TCGA-52-7811 TCGA-56-1622 TCGA-56-5898 TCGA-56-6545 
         911          541         1958          881          555           62 
TCGA-56-7223 TCGA-56-7580 TCGA-56-7730 TCGA-56-7822 TCGA-56-A49D TCGA-56-A4BX 
          30           40            6            1           38           46 
TCGA-58-8393 TCGA-58-A46L TCGA-58-A46M TCGA-60-2698 TCGA-60-2706 TCGA-60-2707 
        1058         1723         1072          311         1958          661 
TCGA-60-2714 TCGA-63-7023 TCGA-66-2737 TCGA-66-2758 TCGA-66-2767 TCGA-66-2770 
        1531         1952           61          639           61          700 
TCGA-66-2773 TCGA-66-2777 TCGA-66-2781 TCGA-66-2787 TCGA-66-2791 TCGA-66-2792 
        1946           61          121         1217         1977          913 
TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-68-7757 
        1952         1645          122         1492           83          211 
TCGA-68-A59J TCGA-77-7139 TCGA-77-7337 TCGA-77-7465 TCGA-77-8009 TCGA-77-8128 
         104         1968         1942          479         1641         1953 
TCGA-77-8133 TCGA-77-8148 TCGA-77-8150 TCGA-77-A5G3 TCGA-77-A5GF TCGA-85-6561 
        1941          293         1961         1959          839          395 
TCGA-85-7696 TCGA-85-7698 TCGA-85-7843 TCGA-85-8049 TCGA-85-8277 TCGA-85-8287 
          18           49           35           60           11           13 
TCGA-85-8352 TCGA-85-8353 TCGA-85-8580 TCGA-85-A511 TCGA-85-A53L TCGA-85-A5B5 
          67           54          445         1972           13          111 
TCGA-90-A4EE TCGA-92-7341 TCGA-94-7943 TCGA-96-7544 TCGA-96-7545 TCGA-96-A4JK 
         331          106          356         1213         1344          273 
TCGA-98-8021 TCGA-98-8023 TCGA-L3-A524 TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HE 
         413          308          449           36           83         1722 

$`1P LOSS WILD-TYPE`
TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 
         136         2417          146         1415          345          396 
TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 
         862          758           50         1331          187           85 
TCGA-18-4721 TCGA-18-5595 TCGA-21-1070 TCGA-21-1076 TCGA-21-1078 TCGA-21-1079 
        2754          827         3636         1852          474          965 
TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 TCGA-21-5784 
        3724          284         3644          267          962         1268 
TCGA-21-5787 TCGA-21-A5DI TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 
         329          979         1945          131         1952           53 
TCGA-22-1012 TCGA-22-1016 TCGA-22-4591 TCGA-22-4594 TCGA-22-4601 TCGA-22-4605 
         429          822          623         1470         1057         1946 
TCGA-22-4607 TCGA-22-4613 TCGA-22-5472 TCGA-22-5478 TCGA-22-5480 TCGA-22-5481 
         587          358         1964           24         1952         1952 
TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 
         357          573          916         1912         1713          506 
TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4533 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 
          29         2524         1940         1311         5287         1966 
TCGA-33-4587 TCGA-33-4589 TCGA-33-6738 TCGA-34-2604 TCGA-34-2608 TCGA-34-2609 
        1970         1948          822          958         1000          951 
TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 
        1528         2062         1715          707          365          428 
TCGA-34-5927 TCGA-34-5928 TCGA-34-8454 TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 
         941          552          166          120           13           12 
TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-39-5011 
         247          227          238          207           12         1454 
TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5028 TCGA-39-5030 
        1361         1947         1996         1964           52           59 
TCGA-39-5031 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 TCGA-39-5040 
         833          474         1084         1086          544         1964 
TCGA-43-2576 TCGA-43-2578 TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 
        1223          684         1007          349          849          376 
TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-7656 TCGA-43-7658 TCGA-43-8115 
         757          310         1936          212         1970          407 
TCGA-43-8116 TCGA-43-8118 TCGA-43-A475 TCGA-43-A56U TCGA-46-6025 TCGA-52-7809 
         358         1971          296          432          324         1948 
TCGA-52-7810 TCGA-52-7812 TCGA-56-5897 TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 
         923         1967            3           26           30           13 
TCGA-56-7579 TCGA-56-7582 TCGA-56-7731 TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 
          44           26         1961           41          178           55 
TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A4BW 
          36           63           17           16           34            2 
TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8388 
          30           25            4            4            8          378 
TCGA-58-8390 TCGA-58-8391 TCGA-58-A46J TCGA-58-A46N TCGA-60-2695 TCGA-60-2696 
         911         2167         2589          910          642          109 
TCGA-60-2703 TCGA-60-2704 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 
        1950         1943         1963         1505         1963         1260 
TCGA-60-2712 TCGA-60-2713 TCGA-60-2715 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 
         274         1731         1075         1475         1297           97 
TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 
         983          908         1092          717          816          358 
TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-66-2727 TCGA-66-2734 
        1973         1957         1955         1947         1967         1311 
TCGA-66-2742 TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 
         641           30           31           61           28           30 
TCGA-66-2757 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2768 
          30          762           30           61           31           61 
TCGA-66-2769 TCGA-66-2771 TCGA-66-2778 TCGA-66-2780 TCGA-66-2782 TCGA-66-2783 
        1947          578          578         1956         1954          759 
TCGA-66-2785 TCGA-66-2786 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-68-7756 
          60          790          699         1955          699          202 
TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 
         244           96          121         1950         1941         1942 
TCGA-77-6845 TCGA-77-7138 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7338 
        1952         1959           15         1286         1954         1952 
TCGA-77-7463 TCGA-77-8007 TCGA-77-8008 TCGA-77-8130 TCGA-77-8131 TCGA-77-8136 
        1954         1960         1945         1945         1941         1947 
TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8144 TCGA-77-8145 TCGA-77-8153 
        1946         1951         1962          833         1943         1684 
TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G6 TCGA-77-A5G7 
        1092           10         1953         1942         1955         1963 
TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GH TCGA-85-6560 TCGA-85-6798 
        1290         1280         1939          713          364           34 
TCGA-85-7697 TCGA-85-7699 TCGA-85-7710 TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 
          10            1         1965          911           60           26 
TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 TCGA-85-8288 
          16          960          428          513           13           54 
TCGA-85-8350 TCGA-85-8351 TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 
          60           55           61           61           22           21 
TCGA-85-8582 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A4QQ 
         424            3          475           15         1972         1960 
TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 TCGA-85-A512 TCGA-85-A513 
          25           19         1973         1967         1987           24 
TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 TCGA-90-7964 TCGA-90-A4ED 
         758          289           89          358          428          244 
TCGA-90-A59Q TCGA-92-7340 TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 
         269           82          122          160           70           87 
TCGA-94-A4VJ TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8022 
         430          189          211          183          256          224 
TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-NC-A5HG TCGA-NC-A5HI 
         222           35         1548         1135 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                1                 1 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             3016              5287 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            581.5             691.5 
[1] "1.0 - 3016.0 (581.5)" "1.0 - 5287.0 (691.5)"
[1] "hr=" "1.1"
D41V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  1P LOSS MUTATED         0       18       37        0        17        23
  1P LOSS WILD-TYPE       1       54      100        1        35        48
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  1P LOSS MUTATED           19          8        0
  1P LOSS WILD-TYPE         38         12        6
D41V3, multiclass
            clus
vv           1P LOSS MUTATED 1P LOSS WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                18                54
  STAGE IB                37               100
  STAGE II                 0                 1
  STAGE IIA               17                35
  STAGE IIB               23                48
  STAGE IIIA              19                38
  STAGE IIIB               8                12
  STAGE IV                 0                 6
[1] 9 2
[1] 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    27  72  17   6
  1P LOSS WILD-TYPE  71 182  31  14
D41V4, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  T1              27                71
  T2              72               182
  T3              17                31
  T4               6                14
[1] 4 2
[1] 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    64  44  10   2
  1P LOSS WILD-TYPE 197  69  25   3
D41V5, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  N0              64               197
  N1              44                69
  N2              10                25
  N3               2                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A  MX
  1P LOSS MUTATED   106   0   0  13
  1P LOSS WILD-TYPE 252   5   1  37
D41V6, multiclass
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  M0              106               252
  M1                0                 5
  M1A               0                 1
  MX               13                37
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V7, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    20 102
  1P LOSS WILD-TYPE  87 211
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     20  102
  1P LOSS WILD-TYPE   87  211
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE              20                87
  MALE               102               211
[1] 2 2
[1] FALSE
D41V8, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  1P LOSS MUTATED                                       3
  1P LOSS WILD-TYPE                                     9
                   vv
clus                LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  1P LOSS MUTATED                                        1
  1P LOSS WILD-TYPE                                      5
                   vv
clus                LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  1P LOSS MUTATED                                         0
  1P LOSS WILD-TYPE                                       1
                   vv
clus                LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  1P LOSS MUTATED                                                           118
  1P LOSS WILD-TYPE                                                         283
D41V9, multiclass
                                                             clus
vv                                                            1P LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     3
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             118
                                                             clus
vv                                                            1P LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       9
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               283
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V10, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     6 116
  1P LOSS WILD-TYPE   7 291
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      6  116
  1P LOSS WILD-TYPE    7  291
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  NO                6                 7
  YES             116               291
[1] 2 2
[1] FALSE
D41V11, continuous
                   vv
clus                 R0  R1  R2  RX
  1P LOSS MUTATED   104   1   2   4
  1P LOSS WILD-TYPE 238   7   2  14
D41V12, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  R0             104               238
  R1               1                 7
  R2               2                 2
  RX               4                14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1P LOSS MUTATED       2                         5    87
  1P LOSS WILD-TYPE     7                        12   211
D41V13, multiclass
                           clus
vv                          1P LOSS MUTATED 1P LOSS WILD-TYPE
  ASIAN                                   2                 7
  BLACK OR AFRICAN AMERICAN               5                12
  WHITE                                  87               211
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V14, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     5  72
  1P LOSS WILD-TYPE   3 195
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      5   72
  1P LOSS WILD-TYPE    3  195
                        clus
vv                       1P LOSS MUTATED 1P LOSS WILD-TYPE
  HISPANIC OR LATINO                   5                 3
  NOT HISPANIC OR LATINO              72               195
[1] 2 2
[1] FALSE

Clustering(42) Variable = 1Q LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                 0   1
  1Q LOSS MUTATED    26  15
  1Q LOSS WILD-TYPE 239 108
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               41               347 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               15               108 
$`1Q LOSS MUTATED`
TCGA-21-5786 TCGA-22-4593 TCGA-22-4595 TCGA-22-4604 TCGA-22-5471 TCGA-22-5477 
        1032         1067          734          399          965         1346 
TCGA-34-2605 TCGA-37-4129 TCGA-39-5029 TCGA-39-5034 TCGA-43-3394 TCGA-43-A474 
         881          200          740         1107          822          353 
TCGA-43-A56V TCGA-46-6026 TCGA-51-4079 TCGA-52-7811 TCGA-56-5898 TCGA-56-6545 
         366          423           12         1958          555           62 
TCGA-56-7580 TCGA-56-7730 TCGA-56-7822 TCGA-56-A49D TCGA-60-2714 TCGA-60-2719 
          40            6            1           38         1531         1297 
TCGA-63-6202 TCGA-66-2791 TCGA-66-2793 TCGA-68-7755 TCGA-68-7757 TCGA-77-8128 
        1973         1977         1952           83          211         1953 
TCGA-77-8133 TCGA-77-8150 TCGA-77-A5G3 TCGA-85-7843 TCGA-85-8287 TCGA-85-A53L 
        1941         1961         1959           35           13           13 
TCGA-96-7544 TCGA-96-7545 TCGA-96-A4JK TCGA-98-8021 TCGA-98-8023 
        1213         1344          273          413          308 

$`1Q LOSS WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 
         370          136         2464         2417          146         1415 
TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 
         345          396         1810          862          758           50 
TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 
        1331          187           85         2754           92          827 
TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 
        3636         1426         3016         2134         1852         1058 
TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 TCGA-21-1083 
         474          965         3724          284         3644          267 
TCGA-21-5782 TCGA-21-5784 TCGA-21-5787 TCGA-21-A5DI TCGA-22-0940 TCGA-22-0944 
         962         1268          329          979          608          223 
TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 
        1945          131         1952           53          429          822 
TCGA-22-1017 TCGA-22-4591 TCGA-22-4594 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 
        1485          623         1470           17         1161         1057 
TCGA-22-4605 TCGA-22-4607 TCGA-22-4613 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 
        1946          587          358         1964         1933          445 
TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 
          24         1651         1952         1952          357          573 
TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4532 
         916         1912         1713          506           29         2524 
TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 
        1940         2979         1311         5287         1966         1941 
TCGA-33-4586 TCGA-33-4587 TCGA-33-4589 TCGA-33-6738 TCGA-34-2596 TCGA-34-2600 
         428         1970         1948          822           80         1874 
TCGA-34-2604 TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 
         958         1000          951         1528         2062         1715 
TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-8454 
         707          365          428          941          552          166 
TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 
         120           13           12          247          227          238 
TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 
         207           12          103         1454         2253         1361 
TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5030 
        1947         1996         1964         1849           52           59 
TCGA-39-5031 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 TCGA-39-5040 
         833          474         1084         1086          544         1964 
TCGA-43-2576 TCGA-43-2578 TCGA-43-2581 TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 
        1223          684         1176         1007          349          849 
TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-7656 TCGA-43-7657 
         376          757          310         1936          212          236 
TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 TCGA-43-A475 TCGA-43-A56U 
        1970          407          358         1971          296          432 
TCGA-46-6025 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 
         324           12          911          541         1948          923 
TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 
        1967          881            3           26           30           13 
TCGA-56-7223 TCGA-56-7579 TCGA-56-7582 TCGA-56-7731 TCGA-56-8503 TCGA-56-8504 
          30           44           26         1961           41          178 
TCGA-56-8622 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 
          55           36           63           17           16           34 
TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR 
           2           46           30           25            4            4 
TCGA-56-A5DS TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-8393 TCGA-58-A46J 
           8          378          911         2167         1058         2589 
TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 TCGA-60-2696 TCGA-60-2698 
        1723         1072          910          642          109          311 
TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 
        1950         1943         1958          661         1963         1505 
TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2715 TCGA-60-2716 
        1963         1260          274         1731         1075         1475 
TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 
          97          983          908         1092          717          816 
TCGA-60-2726 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 TCGA-66-2727 
         358         1957         1955         1947         1952         1967 
TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 
        1311           61          641           30           31           61 
TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 
          28           30           30          639          762           30 
TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 
          61           31           61           61         1947          700 
TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 
         578         1946           61          578         1956          121 
TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 
        1954          759           60          790         1217          699 
TCGA-66-2789 TCGA-66-2790 TCGA-66-2792 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 
        1955          699          913         1645          122         1492 
TCGA-68-7756 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-77-6842 
         202          244           96          121          104         1950 
TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 
        1941         1942         1952         1959         1968           15 
TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 
        1286         1954         1942         1952         1954          479 
TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 TCGA-77-8130 TCGA-77-8131 TCGA-77-8136 
        1960         1945         1641         1945         1941         1947 
TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 
        1946         1951         1962          833         1943          293 
TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G6 
        1684         1092           10         1953         1942         1955 
TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF TCGA-77-A5GH 
        1963         1290         1280         1939          839          713 
TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 
         364          395           34           18           10           49 
TCGA-85-7699 TCGA-85-7710 TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 
           1         1965          911           60           26           60 
TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 
          16          960          428          513           13           11 
TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 TCGA-85-8354 
          54           60           55           67           54           61 
TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8664 
          61           22           21          445          424            3 
TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M 
         475           15         1972         1960           25           19 
TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 TCGA-85-A5B5 
        1973         1967         1972         1987           24          111 
TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 TCGA-90-7964 TCGA-90-A4ED 
         758          289           89          358          428          244 
TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 
         331          269           82          106          122          160 
TCGA-92-8065 TCGA-94-7033 TCGA-94-7943 TCGA-94-A4VJ TCGA-96-8169 TCGA-96-8170 
          70           87          356          430          189          211 
TCGA-96-A4JL TCGA-98-7454 TCGA-98-8022 TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 
         183          256          224          222           35          449 
TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HE TCGA-NC-A5HG TCGA-NC-A5HI 
          36           83         1722         1548         1135 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                1                 1 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             1977              5287 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
              734               641 
[1] "1.0 - 1977.0 (734.0)" "1.0 - 5287.0 (641.0)"
[1] "hr=" "1.3"
D42V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  1Q LOSS MUTATED         0        6       10        0        11         8
  1Q LOSS WILD-TYPE       1       66      127        1        41        63
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  1Q LOSS MUTATED            9          3        0
  1Q LOSS WILD-TYPE         48         17        6
D42V3, multiclass
            clus
vv           1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                 6                66
  STAGE IB                10               127
  STAGE II                 0                 1
  STAGE IIA               11                41
  STAGE IIB                8                63
  STAGE IIIA               9                48
  STAGE IIIB               3                17
  STAGE IV                 0                 6
[1] 9 2
[1] 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    11  26   8   2
  1Q LOSS WILD-TYPE  87 228  40  18
D42V4, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  T1              11                87
  T2              26               228
  T3               8                40
  T4               2                18
[1] 4 2
[1] 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    24  17   5   1
  1Q LOSS WILD-TYPE 237  96  30   4
D42V5, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  N0              24               237
  N1              17                96
  N2               5                30
  N3               1                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A  MX
  1Q LOSS MUTATED    41   0   0   4
  1Q LOSS WILD-TYPE 317   5   1  46
D42V6, multiclass
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  M0               41               317
  M1                0                 5
  M1A               0                 1
  MX                4                46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V7, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    10  37
  1Q LOSS WILD-TYPE  97 276
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     10   37
  1Q LOSS WILD-TYPE   97  276
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE              10                97
  MALE                37               276
[1] 2 2
[1] FALSE
D42V8, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  1Q LOSS MUTATED                                       0
  1Q LOSS WILD-TYPE                                    12
                   vv
clus                LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  1Q LOSS MUTATED                                        1
  1Q LOSS WILD-TYPE                                      5
                   vv
clus                LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  1Q LOSS MUTATED                                         0
  1Q LOSS WILD-TYPE                                       1
                   vv
clus                LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  1Q LOSS MUTATED                                                            46
  1Q LOSS WILD-TYPE                                                         355
D42V9, multiclass
                                                             clus
vv                                                            1Q LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              46
                                                             clus
vv                                                            1Q LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      12
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               355
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V10, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     3  44
  1Q LOSS WILD-TYPE  10 363
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      3   44
  1Q LOSS WILD-TYPE   10  363
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  NO                3                10
  YES              44               363
[1] 2 2
[1] FALSE
D42V11, continuous
                   vv
clus                 R0  R1  R2  RX
  1Q LOSS MUTATED    37   1   2   1
  1Q LOSS WILD-TYPE 305   7   2  17
D42V12, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  R0              37               305
  R1               1                 7
  R2               2                 2
  RX               1                17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1Q LOSS MUTATED       2                         4    33
  1Q LOSS WILD-TYPE     7                        13   265
D42V13, multiclass
                           clus
vv                          1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  ASIAN                                   2                 7
  BLACK OR AFRICAN AMERICAN               4                13
  WHITE                                  33               265
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V14, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     2  30
  1Q LOSS WILD-TYPE   6 237
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      2   30
  1Q LOSS WILD-TYPE    6  237
                        clus
vv                       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 6
  NOT HISPANIC OR LATINO              30               237
[1] 2 2
[1] FALSE

Clustering(43) Variable = 2P LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                 0   1
  2P LOSS MUTATED    10   6
  2P LOSS WILD-TYPE 255 117
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               16               372 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                6               117 
$`2P LOSS MUTATED`
TCGA-21-5787 TCGA-22-4594 TCGA-22-5481 TCGA-33-4533 TCGA-37-4141 TCGA-37-5819 
         329         1470         1952         1940           12          103 
TCGA-39-5028 TCGA-39-5029 TCGA-43-2578 TCGA-51-4081 TCGA-66-2756 TCGA-66-2763 
          52          740          684          911           30           30 
TCGA-68-A59J TCGA-77-7465 TCGA-85-8352 TCGA-85-A511 
         104          479           67         1972 

$`2P LOSS WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 
         370          136         2464         2417          146         1415 
TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 
         345          396         1810          862          758           50 
TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 
        1331          187           85         2754           92          827 
TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 
        3636         1426         3016         2134         1852         1058 
TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 TCGA-21-1083 
         474          965         3724          284         3644          267 
TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 TCGA-21-A5DI TCGA-22-0940 TCGA-22-0944 
         962         1268         1032          979          608          223 
TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 
        1945          131         1952           53          429          822 
TCGA-22-1017 TCGA-22-4591 TCGA-22-4593 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 
        1485          623         1067          734           17         1161 
TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-4613 TCGA-22-5471 
        1057          399         1946          587          358          965 
TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 
        1964         1933          445         1346           24         1651 
TCGA-22-5480 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 
        1952          357          573          916         1912         1713 
TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 
         506           29         2524         2979         1311         5287 
TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-33-4589 TCGA-33-6738 
        1966         1941          428         1970         1948          822 
TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 
          80         1874          958          881         1000          951 
TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 
        1528         2062         1715          707          365          428 
TCGA-34-5927 TCGA-34-5928 TCGA-34-8454 TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 
         941          552          166          120           13           12 
TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-39-5011 
         200          247          227          238          207         1454 
TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 
        2253         1361         1947         1996         1964         1849 
TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 
          59          833         1107          474         1084         1086 
TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 
         544         1964         1223         1176          822         1007 
TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 
         349          849          376          757          310         1936 
TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 
         212          236         1970          407          358         1971 
TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V TCGA-46-6025 TCGA-46-6026 
         353          296          432          366          324          423 
TCGA-51-4079 TCGA-51-4080 TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 
          12           12          541         1948          923         1958 
TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 
        1967          881            3          555           62           26 
TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 
          30           13           30           44           40           26 
TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 
           6         1961            1           41          178           55 
TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D 
          36           63           17           16           34           38 
TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR 
           2           46           30           25            4            4 
TCGA-56-A5DS TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-8393 TCGA-58-A46J 
           8          378          911         2167         1058         2589 
TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 TCGA-60-2696 TCGA-60-2698 
        1723         1072          910          642          109          311 
TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 
        1950         1943         1958          661         1963         1505 
TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2715 
        1963         1260          274         1731         1531         1075 
TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 
        1475         1297           97          983          908         1092 
TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 
         717          816          358         1973         1957         1955 
TCGA-63-7022 TCGA-63-7023 TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 
        1947         1952         1967         1311           61          641 
TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2757 TCGA-66-2758 
          30           31           61           28           30          639 
TCGA-66-2759 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 
         762           61           31           61           61         1947 
TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 
         700          578         1946           61          578         1956 
TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 
         121         1954          759           60          790         1217 
TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 
         699         1955          699         1977          913         1952 
TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 
        1645          122         1492           83          202          211 
TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 
         244           96          121         1950         1941         1942 
TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 
        1952         1959         1968           15         1286         1954 
TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 
        1942         1952         1954         1960         1945         1641 
TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 
        1953         1945         1941         1941         1947         1946 
TCGA-77-8139 TCGA-77-8140 TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 
        1951         1962          833         1943          293         1961 
TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 
        1684         1092           10         1953         1942         1959 
TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF 
        1955         1963         1290         1280         1939          839 
TCGA-77-A5GH TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 
         713          364          395           34           18           10 
TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 
          49            1         1965           35          911           60 
TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 
          26           60           16          960          428          513 
TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 
          13           11           13           54           60           55 
TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 
          54           61           61           22           21          445 
TCGA-85-8582 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A4QQ 
         424            3          475           15         1972         1960 
TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 TCGA-85-A512 TCGA-85-A513 
          25           19         1973         1967         1987           24 
TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 
          13          111          758          289           89          358 
TCGA-90-7964 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 
         428          244          331          269           82          106 
TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 TCGA-94-7943 TCGA-94-A4VJ 
         122          160           70           87          356          430 
TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL 
        1213         1344          189          211          273          183 
TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-J1-A4AH TCGA-L3-A4E7 
         256          413          224          308          222           35 
TCGA-L3-A524 TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HE TCGA-NC-A5HG TCGA-NC-A5HI 
         449           36           83         1722         1548         1135 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               12                 1 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             1972              5287 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            404.0             651.5 
[1] "12.0 - 1972.0 (404.0)" "1.0 - 5287.0 (651.5)" 
[1] "hr=" "1.7"
D43V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  2P LOSS MUTATED         0        2        3        0         1         3
  2P LOSS WILD-TYPE       1       70      134        1        51        68
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  2P LOSS MUTATED            6          1        0
  2P LOSS WILD-TYPE         51         19        6
D43V3, multiclass
            clus
vv           2P LOSS MUTATED 2P LOSS WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                 2                70
  STAGE IB                 3               134
  STAGE II                 0                 1
  STAGE IIA                1                51
  STAGE IIB                3                68
  STAGE IIIA               6                51
  STAGE IIIB               1                19
  STAGE IV                 0                 6
[1] 9 2
[1] 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     3   9   2   2
  2P LOSS WILD-TYPE  95 245  46  18
D43V4, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  T1               3                95
  T2               9               245
  T3               2                46
  T4               2                18
[1] 4 2
[1] 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     6   6   4   0
  2P LOSS WILD-TYPE 255 107  31   5
D43V5, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  N0               6               255
  N1               6               107
  N2               4                31
  N3               0                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A  MX
  2P LOSS MUTATED    15   0   0   1
  2P LOSS WILD-TYPE 343   5   1  49
D43V6, multiclass
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  M0               15               343
  M1                0                 5
  M1A               0                 1
  MX                1                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V7, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     7   9
  2P LOSS WILD-TYPE 100 304
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      7    9
  2P LOSS WILD-TYPE  100  304
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE               7               100
  MALE                 9               304
[1] 2 2
[1] FALSE
D43V8, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  2P LOSS MUTATED                                       0
  2P LOSS WILD-TYPE                                    12
                   vv
clus                LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  2P LOSS MUTATED                                        0
  2P LOSS WILD-TYPE                                      6
                   vv
clus                LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  2P LOSS MUTATED                                         0
  2P LOSS WILD-TYPE                                       1
                   vv
clus                LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  2P LOSS MUTATED                                                            16
  2P LOSS WILD-TYPE                                                         385
D43V9, multiclass
                                                             clus
vv                                                            2P LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    0
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              16
                                                             clus
vv                                                            2P LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      12
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               385
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V10, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     1  15
  2P LOSS WILD-TYPE  12 392
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      1   15
  2P LOSS WILD-TYPE   12  392
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  NO                1                12
  YES              15               392
[1] 2 2
[1] FALSE
D43V11, continuous
                   vv
clus                 R0  R1  R2  RX
  2P LOSS MUTATED    16   0   0   0
  2P LOSS WILD-TYPE 326   8   4  18
D43V12, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  R0              16               326
  R1               0                 8
  R2               0                 4
  RX               0                18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2P LOSS MUTATED       0                         2    11
  2P LOSS WILD-TYPE     9                        15   287
D43V13, multiclass
                           clus
vv                          2P LOSS MUTATED 2P LOSS WILD-TYPE
  ASIAN                                   0                 9
  BLACK OR AFRICAN AMERICAN               2                15
  WHITE                                  11               287
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V14, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     1  10
  2P LOSS WILD-TYPE   7 257
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      1   10
  2P LOSS WILD-TYPE    7  257
                        clus
vv                       2P LOSS MUTATED 2P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 7
  NOT HISPANIC OR LATINO              10               257
[1] 2 2
[1] FALSE

Clustering(44) Variable = 2Q LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                 0   1
  2Q LOSS MUTATED    21   8
  2Q LOSS WILD-TYPE 244 115
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               29               359 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                8               115 
$`2Q LOSS MUTATED`
TCGA-18-3417 TCGA-21-1082 TCGA-21-5786 TCGA-21-5787 TCGA-22-4594 TCGA-22-4604 
         758         3644         1032          329         1470          399 
TCGA-22-5481 TCGA-33-4533 TCGA-37-4141 TCGA-39-5028 TCGA-43-2578 TCGA-43-7657 
        1952         1940           12           52          684          236 
TCGA-43-8115 TCGA-51-4081 TCGA-60-2713 TCGA-60-2724 TCGA-66-2763 TCGA-66-2767 
         407          911         1731          717           30           61 
TCGA-66-2800 TCGA-68-A59J TCGA-77-7465 TCGA-77-8007 TCGA-77-8136 TCGA-85-7696 
        1492          104          479         1960         1947           18 
TCGA-85-7699 TCGA-85-8288 TCGA-85-8352 TCGA-85-8664 TCGA-85-A511 
           1           54           67            3         1972 

$`2Q LOSS WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 
         370          136         2464         2417          146         1415 
TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3416 TCGA-18-3419 TCGA-18-3421 
         345          396         1810          862           50         1331 
TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1070 
         187           85         2754           92          827         3636 
TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 
        1426         3016         2134         1852         1058          474 
TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 TCGA-21-1083 TCGA-21-5782 TCGA-21-5784 
         965         3724          284          267          962         1268 
TCGA-21-A5DI TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 
         979          608          223         1945          131         1952 
TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 TCGA-22-4593 
          53          429          822         1485          623         1067 
TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 TCGA-22-4605 TCGA-22-4607 
         734           17         1161         1057         1946          587 
TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 
         358          965         1964         1933          445         1346 
TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 
          24         1651         1952          357          573          916 
TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4538 
        1912         1713          506           29         2524         2979 
TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 
        1311         5287         1966         1941          428         1970 
TCGA-33-4589 TCGA-33-6738 TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 
        1948          822           80         1874          958          881 
TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 
        1000          951         1528         2062         1715          707 
TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-8454 TCGA-37-3783 
         365          428          941          552          166          120 
TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 
          13           12          200          247          227          238 
TCGA-37-4135 TCGA-37-5819 TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 
         207          103         1454         2253         1361         1947 
TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 
        1996         1964         1849          740           59          833 
TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 TCGA-39-5040 
        1107          474         1084         1086          544         1964 
TCGA-43-2576 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 
        1223         1176          822         1007          349          849 
TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-7656 TCGA-43-7658 
         376          757          310         1936          212         1970 
TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V 
         358         1971          353          296          432          366 
TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-52-7622 TCGA-52-7809 
         324          423           12           12          541         1948 
TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 
         923         1958         1967          881            3          555 
TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 
          62           26           30           13           30           44 
TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-8503 
          40           26            6         1961            1           41 
TCGA-56-8504 TCGA-56-8622 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 
         178           55           36           63           17           16 
TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ 
          34           38            2           46           30           25 
TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 
           4            4            8          378          911         2167 
TCGA-58-8393 TCGA-58-A46J TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 
        1058         2589         1723         1072          910          642 
TCGA-60-2696 TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 
         109          311         1950         1943         1958          661 
TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 TCGA-60-2714 
        1963         1505         1963         1260          274         1531 
TCGA-60-2715 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 
        1075         1475         1297           97          983          908 
TCGA-60-2723 TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 
        1092          816          358         1973         1957         1955 
TCGA-63-7022 TCGA-63-7023 TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 
        1947         1952         1967         1311           61          641 
TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 
          30           31           61           28           30           30 
TCGA-66-2758 TCGA-66-2759 TCGA-66-2765 TCGA-66-2766 TCGA-66-2768 TCGA-66-2769 
         639          762           61           31           61         1947 
TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 
         700          578         1946           61          578         1956 
TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 
         121         1954          759           60          790         1217 
TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 
         699         1955          699         1977          913         1952 
TCGA-66-2794 TCGA-66-2795 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 
        1645          122           83          202          211          244 
TCGA-68-8251 TCGA-68-A59I TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 
          96          121         1950         1941         1942         1952 
TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 
        1959         1968           15         1286         1954         1942 
TCGA-77-7338 TCGA-77-7463 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 
        1952         1954         1945         1641         1953         1945 
TCGA-77-8131 TCGA-77-8133 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8144 
        1941         1941         1946         1951         1962          833 
TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 
        1943          293         1961         1684         1092           10 
TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 
        1953         1942         1959         1955         1963         1290 
TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6560 TCGA-85-6561 
        1280         1939          839          713          364          395 
TCGA-85-6798 TCGA-85-7697 TCGA-85-7698 TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 
          34           10           49         1965           35          911 
TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 
          60           26           60           16          960          428 
TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 TCGA-85-8350 TCGA-85-8351 
         513           13           11           13           60           55 
TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 
          54           61           61           22           21          445 
TCGA-85-8582 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR 
         424          475           15         1972         1960           25 
TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L 
          19         1973         1967         1987           24           13 
TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 TCGA-90-7964 
         111          758          289           89          358          428 
TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 
         244          331          269           82          106          122 
TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 TCGA-94-7943 TCGA-94-A4VJ TCGA-96-7544 
         160           70           87          356          430         1213 
TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL TCGA-98-7454 
        1344          189          211          273          183          256 
TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 
         413          224          308          222           35          449 
TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HE TCGA-NC-A5HG TCGA-NC-A5HI 
          36           83         1722         1548         1135 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                1                 1 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             3644              5287 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
              479               642 
[1] "1.0 - 3644.0 (479.0)" "1.0 - 5287.0 (642.0)"
[1] "hr=" "1"  
D44V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  2Q LOSS MUTATED         0        3        8        0         4         6
  2Q LOSS WILD-TYPE       1       69      129        1        48        65
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  2Q LOSS MUTATED            7          2        1
  2Q LOSS WILD-TYPE         50         18        5
D44V3, multiclass
            clus
vv           2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                 3                69
  STAGE IB                 8               129
  STAGE II                 0                 1
  STAGE IIA                4                48
  STAGE IIB                6                65
  STAGE IIIA               7                50
  STAGE IIIB               2                18
  STAGE IV                 1                 5
[1] 9 2
[1] 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     5  20   3   3
  2Q LOSS WILD-TYPE  93 234  45  17
D44V4, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  T1               5                93
  T2              20               234
  T3               3                45
  T4               3                17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  2Q LOSS MUTATED    13  14   3   1
  2Q LOSS WILD-TYPE 248  99  32   4
D44V5, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  N0              13               248
  N1              14                99
  N2               3                32
  N3               1                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A  MX
  2Q LOSS MUTATED    27   1   0   3
  2Q LOSS WILD-TYPE 331   4   1  47
D44V6, multiclass
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  M0               27               331
  M1                1                 4
  M1A               0                 1
  MX                3                47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V7, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    10  21
  2Q LOSS WILD-TYPE  97 292
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     10   21
  2Q LOSS WILD-TYPE   97  292
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE              10                97
  MALE                21               292
[1] 2 2
[1] FALSE
D44V8, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  2Q LOSS MUTATED                                       1
  2Q LOSS WILD-TYPE                                    11
                   vv
clus                LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  2Q LOSS MUTATED                                        0
  2Q LOSS WILD-TYPE                                      6
                   vv
clus                LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  2Q LOSS MUTATED                                         0
  2Q LOSS WILD-TYPE                                       1
                   vv
clus                LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  2Q LOSS MUTATED                                                            30
  2Q LOSS WILD-TYPE                                                         371
D44V9, multiclass
                                                             clus
vv                                                            2Q LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    0
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              30
                                                             clus
vv                                                            2Q LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      11
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               371
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V10, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     1  30
  2Q LOSS WILD-TYPE  12 377
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      1   30
  2Q LOSS WILD-TYPE   12  377
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  NO                1                12
  YES              30               377
[1] 2 2
[1] FALSE
D44V11, continuous
                   vv
clus                 R0  R1  R2  RX
  2Q LOSS MUTATED    30   0   0   0
  2Q LOSS WILD-TYPE 312   8   4  18
D44V12, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  R0              30               312
  R1               0                 8
  R2               0                 4
  RX               0                18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2Q LOSS MUTATED       0                         2    22
  2Q LOSS WILD-TYPE     9                        15   276
D44V13, multiclass
                           clus
vv                          2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  ASIAN                                   0                 9
  BLACK OR AFRICAN AMERICAN               2                15
  WHITE                                  22               276
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V14, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     0  21
  2Q LOSS WILD-TYPE   8 246
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      0   21
  2Q LOSS WILD-TYPE    8  246
                        clus
vv                       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 8
  NOT HISPANIC OR LATINO              21               246
[1] 2 2
[1] FALSE

Clustering(45) Variable = 3P LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                 0   1
  3P LOSS MUTATED   173  75
  3P LOSS WILD-TYPE  92  48
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              248               140 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               75                48 
$`3P LOSS MUTATED`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3411 TCGA-18-3412 
         370          136         2464         2417         1415          345 
TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 
        1810          862          758          187           85         2754 
TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 TCGA-21-1075 TCGA-21-1077 TCGA-21-1079 
          92         3636         1426         2134         1058          965 
TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 TCGA-21-5786 TCGA-21-5787 TCGA-21-A5DI 
        3644          267          962         1032          329          979 
TCGA-22-0940 TCGA-22-0944 TCGA-22-1012 TCGA-22-1016 TCGA-22-4591 TCGA-22-4594 
         608          223          429          822          623         1470 
TCGA-22-4599 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-4613 TCGA-22-5471 
        1161          399         1946          587          358          965 
TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 
        1964         1933          445           24         1651         1952 
TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4532 
        1952          357          573          506           29         2524 
TCGA-33-4583 TCGA-33-4587 TCGA-33-4589 TCGA-33-6738 TCGA-34-2596 TCGA-34-2600 
        1941         1970         1948          822           80         1874 
TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 TCGA-34-5231 TCGA-34-5239 TCGA-37-4129 
         958          881         1000         1528          707          200 
TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4141 TCGA-37-5819 TCGA-39-5011 
         247          227          238           12          103         1454 
TCGA-39-5016 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5031 TCGA-39-5035 
        2253         1964         1849           52          833          474 
TCGA-39-5036 TCGA-43-2576 TCGA-43-2581 TCGA-43-3920 TCGA-43-6143 TCGA-43-6770 
        1084         1223         1176         1007          376          310 
TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 
         212          236         1970          407          358         1971 
TCGA-43-A474 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 
         353           12           12          911          541         1948 
TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-6545 TCGA-56-7221 
        1958         1967          881            3           62           30 
TCGA-56-7222 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7731 TCGA-56-7822 
          13           44           40           26         1961            1 
TCGA-56-8503 TCGA-56-8504 TCGA-56-8624 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 
          41          178           36           17           16           34 
TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A5DS TCGA-58-8388 TCGA-58-8390 
          46           30           25            8          378          911 
TCGA-58-8391 TCGA-60-2695 TCGA-60-2696 TCGA-60-2698 TCGA-60-2704 TCGA-60-2707 
        2167          642          109          311         1943          661 
TCGA-60-2708 TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 TCGA-60-2719 TCGA-60-2721 
        1963         1963         1260          274         1297          983 
TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-7020 
         908         1092          717          816          358         1957 
TCGA-63-7021 TCGA-63-7023 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2754 
        1955         1952         1311           61          641           61 
TCGA-66-2755 TCGA-66-2757 TCGA-66-2758 TCGA-66-2763 TCGA-66-2765 TCGA-66-2767 
          28           30          639           30           61           61 
TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 TCGA-66-2773 TCGA-66-2778 TCGA-66-2780 
          61         1947          700         1946          578         1956 
TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 
         121         1954          759          790         1217          699 
TCGA-66-2790 TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2795 TCGA-66-2800 
         699         1977          913         1952          122         1492 
TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I 
          83          202          211          244           96          121 
TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 
        1950         1941         1942         1952         1959         1968 
TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 
          15         1286         1954         1942         1952         1954 
TCGA-77-7465 TCGA-77-8128 TCGA-77-8130 TCGA-77-8133 TCGA-77-8138 TCGA-77-8139 
         479         1953         1945         1941         1946         1951 
TCGA-77-8140 TCGA-77-8144 TCGA-77-8148 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 
        1962          833          293         1684         1092           10 
TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5GH TCGA-85-6560 TCGA-85-6798 
        1959         1955         1963          713          364           34 
TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7844 TCGA-85-7950 
          10           49            1         1965          911           60 
TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8277 TCGA-85-8288 
          16          960          428          513           11           54 
TCGA-85-8351 TCGA-85-8353 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8666 
          55           54           61           22           21          475 
TCGA-85-A4CL TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 
          15         1960           25         1973         1967         1972 
TCGA-85-A512 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-7766 TCGA-90-7767 TCGA-90-7964 
        1987           13          111          289           89          428 
TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 
         244          331          269          106          122          160 
TCGA-92-8065 TCGA-94-A4VJ TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK 
          70          430         1213          189          211          273 
TCGA-98-8021 TCGA-98-8023 TCGA-L3-A4E7 TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HE 
         413          308           35           36           83         1722 
TCGA-NC-A5HG TCGA-NC-A5HI 
        1548         1135 

$`3P LOSS WILD-TYPE`
TCGA-18-3410 TCGA-18-3414 TCGA-18-3419 TCGA-18-3421 TCGA-18-5595 TCGA-21-1072 
         146          396           50         1331          827         3016 
TCGA-21-1076 TCGA-21-1078 TCGA-21-1080 TCGA-21-1081 TCGA-21-5784 TCGA-22-1000 
        1852          474         3724          284         1268         1945 
TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1017 TCGA-22-4593 TCGA-22-4595 
         131         1952           53         1485         1067          734 
TCGA-22-4596 TCGA-22-4601 TCGA-22-5477 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 
          17         1057         1346          916         1912         1713 
TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4586 
        1940         2979         1311         5287         1966          428 
TCGA-34-2609 TCGA-34-5232 TCGA-34-5234 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 
         951         2062         1715          365          428          941 
TCGA-34-5928 TCGA-34-8454 TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4135 
         552          166          120           13           12          207 
TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5029 TCGA-39-5030 TCGA-39-5034 
        1361         1947         1996          740           59         1107 
TCGA-39-5037 TCGA-39-5039 TCGA-39-5040 TCGA-43-2578 TCGA-43-3394 TCGA-43-5668 
        1086          544         1964          684          822          349 
TCGA-43-5670 TCGA-43-6647 TCGA-43-6771 TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V 
         849          757         1936          296          432          366 
TCGA-46-6025 TCGA-46-6026 TCGA-52-7810 TCGA-56-5898 TCGA-56-6546 TCGA-56-7223 
         324          423          923          555           26           30 
TCGA-56-7730 TCGA-56-8622 TCGA-56-8625 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4ZK 
           6           55           63           38            2            4 
TCGA-56-A5DR TCGA-58-8393 TCGA-58-A46J TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N 
           4         1058         2589         1723         1072          910 
TCGA-60-2703 TCGA-60-2706 TCGA-60-2709 TCGA-60-2713 TCGA-60-2714 TCGA-60-2715 
        1950         1958         1505         1731         1531         1075 
TCGA-60-2716 TCGA-60-2720 TCGA-63-6202 TCGA-63-7022 TCGA-66-2727 TCGA-66-2744 
        1475           97         1973         1947         1967           30 
TCGA-66-2753 TCGA-66-2756 TCGA-66-2759 TCGA-66-2766 TCGA-66-2771 TCGA-66-2777 
          31           30          762           31          578           61 
TCGA-66-2785 TCGA-66-2789 TCGA-66-2794 TCGA-68-A59J TCGA-77-8007 TCGA-77-8008 
          60         1955         1645          104         1960         1945 
TCGA-77-8009 TCGA-77-8131 TCGA-77-8136 TCGA-77-8145 TCGA-77-8150 TCGA-77-A5FZ 
        1641         1941         1947         1943         1961         1953 
TCGA-77-A5G1 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF TCGA-85-6561 
        1942         1290         1280         1939          839          395 
TCGA-85-7696 TCGA-85-7843 TCGA-85-8048 TCGA-85-8049 TCGA-85-8276 TCGA-85-8287 
          18           35           26           60           13           13 
TCGA-85-8350 TCGA-85-8352 TCGA-85-8354 TCGA-85-8580 TCGA-85-8582 TCGA-85-8664 
          60           67           61          445          424            3 
TCGA-85-A4PA TCGA-85-A50M TCGA-85-A513 TCGA-90-6837 TCGA-90-7769 TCGA-92-7340 
        1972           19           24          758          358           82 
TCGA-94-7033 TCGA-94-7943 TCGA-96-7545 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8022 
          87          356         1344          183          256          224 
TCGA-J1-A4AH TCGA-L3-A524 
         222          449 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                1                 2 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             3644              5287 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              631               737 
[1] "1.0 - 3644.0 (631.0)" "2.0 - 5287.0 (737.0)"
[1] "hr=" "1.2"
D45V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  3P LOSS MUTATED         1       44       91        0        31        41
  3P LOSS WILD-TYPE       0       28       46        1        21        30
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  3P LOSS MUTATED           32         14        5
  3P LOSS WILD-TYPE         25          6        1
D45V3, multiclass
            clus
vv           3P LOSS MUTATED 3P LOSS WILD-TYPE
  STAGE I                  1                 0
  STAGE IA                44                28
  STAGE IB                91                46
  STAGE II                 0                 1
  STAGE IIA               31                21
  STAGE IIB               41                30
  STAGE IIIA              32                25
  STAGE IIIB              14                 6
  STAGE IV                 5                 1
[1] 9 2
[1] 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    62 157  30  13
  3P LOSS WILD-TYPE  36  97  18   7
D45V4, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  T1              62                36
  T2             157                97
  T3              30                18
  T4              13                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  3P LOSS MUTATED   168  71  18   4
  3P LOSS WILD-TYPE  93  42  17   1
D45V5, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  N0             168                93
  N1              71                42
  N2              18                17
  N3               4                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A  MX
  3P LOSS MUTATED   221   4   1  32
  3P LOSS WILD-TYPE 137   1   0  18
D45V6, multiclass
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  M0              221               137
  M1                4                 1
  M1A               1                 0
  MX               32                18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V7, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    70 192
  3P LOSS WILD-TYPE  37 121
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     70  192
  3P LOSS WILD-TYPE   37  121
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE              70                37
  MALE               192               121
[1] 2 2
[1] FALSE
D45V8, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  3P LOSS MUTATED                                       8
  3P LOSS WILD-TYPE                                     4
                   vv
clus                LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  3P LOSS MUTATED                                        3
  3P LOSS WILD-TYPE                                      3
                   vv
clus                LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  3P LOSS MUTATED                                         1
  3P LOSS WILD-TYPE                                       0
                   vv
clus                LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  3P LOSS MUTATED                                                           250
  3P LOSS WILD-TYPE                                                         151
D45V9, multiclass
                                                             clus
vv                                                            3P LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     8
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             250
                                                             clus
vv                                                            3P LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       4
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               151
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V10, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     9 253
  3P LOSS WILD-TYPE   4 154
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      9  253
  3P LOSS WILD-TYPE    4  154
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  NO                9                 4
  YES             253               154
[1] 2 2
[1] FALSE
D45V11, continuous
                   vv
clus                 R0  R1  R2  RX
  3P LOSS MUTATED   215   3   3  11
  3P LOSS WILD-TYPE 127   5   1   7
D45V12, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  R0             215               127
  R1               3                 5
  R2               3                 1
  RX              11                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3P LOSS MUTATED       3                        10   184
  3P LOSS WILD-TYPE     6                         7   114
D45V13, multiclass
                           clus
vv                          3P LOSS MUTATED 3P LOSS WILD-TYPE
  ASIAN                                   3                 6
  BLACK OR AFRICAN AMERICAN              10                 7
  WHITE                                 184               114
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V14, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     6 157
  3P LOSS WILD-TYPE   2 110
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      6  157
  3P LOSS WILD-TYPE    2  110
                        clus
vv                       3P LOSS MUTATED 3P LOSS WILD-TYPE
  HISPANIC OR LATINO                   6                 2
  NOT HISPANIC OR LATINO             157               110
[1] 2 2
[1] FALSE

Clustering(46) Variable = 3Q LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                 0   1
  3Q LOSS MUTATED    36  18
  3Q LOSS WILD-TYPE 229 105
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               54               334 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               18               105 
$`3Q LOSS MUTATED`
TCGA-18-3408 TCGA-18-3412 TCGA-18-3416 TCGA-18-5592 TCGA-21-1075 TCGA-21-1079 
        2464          345          862           92         2134          965 
TCGA-21-1082 TCGA-22-0944 TCGA-22-1016 TCGA-22-4594 TCGA-22-4604 TCGA-22-5483 
        3644          223          822         1470          399          573 
TCGA-33-4583 TCGA-33-6738 TCGA-37-4129 TCGA-39-5011 TCGA-39-5027 TCGA-43-2581 
        1941          822          200         1454         1849         1176 
TCGA-43-A474 TCGA-52-7811 TCGA-56-1622 TCGA-56-7221 TCGA-56-7579 TCGA-56-7582 
         353         1958          881           30           44           26 
TCGA-56-8503 TCGA-58-8388 TCGA-60-2696 TCGA-60-2698 TCGA-60-2722 TCGA-63-7021 
          41          378          109          311          908         1955 
TCGA-66-2737 TCGA-66-2754 TCGA-66-2757 TCGA-66-2769 TCGA-66-2782 TCGA-66-2788 
          61           61           30         1947         1954          699 
TCGA-66-2791 TCGA-66-2793 TCGA-66-2795 TCGA-77-6843 TCGA-77-6844 TCGA-77-8130 
        1977         1952          122         1941         1942         1945 
TCGA-77-8154 TCGA-85-7698 TCGA-85-8070 TCGA-85-8071 TCGA-85-8481 TCGA-85-A50Z 
        1092           49          960          428           21         1973 
TCGA-85-A53L TCGA-90-A4ED TCGA-92-7341 TCGA-96-8169 TCGA-98-8023 TCGA-NC-A5HE 
          13          244          106          189          308         1722 

$`3Q LOSS WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 TCGA-18-3414 
         370          136         2417          146         1415          396 
TCGA-18-3415 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 
        1810          758           50         1331          187           85 
TCGA-18-4721 TCGA-18-5595 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 TCGA-21-1076 
        2754          827         3636         1426         3016         1852 
TCGA-21-1077 TCGA-21-1078 TCGA-21-1080 TCGA-21-1081 TCGA-21-1083 TCGA-21-5782 
        1058          474         3724          284          267          962 
TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-21-A5DI TCGA-22-0940 TCGA-22-1000 
        1268         1032          329          979          608         1945 
TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1017 TCGA-22-4591 
         131         1952           53          429         1485          623 
TCGA-22-4593 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 TCGA-22-4605 
        1067          734           17         1161         1057         1946 
TCGA-22-4607 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 
         587          358          965         1964         1933          445 
TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 
        1346           24         1651         1952         1952          357 
TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4532 
         916         1912         1713          506           29         2524 
TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4586 
        1940         2979         1311         5287         1966          428 
TCGA-33-4587 TCGA-33-4589 TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 
        1970         1948           80         1874          958          881 
TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 
        1000          951         1528         2062         1715          707 
TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-8454 TCGA-37-3783 
         365          428          941          552          166          120 
TCGA-37-3789 TCGA-37-3792 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 
          13           12          247          227          238          207 
TCGA-37-4141 TCGA-37-5819 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 
          12          103         2253         1361         1947         1996 
TCGA-39-5024 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 
        1964           52          740           59          833         1107 
TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 
         474         1084         1086          544         1964         1223 
TCGA-43-2578 TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 
         684          822         1007          349          849          376 
TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 
         757          310         1936          212          236         1970 
TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V 
         407          358         1971          296          432          366 
TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 
         324          423           12           12          911          541 
TCGA-52-7809 TCGA-52-7810 TCGA-52-7812 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 
        1948          923         1967            3          555           62 
TCGA-56-6546 TCGA-56-7222 TCGA-56-7223 TCGA-56-7580 TCGA-56-7730 TCGA-56-7731 
          26           13           30           40            6         1961 
TCGA-56-7822 TCGA-56-8504 TCGA-56-8622 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 
           1          178           55           36           63           17 
TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY 
          16           34           38            2           46           30 
TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8390 TCGA-58-8391 
          25            4            4            8          911         2167 
TCGA-58-8393 TCGA-58-A46J TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 
        1058         2589         1723         1072          910          642 
TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 
        1950         1943         1958          661         1963         1505 
TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2715 
        1963         1260          274         1731         1531         1075 
TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2723 TCGA-60-2724 
        1475         1297           97          983         1092          717 
TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 TCGA-63-7020 TCGA-63-7022 TCGA-63-7023 
         816          358         1973         1957         1947         1952 
TCGA-66-2727 TCGA-66-2734 TCGA-66-2742 TCGA-66-2744 TCGA-66-2753 TCGA-66-2755 
        1967         1311          641           30           31           28 
TCGA-66-2756 TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 
          30          639          762           30           61           31 
TCGA-66-2767 TCGA-66-2768 TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 
          61           61          700          578         1946           61 
TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 
         578         1956          121          759           60          790 
TCGA-66-2787 TCGA-66-2789 TCGA-66-2790 TCGA-66-2792 TCGA-66-2794 TCGA-66-2800 
        1217         1955          699          913         1645         1492 
TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I 
          83          202          211          244           96          121 
TCGA-68-A59J TCGA-77-6842 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 
         104         1950         1952         1959         1968           15 
TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 
        1286         1954         1942         1952         1954          479 
TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8131 TCGA-77-8133 
        1960         1945         1641         1953         1941         1941 
TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8144 TCGA-77-8145 
        1947         1946         1951         1962          833         1943 
TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 
         293         1961         1684           10         1953         1942 
TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB 
        1959         1955         1963         1290         1280         1939 
TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 
         839          713          364          395           34           18 
TCGA-85-7697 TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 
          10            1         1965           35          911           60 
TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 
          26           60           16          513           13           11 
TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 
          13           54           60           55           67           54 
TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 TCGA-85-8580 TCGA-85-8582 TCGA-85-8664 
          61           61           22          445          424            3 
TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M 
         475           15         1972         1960           25           19 
TCGA-85-A510 TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 TCGA-85-A5B5 TCGA-90-6837 
        1967         1972         1987           24          111          758 
TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 TCGA-90-7964 TCGA-90-A4EE TCGA-90-A59Q 
         289           89          358          428          331          269 
TCGA-92-7340 TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 TCGA-94-7943 
          82          122          160           70           87          356 
TCGA-94-A4VJ TCGA-96-7544 TCGA-96-7545 TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL 
         430         1213         1344          211          273          183 
TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 
         256          413          224          222           35          449 
TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HG TCGA-NC-A5HI 
          36           83         1548         1135 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               13                 1 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             3644              5287 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            760.5             640.0 
[1] "13.0 - 3644.0 (760.5)" "1.0 - 5287.0 (640.0)" 
[1] "hr=" "1"  
D46V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  3Q LOSS MUTATED         0        7       18        0         8        13
  3Q LOSS WILD-TYPE       1       65      119        1        44        58
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  3Q LOSS MUTATED            9          4        0
  3Q LOSS WILD-TYPE         48         16        6
D46V3, multiclass
            clus
vv           3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                 7                65
  STAGE IB                18               119
  STAGE II                 0                 1
  STAGE IIA                8                44
  STAGE IIB               13                58
  STAGE IIIA               9                48
  STAGE IIIB               4                16
  STAGE IV                 0                 6
[1] 9 2
[1] 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    12  32  13   3
  3Q LOSS WILD-TYPE  86 222  35  17
D46V4, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  T1              12                86
  T2              32               222
  T3              13                35
  T4               3                17
[1] 4 2
[1] 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    37  19   3   1
  3Q LOSS WILD-TYPE 224  94  32   4
D46V5, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  N0              37               224
  N1              19                94
  N2               3                32
  N3               1                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A  MX
  3Q LOSS MUTATED    56   0   0   3
  3Q LOSS WILD-TYPE 302   5   1  47
D46V6, multiclass
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  M0               56               302
  M1                0                 5
  M1A               0                 1
  MX                3                47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V7, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    12  48
  3Q LOSS WILD-TYPE  95 265
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     12   48
  3Q LOSS WILD-TYPE   95  265
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE              12                95
  MALE                48               265
[1] 2 2
[1] FALSE
D46V8, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  3Q LOSS MUTATED                                       1
  3Q LOSS WILD-TYPE                                    11
                   vv
clus                LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  3Q LOSS MUTATED                                        2
  3Q LOSS WILD-TYPE                                      4
                   vv
clus                LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  3Q LOSS MUTATED                                         0
  3Q LOSS WILD-TYPE                                       1
                   vv
clus                LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  3Q LOSS MUTATED                                                            57
  3Q LOSS WILD-TYPE                                                         344
D46V9, multiclass
                                                             clus
vv                                                            3Q LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              57
                                                             clus
vv                                                            3Q LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      11
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               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"
D46V10, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     1  59
  3Q LOSS WILD-TYPE  12 348
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      1   59
  3Q LOSS WILD-TYPE   12  348
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  NO                1                12
  YES              59               348
[1] 2 2
[1] FALSE
D46V11, continuous
                   vv
clus                 R0  R1  R2  RX
  3Q LOSS MUTATED    49   2   0   3
  3Q LOSS WILD-TYPE 293   6   4  15
D46V12, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  R0              49               293
  R1               2                 6
  R2               0                 4
  RX               3                15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3Q LOSS MUTATED       2                         2    40
  3Q LOSS WILD-TYPE     7                        15   258
D46V13, multiclass
                           clus
vv                          3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  ASIAN                                   2                 7
  BLACK OR AFRICAN AMERICAN               2                15
  WHITE                                  40               258
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V14, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     1  35
  3Q LOSS WILD-TYPE   7 232
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      1   35
  3Q LOSS WILD-TYPE    7  232
                        clus
vv                       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 7
  NOT HISPANIC OR LATINO              35               232
[1] 2 2
[1] FALSE

Clustering(47) Variable = 4P LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                 0   1
  4P LOSS MUTATED   170  72
  4P LOSS WILD-TYPE  95  51
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              242               146 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               72                51 
$`4P LOSS MUTATED`
TCGA-18-3407 TCGA-18-3411 TCGA-18-3412 TCGA-18-3415 TCGA-18-3417 TCGA-18-3421 
         136         1415          345         1810          758         1331 
TCGA-18-4083 TCGA-18-4086 TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 
         187           85           92         3636         1426         3016 
TCGA-21-1076 TCGA-21-1077 TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 
        1852         1058          965         3724          284         3644 
TCGA-21-1083 TCGA-21-5782 TCGA-21-5786 TCGA-21-5787 TCGA-22-0940 TCGA-22-0944 
         267          962         1032          329          608          223 
TCGA-22-1000 TCGA-22-1011 TCGA-22-1012 TCGA-22-4593 TCGA-22-4594 TCGA-22-4595 
        1945           53          429         1067         1470          734 
TCGA-22-4599 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-5471 TCGA-22-5472 
        1161          399         1946          587          965         1964 
TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5479 TCGA-22-5482 TCGA-22-5483 
        1933          445         1346         1651          357          573 
TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-33-4532 TCGA-33-4533 TCGA-33-4538 
         916         1912         1713         2524         1940         2979 
TCGA-33-4547 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-33-4589 
        1311         1966         1941          428         1970         1948 
TCGA-33-6738 TCGA-34-2600 TCGA-34-2605 TCGA-34-5231 TCGA-34-5232 TCGA-34-5241 
         822         1874          881         1528         2062          428 
TCGA-34-5927 TCGA-34-5928 TCGA-37-3783 TCGA-37-3789 TCGA-37-4133 TCGA-37-4135 
         941          552          120           13          238          207 
TCGA-37-4141 TCGA-37-5819 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5027 
          12          103         2253         1361         1947         1849 
TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5037 TCGA-39-5040 TCGA-43-2578 
         833         1107          474         1086         1964          684 
TCGA-43-3394 TCGA-43-6143 TCGA-43-6771 TCGA-43-7656 TCGA-43-7657 TCGA-43-8115 
         822          376         1936          212          236          407 
TCGA-43-8118 TCGA-43-A474 TCGA-43-A56U TCGA-43-A56V TCGA-46-6025 TCGA-46-6026 
        1971          353          432          366          324          423 
TCGA-51-4081 TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 TCGA-56-5898 
         911         1948          923         1958         1967          555 
TCGA-56-6545 TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7582 
          62           30           13           30           44           26 
TCGA-56-7730 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4ZK TCGA-56-A5DR 
           6           38            2           46            4            4 
TCGA-58-8393 TCGA-58-A46J TCGA-58-A46L TCGA-58-A46M TCGA-60-2695 TCGA-60-2696 
        1058         2589         1723         1072          642          109 
TCGA-60-2698 TCGA-60-2703 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 
         311         1950         1958          661         1963         1505 
TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2719 
        1963         1260          274         1731         1531         1297 
TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2726 
          97          983          908         1092          717          358 
TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 TCGA-66-2727 TCGA-66-2734 
        1957         1955         1947         1952         1967         1311 
TCGA-66-2737 TCGA-66-2742 TCGA-66-2753 TCGA-66-2754 TCGA-66-2758 TCGA-66-2759 
          61          641           31           61          639          762 
TCGA-66-2765 TCGA-66-2767 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 
          61           61          578         1946           61          578 
TCGA-66-2780 TCGA-66-2781 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2791 
        1956          121          759           60          790         1977 
TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 
         913         1952         1645          122         1492           83 
TCGA-68-7756 TCGA-68-A59J TCGA-77-6843 TCGA-77-6845 TCGA-77-7139 TCGA-77-7141 
         202          104         1941         1952         1968           15 
TCGA-77-7142 TCGA-77-7335 TCGA-77-7463 TCGA-77-7465 TCGA-77-8009 TCGA-77-8128 
        1286         1954         1954          479         1641         1953 
TCGA-77-8130 TCGA-77-8133 TCGA-77-8138 TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 
        1945         1941         1946          833         1943          293 
TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-A5G3 TCGA-77-A5G7 TCGA-77-A5G8 
        1961         1684         1092         1959         1963         1290 
TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6560 TCGA-85-6561 
        1280         1939          839          713          364          395 
TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 TCGA-85-7843 TCGA-85-8048 
          18           10           49            1           35           26 
TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 
          60           16          960          428          513           13 
TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8352 TCGA-85-8353 
          11           13           54           60           67           54 
TCGA-85-8354 TCGA-85-8580 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4QQ 
          61          445            3          475           15         1960 
TCGA-85-A4QR TCGA-85-A510 TCGA-85-A512 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-7766 
          25         1967         1987           13          111          289 
TCGA-90-7964 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 
         428          244          331          269           82          106 
TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-7943 TCGA-96-A4JK TCGA-98-7454 
         122          160           70          356          273          256 
TCGA-98-8021 TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HE 
         413           35          449           36           83         1722 
TCGA-NC-A5HG TCGA-NC-A5HI 
        1548         1135 

$`4P LOSS WILD-TYPE`
TCGA-18-3406 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3414 TCGA-18-3416 
         370         2464         2417          146          396          862 
TCGA-18-3419 TCGA-18-4721 TCGA-18-5595 TCGA-21-1075 TCGA-21-1078 TCGA-21-5784 
          50         2754          827         2134          474         1268 
TCGA-21-A5DI TCGA-22-1002 TCGA-22-1005 TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 
         979          131         1952          822         1485          623 
TCGA-22-4596 TCGA-22-4601 TCGA-22-4613 TCGA-22-5478 TCGA-22-5480 TCGA-22-5481 
          17         1057          358           24         1952         1952 
TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4566 TCGA-34-2596 TCGA-34-2604 TCGA-34-2608 
         506           29         5287           80          958         1000 
TCGA-34-2609 TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 TCGA-34-8454 TCGA-37-3792 
         951         1715          707          365          166           12 
TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-39-5011 TCGA-39-5022 TCGA-39-5024 
         200          247          227         1454         1996         1964 
TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5036 TCGA-39-5039 TCGA-43-2576 
          52          740           59         1084          544         1223 
TCGA-43-2581 TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 TCGA-43-6647 TCGA-43-6770 
        1176         1007          349          849          757          310 
TCGA-43-7658 TCGA-43-8116 TCGA-43-A475 TCGA-51-4079 TCGA-51-4080 TCGA-52-7622 
        1970          358          296           12           12          541 
TCGA-56-1622 TCGA-56-5897 TCGA-56-6546 TCGA-56-7580 TCGA-56-7731 TCGA-56-7822 
         881            3           26           40         1961            1 
TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 
          41          178           55           36           63           17 
TCGA-56-8628 TCGA-56-8629 TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A5DS TCGA-58-8388 
          16           34           30           25            8          378 
TCGA-58-8390 TCGA-58-8391 TCGA-58-A46N TCGA-60-2704 TCGA-60-2715 TCGA-60-2716 
         911         2167          910         1943         1075         1475 
TCGA-60-2725 TCGA-63-6202 TCGA-66-2744 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 
         816         1973           30           28           30           30 
TCGA-66-2763 TCGA-66-2766 TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 TCGA-66-2782 
          30           31           61         1947          700         1954 
TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-68-7757 TCGA-68-8250 
        1217          699         1955          699          211          244 
TCGA-68-8251 TCGA-68-A59I TCGA-77-6842 TCGA-77-6844 TCGA-77-7138 TCGA-77-7337 
          96          121         1950         1942         1959         1942 
TCGA-77-7338 TCGA-77-8007 TCGA-77-8008 TCGA-77-8131 TCGA-77-8136 TCGA-77-8139 
        1952         1960         1945         1941         1947         1951 
TCGA-77-8140 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G6 TCGA-85-6798 
        1962           10         1953         1942         1955           34 
TCGA-85-7710 TCGA-85-7844 TCGA-85-7950 TCGA-85-8351 TCGA-85-8355 TCGA-85-8479 
        1965          911           60           55           61           22 
TCGA-85-8481 TCGA-85-8582 TCGA-85-A4PA TCGA-85-A50M TCGA-85-A50Z TCGA-85-A511 
          21          424         1972           19         1973         1972 
TCGA-85-A513 TCGA-90-6837 TCGA-90-7767 TCGA-90-7769 TCGA-94-7033 TCGA-94-A4VJ 
          24          758           89          358           87          430 
TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-8022 
        1213         1344          189          211          183          224 
TCGA-98-8023 TCGA-J1-A4AH 
         308          222 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                1                 1 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             3724              5287 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            698.5             523.5 
[1] "1.0 - 3724.0 (698.5)" "1.0 - 5287.0 (523.5)"
[1] "hr=" "1.2"
D47V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  4P LOSS MUTATED         0       40       94        1        35        37
  4P LOSS WILD-TYPE       1       32       43        0        17        34
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  4P LOSS MUTATED           36         13        2
  4P LOSS WILD-TYPE         21          7        4
D47V3, multiclass
            clus
vv           4P LOSS MUTATED 4P LOSS WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                40                32
  STAGE IB                94                43
  STAGE II                 1                 0
  STAGE IIA               35                17
  STAGE IIB               37                34
  STAGE IIIA              36                21
  STAGE IIIB              13                 7
  STAGE IV                 2                 4
[1] 9 2
[1] 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    57 166  27  10
  4P LOSS WILD-TYPE  41  88  21  10
D47V4, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  T1              57                41
  T2             166                88
  T3              27                21
  T4              10                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  4P LOSS MUTATED   157  72  24   4
  4P LOSS WILD-TYPE 104  41  11   1
D47V5, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  N0             157               104
  N1              72                41
  N2              24                11
  N3               4                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A  MX
  4P LOSS MUTATED   226   2   0  28
  4P LOSS WILD-TYPE 132   3   1  22
D47V6, multiclass
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  M0              226               132
  M1                2                 3
  M1A               0                 1
  MX               28                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V7, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    62 198
  4P LOSS WILD-TYPE  45 115
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     62  198
  4P LOSS WILD-TYPE   45  115
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE              62                45
  MALE               198               115
[1] 2 2
[1] FALSE
D47V8, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  4P LOSS MUTATED                                       7
  4P LOSS WILD-TYPE                                     5
                   vv
clus                LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  4P LOSS MUTATED                                        1
  4P LOSS WILD-TYPE                                      5
                   vv
clus                LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  4P LOSS MUTATED                                         1
  4P LOSS WILD-TYPE                                       0
                   vv
clus                LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  4P LOSS MUTATED                                                           251
  4P LOSS WILD-TYPE                                                         150
D47V9, multiclass
                                                             clus
vv                                                            4P LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     7
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             251
                                                             clus
vv                                                            4P LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       5
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               150
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V10, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    11 249
  4P LOSS WILD-TYPE   2 158
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     11  249
  4P LOSS WILD-TYPE    2  158
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  NO               11                 2
  YES             249               158
[1] 2 2
[1] FALSE
D47V11, continuous
                   vv
clus                 R0  R1  R2  RX
  4P LOSS MUTATED   213   4   4  10
  4P LOSS WILD-TYPE 129   4   0   8
D47V12, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  R0             213               129
  R1               4                 4
  R2               4                 0
  RX              10                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4P LOSS MUTATED       3                        10   187
  4P LOSS WILD-TYPE     6                         7   111
D47V13, multiclass
                           clus
vv                          4P LOSS MUTATED 4P LOSS WILD-TYPE
  ASIAN                                   3                 6
  BLACK OR AFRICAN AMERICAN              10                 7
  WHITE                                 187               111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V14, binary
                   cls
clus                  0   1
  4P LOSS MUTATED     5 160
  4P LOSS WILD-TYPE   3 107
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      5  160
  4P LOSS WILD-TYPE    3  107
                        clus
vv                       4P LOSS MUTATED 4P LOSS WILD-TYPE
  HISPANIC OR LATINO                   5                 3
  NOT HISPANIC OR LATINO             160               107
[1] 2 2
[1] FALSE

Clustering(48) Variable = 4Q LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                 0   1
  4Q LOSS MUTATED   159  72
  4Q LOSS WILD-TYPE 106  51
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              231               157 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               72                51 
$`4Q LOSS MUTATED`
TCGA-18-3407 TCGA-18-3411 TCGA-18-3412 TCGA-18-3415 TCGA-18-3417 TCGA-18-4083 
         136         1415          345         1810          758          187 
TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 
          85         2754           92         3636         1426         3016 
TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 
        2134         1852         1058          965         3724          284 
TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 TCGA-21-5786 TCGA-21-5787 TCGA-22-0944 
        3644          267          962         1032          329          223 
TCGA-22-1000 TCGA-22-1011 TCGA-22-1012 TCGA-22-4594 TCGA-22-4595 TCGA-22-4599 
        1945           53          429         1470          734         1161 
TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 
         399         1946          587          358          965         1964 
TCGA-22-5473 TCGA-22-5474 TCGA-22-5479 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 
        1933          445         1651          357          573          916 
TCGA-22-5489 TCGA-22-5491 TCGA-33-4532 TCGA-33-4533 TCGA-33-4538 TCGA-33-4566 
        1912         1713         2524         1940         2979         5287 
TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-33-4589 TCGA-34-2600 
        1966         1941          428         1970         1948         1874 
TCGA-34-2605 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-37-4133 TCGA-37-4135 
         881          428          941          552          238          207 
TCGA-37-4141 TCGA-37-5819 TCGA-39-5019 TCGA-39-5021 TCGA-39-5027 TCGA-39-5031 
          12          103         1361         1947         1849          833 
TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-39-5040 TCGA-43-2578 
        1107          474         1084         1086         1964          684 
TCGA-43-3394 TCGA-43-6143 TCGA-43-6771 TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 
         822          376         1936          236         1970          407 
TCGA-43-8118 TCGA-43-A474 TCGA-43-A56U TCGA-43-A56V TCGA-46-6025 TCGA-46-6026 
        1971          353          432          366          324          423 
TCGA-51-4079 TCGA-51-4081 TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 TCGA-56-5898 
          12          911         1948          923         1958          555 
TCGA-56-6545 TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 TCGA-56-7582 TCGA-56-7730 
          62           30           13           30           26            6 
TCGA-56-8625 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BX TCGA-56-A4ZJ TCGA-56-A4ZK 
          63           34           38           46           25            4 
TCGA-56-A5DR TCGA-58-8390 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46L TCGA-58-A46M 
           4          911         1058         2589         1723         1072 
TCGA-60-2695 TCGA-60-2696 TCGA-60-2698 TCGA-60-2703 TCGA-60-2706 TCGA-60-2707 
         642          109          311         1950         1958          661 
TCGA-60-2708 TCGA-60-2709 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2719 
        1963         1505          274         1731         1531         1297 
TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2726 
          97          983          908         1092          717          358 
TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 TCGA-66-2727 TCGA-66-2734 
        1957         1955         1947         1952         1967         1311 
TCGA-66-2737 TCGA-66-2742 TCGA-66-2753 TCGA-66-2754 TCGA-66-2757 TCGA-66-2758 
          61          641           31           61           30          639 
TCGA-66-2763 TCGA-66-2765 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 
          30           61          578         1946           61          578 
TCGA-66-2780 TCGA-66-2781 TCGA-66-2785 TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 
        1956          121           60         1977          913         1952 
TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 
        1645          122         1492           83          202          211 
TCGA-68-A59I TCGA-68-A59J TCGA-77-6843 TCGA-77-6845 TCGA-77-7139 TCGA-77-7141 
         121          104         1941         1952         1968           15 
TCGA-77-7142 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 TCGA-77-8009 TCGA-77-8128 
        1286         1954          479         1960         1641         1953 
TCGA-77-8130 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8144 TCGA-77-8145 
        1945         1941         1947         1946          833         1943 
TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-A5G3 TCGA-77-A5G6 
         293         1961         1684         1092         1959         1955 
TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF TCGA-77-A5GH 
        1963         1290         1280         1939          839          713 
TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7699 TCGA-85-8048 
         364          395           34           18            1           26 
TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 
          60           16          960          513           13           11 
TCGA-85-8287 TCGA-85-8350 TCGA-85-8352 TCGA-85-8353 TCGA-85-8479 TCGA-85-8580 
          13           60           67           54           22          445 
TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A510 
           3          475           15         1960           25         1967 
TCGA-85-A512 TCGA-85-A53L TCGA-90-7769 TCGA-90-7964 TCGA-90-A4ED TCGA-90-A4EE 
        1987           13          358          428          244          331 
TCGA-90-A59Q TCGA-92-7340 TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-7943 
         269           82          122          160           70          356 
TCGA-96-A4JK TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-L3-A524 TCGA-LA-A446 
         273          256          413          224          449           36 
TCGA-MF-A522 TCGA-NC-A5HE TCGA-NC-A5HI 
          83         1722         1135 

$`4Q LOSS WILD-TYPE`
TCGA-18-3406 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3414 TCGA-18-3416 
         370         2464         2417          146          396          862 
TCGA-18-3419 TCGA-18-3421 TCGA-18-5595 TCGA-21-1078 TCGA-21-5784 TCGA-21-A5DI 
          50         1331          827          474         1268          979 
TCGA-22-0940 TCGA-22-1002 TCGA-22-1005 TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 
         608          131         1952          822         1485          623 
TCGA-22-4593 TCGA-22-4596 TCGA-22-4601 TCGA-22-5477 TCGA-22-5478 TCGA-22-5480 
        1067           17         1057         1346           24         1952 
TCGA-22-5481 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4547 TCGA-33-6738 TCGA-34-2596 
        1952          506           29         1311          822           80 
TCGA-34-2604 TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 
         958         1000          951         1528         2062         1715 
TCGA-34-5239 TCGA-34-5240 TCGA-34-8454 TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 
         707          365          166          120           13           12 
TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-39-5011 TCGA-39-5016 TCGA-39-5022 
         200          247          227         1454         2253         1996 
TCGA-39-5024 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5039 TCGA-43-2576 
        1964           52          740           59          544         1223 
TCGA-43-2581 TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 TCGA-43-6647 TCGA-43-6770 
        1176         1007          349          849          757          310 
TCGA-43-7656 TCGA-43-8116 TCGA-43-A475 TCGA-51-4080 TCGA-52-7622 TCGA-52-7812 
         212          358          296           12          541         1967 
TCGA-56-1622 TCGA-56-5897 TCGA-56-6546 TCGA-56-7579 TCGA-56-7580 TCGA-56-7731 
         881            3           26           44           40         1961 
TCGA-56-7822 TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 TCGA-56-8624 TCGA-56-8626 
           1           41          178           55           36           17 
TCGA-56-8628 TCGA-56-A4BW TCGA-56-A4BY TCGA-56-A5DS TCGA-58-8388 TCGA-58-8391 
          16            2           30            8          378         2167 
TCGA-58-A46N TCGA-60-2704 TCGA-60-2710 TCGA-60-2711 TCGA-60-2715 TCGA-60-2716 
         910         1943         1963         1260         1075         1475 
TCGA-60-2725 TCGA-63-6202 TCGA-66-2744 TCGA-66-2755 TCGA-66-2756 TCGA-66-2759 
         816         1973           30           28           30          762 
TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 TCGA-66-2782 
          31           61           61         1947          700         1954 
TCGA-66-2783 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 
         759          790         1217          699         1955          699 
TCGA-68-8250 TCGA-68-8251 TCGA-77-6842 TCGA-77-6844 TCGA-77-7138 TCGA-77-7335 
         244           96         1950         1942         1959         1954 
TCGA-77-7337 TCGA-77-7338 TCGA-77-8008 TCGA-77-8131 TCGA-77-8139 TCGA-77-8140 
        1942         1952         1945         1941         1951         1962 
TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-85-7697 TCGA-85-7698 TCGA-85-7710 
          10         1953         1942           10           49         1965 
TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 TCGA-85-8071 TCGA-85-8288 TCGA-85-8351 
          35          911           60          428           54           55 
TCGA-85-8354 TCGA-85-8355 TCGA-85-8481 TCGA-85-8582 TCGA-85-A4PA TCGA-85-A50M 
          61           61           21          424         1972           19 
TCGA-85-A50Z TCGA-85-A511 TCGA-85-A513 TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7766 
        1973         1972           24          111          758          289 
TCGA-90-7767 TCGA-92-7341 TCGA-94-7033 TCGA-94-A4VJ TCGA-96-7544 TCGA-96-7545 
          89          106           87          430         1213         1344 
TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-8023 TCGA-J1-A4AH TCGA-L3-A4E7 
         189          211          183          308          222           35 
TCGA-NC-A5HG 
        1548 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                1                 1 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             5287              2464 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              661               608 
[1] "1.0 - 5287.0 (661.0)" "1.0 - 2464.0 (608.0)"
[1] "hr=" "1.2"
D48V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  4Q LOSS MUTATED         0       40       90        1        26        40
  4Q LOSS WILD-TYPE       1       32       47        0        26        31
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  4Q LOSS MUTATED           33         11        2
  4Q LOSS WILD-TYPE         24          9        4
D48V3, multiclass
            clus
vv           4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                40                32
  STAGE IB                90                47
  STAGE II                 1                 0
  STAGE IIA               26                26
  STAGE IIB               40                31
  STAGE IIIA              33                24
  STAGE IIIB              11                 9
  STAGE IV                 2                 4
[1] 9 2
[1] 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    51 158  27   9
  4Q LOSS WILD-TYPE  47  96  21  11
D48V4, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  T1              51                47
  T2             158                96
  T3              27                21
  T4               9                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  4Q LOSS MUTATED   153  69  18   2
  4Q LOSS WILD-TYPE 108  44  17   3
D48V5, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  N0             153               108
  N1              69                44
  N2              18                17
  N3               2                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A  MX
  4Q LOSS MUTATED   211   2   0  28
  4Q LOSS WILD-TYPE 147   3   1  22
D48V6, multiclass
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  M0              211               147
  M1                2                 3
  M1A               0                 1
  MX               28                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V7, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    64 181
  4Q LOSS WILD-TYPE  43 132
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     64  181
  4Q LOSS WILD-TYPE   43  132
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE              64                43
  MALE               181               132
[1] 2 2
[1] FALSE
D48V8, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  4Q LOSS MUTATED                                       5
  4Q LOSS WILD-TYPE                                     7
                   vv
clus                LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  4Q LOSS MUTATED                                        2
  4Q LOSS WILD-TYPE                                      4
                   vv
clus                LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  4Q LOSS MUTATED                                         1
  4Q LOSS WILD-TYPE                                       0
                   vv
clus                LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  4Q LOSS MUTATED                                                           237
  4Q LOSS WILD-TYPE                                                         164
D48V9, multiclass
                                                             clus
vv                                                            4Q LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     5
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             237
                                                             clus
vv                                                            4Q LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       7
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               164
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V10, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    11 234
  4Q LOSS WILD-TYPE   2 173
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     11  234
  4Q LOSS WILD-TYPE    2  173
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  NO               11                 2
  YES             234               173
[1] 2 2
[1] FALSE
D48V11, continuous
                   vv
clus                 R0  R1  R2  RX
  4Q LOSS MUTATED   199   4   3  12
  4Q LOSS WILD-TYPE 143   4   1   6
D48V12, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  R0             199               143
  R1               4                 4
  R2               3                 1
  RX              12                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4Q LOSS MUTATED       4                        10   172
  4Q LOSS WILD-TYPE     5                         7   126
D48V13, multiclass
                           clus
vv                          4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  ASIAN                                   4                 5
  BLACK OR AFRICAN AMERICAN              10                 7
  WHITE                                 172               126
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V14, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED     4 151
  4Q LOSS WILD-TYPE   4 116
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      4  151
  4Q LOSS WILD-TYPE    4  116
                        clus
vv                       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   4                 4
  NOT HISPANIC OR LATINO             151               116
[1] 2 2
[1] FALSE

Clustering(49) Variable = 5P LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                 0   1
  5P LOSS MUTATED    44  17
  5P LOSS WILD-TYPE 221 106
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               61               327 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               17               106 
$`5P LOSS MUTATED`
TCGA-18-3409 TCGA-18-3410 TCGA-18-4083 TCGA-21-1070 TCGA-21-1079 TCGA-22-4607 
        2417          146          187         3636          965          587 
TCGA-22-5472 TCGA-22-5479 TCGA-22-5485 TCGA-22-5491 TCGA-33-4532 TCGA-33-4538 
        1964         1651          916         1713         2524         2979 
TCGA-33-4547 TCGA-34-2605 TCGA-34-5231 TCGA-37-4130 TCGA-39-5037 TCGA-43-2578 
        1311          881         1528          247         1086          684 
TCGA-43-8118 TCGA-51-4079 TCGA-52-7810 TCGA-56-5897 TCGA-56-5898 TCGA-56-7221 
        1971           12          923            3          555           30 
TCGA-56-7730 TCGA-56-8622 TCGA-56-A49D TCGA-58-A46L TCGA-60-2706 TCGA-60-2707 
           6           55           38         1723         1958          661 
TCGA-60-2708 TCGA-60-2710 TCGA-60-2713 TCGA-60-2722 TCGA-63-7023 TCGA-66-2734 
        1963         1963         1731          908         1952         1311 
TCGA-66-2755 TCGA-66-2785 TCGA-66-2789 TCGA-66-2791 TCGA-66-2793 TCGA-68-8250 
          28           60         1955         1977         1952          244 
TCGA-68-8251 TCGA-77-7139 TCGA-77-8140 TCGA-77-8148 TCGA-77-8153 TCGA-77-8154 
          96         1968         1962          293         1684         1092 
TCGA-85-6561 TCGA-85-7698 TCGA-85-7950 TCGA-85-8276 TCGA-85-8288 TCGA-85-8352 
         395           49           60           13           54           67 
TCGA-85-8355 TCGA-90-7964 TCGA-92-8063 TCGA-94-7033 TCGA-94-7943 TCGA-NC-A5HG 
          61          428          122           87          356         1548 
TCGA-NC-A5HI 
        1135 

$`5P LOSS WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 
         370          136         2464         1415          345          396 
TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4086 
        1810          862          758           50         1331           85 
TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 
        2754           92          827         1426         3016         2134 
TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 
        1852         1058          474         3724          284         3644 
TCGA-21-1083 TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-21-A5DI 
         267          962         1268         1032          329          979 
TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 
         608          223         1945          131         1952           53 
TCGA-22-1012 TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 
         429          822         1485          623         1067         1470 
TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 
         734           17         1161         1057          399         1946 
TCGA-22-4613 TCGA-22-5471 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 
         358          965         1933          445         1346           24 
TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 TCGA-22-5489 TCGA-22-5492 
        1952         1952          357          573         1912          506 
TCGA-22-A5C4 TCGA-33-4533 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 
          29         1940         5287         1966         1941          428 
TCGA-33-4587 TCGA-33-4589 TCGA-33-6738 TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 
        1970         1948          822           80         1874          958 
TCGA-34-2608 TCGA-34-2609 TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 
        1000          951         2062         1715          707          365 
TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-8454 TCGA-37-3783 TCGA-37-3789 
         428          941          552          166          120           13 
TCGA-37-3792 TCGA-37-4129 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 
          12          200          227          238          207           12 
TCGA-37-5819 TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 
         103         1454         2253         1361         1947         1996 
TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 
        1964         1849           52          740           59          833 
TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 
        1107          474         1084          544         1964         1223 
TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 
        1176          822         1007          349          849          376 
TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 
         757          310         1936          212          236         1970 
TCGA-43-8115 TCGA-43-8116 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V 
         407          358          353          296          432          366 
TCGA-46-6025 TCGA-46-6026 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 
         324          423           12          911          541         1948 
TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-6545 TCGA-56-6546 TCGA-56-7222 
        1958         1967          881           62           26           13 
TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7731 TCGA-56-7822 
          30           44           40           26         1961            1 
TCGA-56-8503 TCGA-56-8504 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 
          41          178           36           63           17           16 
TCGA-56-8629 TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK 
          34            2           46           30           25            4 
TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-8393 
           4            8          378          911         2167         1058 
TCGA-58-A46J TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 TCGA-60-2696 TCGA-60-2698 
        2589         1072          910          642          109          311 
TCGA-60-2703 TCGA-60-2704 TCGA-60-2709 TCGA-60-2711 TCGA-60-2712 TCGA-60-2714 
        1950         1943         1505         1260          274         1531 
TCGA-60-2715 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2723 
        1075         1475         1297           97          983         1092 
TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 
         717          816          358         1973         1957         1955 
TCGA-63-7022 TCGA-66-2727 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 TCGA-66-2753 
        1947         1967           61          641           30           31 
TCGA-66-2754 TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 
          61           30           30          639          762           30 
TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 
          61           31           61           61         1947          700 
TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 
         578         1946           61          578         1956          121 
TCGA-66-2782 TCGA-66-2783 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2790 
        1954          759          790         1217          699          699 
TCGA-66-2792 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 
         913         1645          122         1492           83          202 
TCGA-68-7757 TCGA-68-A59I TCGA-68-A59J TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 
         211          121          104         1950         1941         1942 
TCGA-77-6845 TCGA-77-7138 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 
        1952         1959           15         1286         1954         1942 
TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 
        1952         1954          479         1960         1945         1641 
TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 
        1953         1945         1941         1941         1947         1946 
TCGA-77-8139 TCGA-77-8144 TCGA-77-8145 TCGA-77-8150 TCGA-77-8156 TCGA-77-A5FZ 
        1951          833         1943         1961           10         1953 
TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA 
        1942         1959         1955         1963         1290         1280 
TCGA-77-A5GB TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6560 TCGA-85-6798 TCGA-85-7696 
        1939          839          713          364           34           18 
TCGA-85-7697 TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 TCGA-85-8048 
          10            1         1965           35          911           26 
TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8277 
          60           16          960          428          513           11 
TCGA-85-8287 TCGA-85-8350 TCGA-85-8351 TCGA-85-8353 TCGA-85-8354 TCGA-85-8479 
          13           60           55           54           61           22 
TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL 
          21          445          424            3          475           15 
TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 
        1972         1960           25           19         1973         1967 
TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 
        1972         1987           24           13          111          758 
TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q 
         289           89          358          244          331          269 
TCGA-92-7340 TCGA-92-7341 TCGA-92-8064 TCGA-92-8065 TCGA-94-A4VJ TCGA-96-7544 
          82          106          160           70          430         1213 
TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL TCGA-98-7454 
        1344          189          211          273          183          256 
TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 
         413          224          308          222           35          449 
TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HE 
          36           83         1722 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                3                 1 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             3636              5287 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
              908               608 
[1] "3.0 - 3636.0 (908.0)" "1.0 - 5287.0 (608.0)"
[1] "hr=" "1.5"
D49V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  5P LOSS MUTATED         0       13       21        0         7         7
  5P LOSS WILD-TYPE       1       59      116        1        45        64
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  5P LOSS MUTATED           11          4        0
  5P LOSS WILD-TYPE         46         16        6
D49V3, multiclass
            clus
vv           5P LOSS MUTATED 5P LOSS WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                13                59
  STAGE IB                21               116
  STAGE II                 0                 1
  STAGE IIA                7                45
  STAGE IIB                7                64
  STAGE IIIA              11                46
  STAGE IIIB               4                16
  STAGE IV                 0                 6
[1] 9 2
[1] 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    22  33   7   3
  5P LOSS WILD-TYPE  76 221  41  17
D49V4, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  T1              22                76
  T2              33               221
  T3               7                41
  T4               3                17
[1] 4 2
[1] 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    41  14   6   2
  5P LOSS WILD-TYPE 220  99  29   3
D49V5, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  N0              41               220
  N1              14                99
  N2               6                29
  N3               2                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A  MX
  5P LOSS MUTATED    56   0   0   7
  5P LOSS WILD-TYPE 302   5   1  43
D49V6, multiclass
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  M0               56               302
  M1                0                 5
  M1A               0                 1
  MX                7                43
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V7, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    13  52
  5P LOSS WILD-TYPE  94 261
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     13   52
  5P LOSS WILD-TYPE   94  261
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE              13                94
  MALE                52               261
[1] 2 2
[1] FALSE
D49V8, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  5P LOSS MUTATED                                       3
  5P LOSS WILD-TYPE                                     9
                   vv
clus                LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  5P LOSS MUTATED                                        1
  5P LOSS WILD-TYPE                                      5
                   vv
clus                LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  5P LOSS MUTATED                                         0
  5P LOSS WILD-TYPE                                       1
                   vv
clus                LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  5P LOSS MUTATED                                                            61
  5P LOSS WILD-TYPE                                                         340
D49V9, multiclass
                                                             clus
vv                                                            5P LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     3
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              61
                                                             clus
vv                                                            5P LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       9
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               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"
D49V10, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     4  61
  5P LOSS WILD-TYPE   9 346
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      4   61
  5P LOSS WILD-TYPE    9  346
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  NO                4                 9
  YES              61               346
[1] 2 2
[1] FALSE
D49V11, continuous
                   vv
clus                 R0  R1  R2  RX
  5P LOSS MUTATED    47   2   0   5
  5P LOSS WILD-TYPE 295   6   4  13
D49V12, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  R0              47               295
  R1               2                 6
  R2               0                 4
  RX               5                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5P LOSS MUTATED       1                         3    46
  5P LOSS WILD-TYPE     8                        14   252
D49V13, multiclass
                           clus
vv                          5P LOSS MUTATED 5P LOSS WILD-TYPE
  ASIAN                                   1                 8
  BLACK OR AFRICAN AMERICAN               3                14
  WHITE                                  46               252
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V14, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     3  39
  5P LOSS WILD-TYPE   5 228
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      3   39
  5P LOSS WILD-TYPE    5  228
                        clus
vv                       5P LOSS MUTATED 5P LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 5
  NOT HISPANIC OR LATINO              39               228
[1] 2 2
[1] FALSE

Clustering(50) Variable = 5Q LOSS MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                 0   1
  5Q LOSS MUTATED   162  62
  5Q LOSS WILD-TYPE 103  61
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              224               164 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               62                61 
$`5Q LOSS MUTATED`
TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 
        2464         2417          146         1415          345          396 
TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 
        1810          862          758          187           85         2754 
TCGA-21-1070 TCGA-21-1072 TCGA-21-1075 TCGA-21-1079 TCGA-21-1082 TCGA-21-5784 
        3636         3016         2134          965         3644         1268 
TCGA-21-5786 TCGA-21-5787 TCGA-22-0940 TCGA-22-0944 TCGA-22-1002 TCGA-22-1011 
        1032          329          608          223          131           53 
TCGA-22-4591 TCGA-22-4593 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 
         623         1067         1161         1057          399         1946 
TCGA-22-4607 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 
         587          358          965         1964         1933          445 
TCGA-22-5477 TCGA-22-5479 TCGA-22-5485 TCGA-22-5491 TCGA-33-4532 TCGA-33-4533 
        1346         1651          916         1713         2524         1940 
TCGA-33-4538 TCGA-33-4547 TCGA-33-4586 TCGA-33-4587 TCGA-33-6738 TCGA-34-2600 
        2979         1311          428         1970          822         1874 
TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 TCGA-34-5239 
         958          881         1000          951         1528          707 
TCGA-34-5927 TCGA-34-8454 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 
         941          166          247          227          238          207 
TCGA-39-5011 TCGA-39-5016 TCGA-39-5024 TCGA-39-5027 TCGA-39-5029 TCGA-39-5030 
        1454         2253         1964         1849          740           59 
TCGA-39-5031 TCGA-39-5036 TCGA-39-5037 TCGA-43-2576 TCGA-43-2578 TCGA-43-2581 
         833         1084         1086         1223          684         1176 
TCGA-43-3394 TCGA-43-5668 TCGA-43-5670 TCGA-43-6647 TCGA-43-6770 TCGA-43-7656 
         822          349          849          757          310          212 
TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56U TCGA-46-6025 TCGA-46-6026 
         358         1971          353          432          324          423 
TCGA-51-4079 TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 
          12          911          541         1948          923         1958 
TCGA-56-5897 TCGA-56-5898 TCGA-56-6546 TCGA-56-7221 TCGA-56-7579 TCGA-56-7582 
           3          555           26           30           44           26 
TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-8622 TCGA-56-8625 TCGA-56-8628 
           6         1961            1           55           63           16 
TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK 
          34           38           46           30           25            4 
TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-A46J 
           4            8          378          911         2167         2589 
TCGA-58-A46L TCGA-60-2695 TCGA-60-2696 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 
        1723          642          109         1958          661         1963 
TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 TCGA-60-2713 TCGA-60-2714 TCGA-60-2720 
        1505         1963         1260         1731         1531           97 
TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 TCGA-63-6202 TCGA-63-7020 TCGA-63-7022 
         983          908         1092         1973         1957         1947 
TCGA-63-7023 TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2753 
        1952         1967         1311           61          641           31 
TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2759 TCGA-66-2763 TCGA-66-2766 
          28           30           30          762           30           31 
TCGA-66-2769 TCGA-66-2773 TCGA-66-2777 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 
        1947         1946           61         1956          121         1954 
TCGA-66-2785 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2791 TCGA-66-2793 
          60         1217          699         1955         1977         1952 
TCGA-66-2794 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 
        1645         1492           83          202          211          244 
TCGA-68-8251 TCGA-77-7139 TCGA-77-7141 TCGA-77-7338 TCGA-77-8007 TCGA-77-8128 
          96         1968           15         1952         1960         1953 
TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8145 TCGA-77-8148 
        1947         1946         1951         1962         1943          293 
TCGA-77-8153 TCGA-77-8154 TCGA-77-A5G3 TCGA-77-A5G8 TCGA-77-A5GH TCGA-85-6560 
        1684         1092         1959         1290          713          364 
TCGA-85-6561 TCGA-85-6798 TCGA-85-7697 TCGA-85-7698 TCGA-85-7710 TCGA-85-7843 
         395           34           10           49         1965           35 
TCGA-85-7950 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 
          60           16          960          428          513           13 
TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 
          11           13           54           55           67           54 
TCGA-85-8354 TCGA-85-8355 TCGA-85-8481 TCGA-85-8580 TCGA-85-8666 TCGA-85-A4QR 
          61           61           21          445          475           25 
TCGA-85-A511 TCGA-85-A512 TCGA-85-A5B5 TCGA-90-7766 TCGA-90-7767 TCGA-90-7964 
        1972         1987          111          289           89          428 
TCGA-90-A4EE TCGA-92-8063 TCGA-92-8064 TCGA-94-7033 TCGA-94-7943 TCGA-96-7544 
         331          122          160           87          356         1213 
TCGA-96-7545 TCGA-96-A4JK TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-L3-A524 
        1344          273          413          224          308          449 
TCGA-NC-A5HG TCGA-NC-A5HI 
        1548         1135 

$`5Q LOSS WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3419 TCGA-18-3421 TCGA-18-5592 TCGA-18-5595 
         370          136           50         1331           92          827 
TCGA-21-1071 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1080 TCGA-21-1081 
        1426         1852         1058          474         3724          284 
TCGA-21-1083 TCGA-21-5782 TCGA-21-A5DI TCGA-22-1000 TCGA-22-1005 TCGA-22-1012 
         267          962          979         1945         1952          429 
TCGA-22-1016 TCGA-22-1017 TCGA-22-4594 TCGA-22-4595 TCGA-22-4596 TCGA-22-5478 
         822         1485         1470          734           17           24 
TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 TCGA-22-5489 TCGA-22-5492 
        1952         1952          357          573         1912          506 
TCGA-22-A5C4 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-33-4589 TCGA-34-2596 
          29         5287         1966         1941         1948           80 
TCGA-34-5232 TCGA-34-5234 TCGA-34-5240 TCGA-34-5241 TCGA-34-5928 TCGA-37-3783 
        2062         1715          365          428          552          120 
TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-37-4141 TCGA-37-5819 TCGA-39-5019 
          13           12          200           12          103         1361 
TCGA-39-5021 TCGA-39-5022 TCGA-39-5028 TCGA-39-5034 TCGA-39-5035 TCGA-39-5039 
        1947         1996           52         1107          474          544 
TCGA-39-5040 TCGA-43-3920 TCGA-43-6143 TCGA-43-6771 TCGA-43-7657 TCGA-43-7658 
        1964         1007          376         1936          236         1970 
TCGA-43-8115 TCGA-43-A475 TCGA-43-A56V TCGA-51-4080 TCGA-52-7812 TCGA-56-1622 
         407          296          366           12         1967          881 
TCGA-56-6545 TCGA-56-7222 TCGA-56-7223 TCGA-56-7580 TCGA-56-8503 TCGA-56-8504 
          62           13           30           40           41          178 
TCGA-56-8624 TCGA-56-8626 TCGA-56-A4BW TCGA-58-8393 TCGA-58-A46M TCGA-58-A46N 
          36           17            2         1058         1072          910 
TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2712 TCGA-60-2715 TCGA-60-2716 
         311         1950         1943          274         1075         1475 
TCGA-60-2719 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-7021 TCGA-66-2744 
        1297          717          816          358         1955           30 
TCGA-66-2754 TCGA-66-2758 TCGA-66-2765 TCGA-66-2767 TCGA-66-2768 TCGA-66-2770 
          61          639           61           61           61          700 
TCGA-66-2771 TCGA-66-2778 TCGA-66-2783 TCGA-66-2786 TCGA-66-2790 TCGA-66-2792 
         578          578          759          790          699          913 
TCGA-66-2795 TCGA-68-A59I TCGA-68-A59J TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 
         122          121          104         1950         1941         1942 
TCGA-77-6845 TCGA-77-7138 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7463 
        1952         1959         1286         1954         1942         1954 
TCGA-77-7465 TCGA-77-8008 TCGA-77-8009 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 
         479         1945         1641         1945         1941         1941 
TCGA-77-8144 TCGA-77-8150 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G6 
         833         1961           10         1953         1942         1955 
TCGA-77-A5G7 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF TCGA-85-7696 TCGA-85-7699 
        1963         1280         1939          839           18            1 
TCGA-85-7844 TCGA-85-8048 TCGA-85-8049 TCGA-85-8350 TCGA-85-8479 TCGA-85-8582 
         911           26           60           60           22          424 
TCGA-85-8664 TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50M TCGA-85-A50Z 
           3           15         1972         1960           19         1973 
TCGA-85-A510 TCGA-85-A513 TCGA-85-A53L TCGA-90-6837 TCGA-90-7769 TCGA-90-A4ED 
        1967           24           13          758          358          244 
TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-92-8065 TCGA-94-A4VJ TCGA-96-8169 
         269           82          106           70          430          189 
TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-LA-A446 
         211          183          256          222           35           36 
TCGA-MF-A522 TCGA-NC-A5HE 
          83         1722 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                1                 1 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             3644              5287 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            691.5             575.5 
[1] "1.0 - 3644.0 (691.5)" "1.0 - 5287.0 (575.5)"
[1] "hr=" "1.5"
D50V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  5Q LOSS MUTATED         0       44       80        1        30        32
  5Q LOSS WILD-TYPE       1       28       57        0        22        39
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  5Q LOSS MUTATED           37         13        5
  5Q LOSS WILD-TYPE         20          7        1
D50V3, multiclass
            clus
vv           5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                44                28
  STAGE IB                80                57
  STAGE II                 1                 0
  STAGE IIA               30                22
  STAGE IIB               32                39
  STAGE IIIA              37                20
  STAGE IIIB              13                 7
  STAGE IV                 5                 1
[1] 9 2
[1] 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    60 144  26  14
  5Q LOSS WILD-TYPE  38 110  22   6
D50V4, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  T1              60                38
  T2             144               110
  T3              26                22
  T4              14                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  5Q LOSS MUTATED   159  59  22   2
  5Q LOSS WILD-TYPE 102  54  13   3
D50V5, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  N0             159               102
  N1              59                54
  N2              22                13
  N3               2                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A  MX
  5Q LOSS MUTATED   205   4   1  32
  5Q LOSS WILD-TYPE 153   1   0  18
D50V6, multiclass
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  M0              205               153
  M1                4                 1
  M1A               1                 0
  MX               32                18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V7, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    63 181
  5Q LOSS WILD-TYPE  44 132
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     63  181
  5Q LOSS WILD-TYPE   44  132
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE              63                44
  MALE               181               132
[1] 2 2
[1] FALSE
D50V8, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  5Q LOSS MUTATED                                       8
  5Q LOSS WILD-TYPE                                     4
                   vv
clus                LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  5Q LOSS MUTATED                                        2
  5Q LOSS WILD-TYPE                                      4
                   vv
clus                LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  5Q LOSS MUTATED                                         1
  5Q LOSS WILD-TYPE                                       0
                   vv
clus                LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  5Q LOSS MUTATED                                                           233
  5Q LOSS WILD-TYPE                                                         168
D50V9, multiclass
                                                             clus
vv                                                            5Q LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     8
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             233
                                                             clus
vv                                                            5Q LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       4
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               168
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V10, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    10 234
  5Q LOSS WILD-TYPE   3 173
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     10  234
  5Q LOSS WILD-TYPE    3  173
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  NO               10                 3
  YES             234               173
[1] 2 2
[1] FALSE
D50V11, continuous
                   vv
clus                 R0  R1  R2  RX
  5Q LOSS MUTATED   193   6   2  11
  5Q LOSS WILD-TYPE 149   2   2   7
D50V12, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  R0             193               149
  R1               6                 2
  R2               2                 2
  RX              11                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5Q LOSS MUTATED       3                        12   174
  5Q LOSS WILD-TYPE     6                         5   124
D50V13, multiclass
                           clus
vv                          5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  ASIAN                                   3                 6
  BLACK OR AFRICAN AMERICAN              12                 5
  WHITE                                 174               124
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V14, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED     6 157
  5Q LOSS WILD-TYPE   2 110
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      6  157
  5Q LOSS WILD-TYPE    2  110
                        clus
vv                       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   6                 2
  NOT HISPANIC OR LATINO             157               110
[1] 2 2
[1] FALSE

Clustering(51) Variable = 6P LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                 0   1
  6P LOSS MUTATED    56  29
  6P LOSS WILD-TYPE 209  94
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               85               303 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               29                94 
$`6P LOSS MUTATED`
TCGA-18-3408 TCGA-18-3412 TCGA-18-3415 TCGA-18-3416 TCGA-18-4083 TCGA-18-4721 
        2464          345         1810          862          187         2754 
TCGA-18-5592 TCGA-21-1076 TCGA-22-0940 TCGA-22-1012 TCGA-22-4595 TCGA-22-4596 
          92         1852          608          429          734           17 
TCGA-22-4599 TCGA-22-5473 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5483 
        1161         1933         1346           24         1651          573 
TCGA-22-5492 TCGA-33-4547 TCGA-33-4583 TCGA-34-2596 TCGA-34-2604 TCGA-37-5819 
         506         1311         1941           80          958          103 
TCGA-39-5016 TCGA-39-5021 TCGA-39-5027 TCGA-39-5034 TCGA-39-5037 TCGA-39-5039 
        2253         1947         1849         1107         1086          544 
TCGA-43-6143 TCGA-43-8115 TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56V 
         376          407         1971          353          296          366 
TCGA-46-6025 TCGA-51-4081 TCGA-52-7622 TCGA-56-7579 TCGA-56-7582 TCGA-56-8624 
         324          911          541           44           26           36 
TCGA-56-A4ZK TCGA-60-2698 TCGA-60-2707 TCGA-60-2722 TCGA-60-2726 TCGA-63-7020 
           4          311          661          908          358         1957 
TCGA-63-7021 TCGA-66-2758 TCGA-66-2780 TCGA-66-2782 TCGA-66-2786 TCGA-66-2789 
        1955          639         1956         1954          790         1955 
TCGA-66-2792 TCGA-66-2794 TCGA-68-7755 TCGA-68-7756 TCGA-68-A59I TCGA-77-8007 
         913         1645           83          202          121         1960 
TCGA-77-8009 TCGA-77-8128 TCGA-77-8131 TCGA-77-8140 TCGA-77-8150 TCGA-77-A5G3 
        1641         1953         1941         1962         1961         1959 
TCGA-77-A5G8 TCGA-85-7696 TCGA-85-7698 TCGA-85-7950 TCGA-85-8049 TCGA-85-8070 
        1290           18           49           60           60          960 
TCGA-85-8277 TCGA-85-8666 TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A510 TCGA-85-A512 
          11          475         1960           25         1967         1987 
TCGA-85-A5B5 TCGA-90-7767 TCGA-92-7341 TCGA-92-8064 TCGA-92-8065 TCGA-96-7544 
         111           89          106          160           70         1213 
TCGA-96-A4JK 
         273 

$`6P LOSS WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 TCGA-18-3414 
         370          136         2417          146         1415          396 
TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4086 TCGA-18-5595 TCGA-21-1070 
         758           50         1331           85          827         3636 
TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 
        1426         3016         2134         1058          474          965 
TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 TCGA-21-5784 
        3724          284         3644          267          962         1268 
TCGA-21-5786 TCGA-21-5787 TCGA-21-A5DI TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 
        1032          329          979          223         1945          131 
TCGA-22-1005 TCGA-22-1011 TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 TCGA-22-4593 
        1952           53          822         1485          623         1067 
TCGA-22-4594 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-4613 
        1470         1057          399         1946          587          358 
TCGA-22-5471 TCGA-22-5472 TCGA-22-5474 TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 
         965         1964          445         1952         1952          357 
TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4533 
         916         1912         1713           29         2524         1940 
TCGA-33-4538 TCGA-33-4566 TCGA-33-4582 TCGA-33-4586 TCGA-33-4587 TCGA-33-4589 
        2979         5287         1966          428         1970         1948 
TCGA-33-6738 TCGA-34-2600 TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 
         822         1874          881         1000          951         1528 
TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 
        2062         1715          707          365          428          941 
TCGA-34-5928 TCGA-34-8454 TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 
         552          166          120           13           12          200 
TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-39-5011 
         247          227          238          207           12         1454 
TCGA-39-5019 TCGA-39-5022 TCGA-39-5024 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 
        1361         1996         1964           52          740           59 
TCGA-39-5031 TCGA-39-5035 TCGA-39-5036 TCGA-39-5040 TCGA-43-2576 TCGA-43-2578 
         833          474         1084         1964         1223          684 
TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 TCGA-43-6647 
        1176          822         1007          349          849          757 
TCGA-43-6770 TCGA-43-6771 TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 TCGA-43-8116 
         310         1936          212          236         1970          358 
TCGA-43-A56U TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-52-7809 TCGA-52-7810 
         432          423           12           12         1948          923 
TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 
        1958         1967          881            3          555           62 
TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 TCGA-56-7580 TCGA-56-7730 
          26           30           13           30           40            6 
TCGA-56-7731 TCGA-56-7822 TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 TCGA-56-8625 
        1961            1           41          178           55           63 
TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX 
          17           16           34           38            2           46 
TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8388 TCGA-58-8390 
          30           25            4            8          378          911 
TCGA-58-8391 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N 
        2167         1058         2589         1723         1072          910 
TCGA-60-2695 TCGA-60-2696 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2708 
         642          109         1950         1943         1958         1963 
TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 
        1505         1963         1260          274         1731         1531 
TCGA-60-2715 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2723 
        1075         1475         1297           97          983         1092 
TCGA-60-2724 TCGA-60-2725 TCGA-63-6202 TCGA-63-7022 TCGA-63-7023 TCGA-66-2727 
         717          816         1973         1947         1952         1967 
TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 
        1311           61          641           30           31           61 
TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 
          28           30           30          762           30           61 
TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 
          31           61           61         1947          700          578 
TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2781 TCGA-66-2783 TCGA-66-2785 
        1946           61          578          121          759           60 
TCGA-66-2787 TCGA-66-2788 TCGA-66-2790 TCGA-66-2791 TCGA-66-2793 TCGA-66-2795 
        1217          699          699         1977         1952          122 
TCGA-66-2800 TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59J TCGA-77-6842 
        1492          211          244           96          104         1950 
TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 
        1941         1942         1952         1959         1968           15 
TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 
        1286         1954         1942         1952         1954          479 
TCGA-77-8008 TCGA-77-8130 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 
        1945         1945         1941         1947         1946         1951 
TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 
         833         1943          293         1684         1092           10 
TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5GA TCGA-77-A5GB 
        1953         1942         1955         1963         1280         1939 
TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 TCGA-85-7697 
         839          713          364          395           34           10 
TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 TCGA-85-8048 TCGA-85-8052 
           1         1965           35          911           26           16 
TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 
         428          513           13           13           54           60 
TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 
          55           67           54           61           61           22 
TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8664 TCGA-85-A4CL TCGA-85-A4PA 
          21          445          424            3           15         1972 
TCGA-85-A50M TCGA-85-A50Z TCGA-85-A511 TCGA-85-A513 TCGA-85-A53L TCGA-90-6837 
          19         1973         1972           24           13          758 
TCGA-90-7766 TCGA-90-7769 TCGA-90-7964 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q 
         289          358          428          244          331          269 
TCGA-92-7340 TCGA-92-8063 TCGA-94-7033 TCGA-94-7943 TCGA-94-A4VJ TCGA-96-7545 
          82          122           87          356          430         1344 
TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 
         189          211          183          256          413          224 
TCGA-98-8023 TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-MF-A522 
         308          222           35          449           36           83 
TCGA-NC-A5HE TCGA-NC-A5HG TCGA-NC-A5HI 
        1722         1548         1135 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                4                 1 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             2754              5287 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
              661               641 
[1] "4.0 - 2754.0 (661.0)" "1.0 - 5287.0 (641.0)"
[1] "hr=" "1"  
D51V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  6P LOSS MUTATED         0       11       32        0        13        23
  6P LOSS WILD-TYPE       1       61      105        1        39        48
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  6P LOSS MUTATED           12          2        2
  6P LOSS WILD-TYPE         45         18        4
D51V3, multiclass
            clus
vv           6P LOSS MUTATED 6P LOSS WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                11                61
  STAGE IB                32               105
  STAGE II                 0                 1
  STAGE IIA               13                39
  STAGE IIB               23                48
  STAGE IIIA              12                45
  STAGE IIIB               2                18
  STAGE IV                 2                 4
[1] 9 2
[1] 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    20  55  17   3
  6P LOSS WILD-TYPE  78 199  31  17
D51V4, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  T1              20                78
  T2              55               199
  T3              17                31
  T4               3                17
[1] 4 2
[1] 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    54  32   6   1
  6P LOSS WILD-TYPE 207  81  29   4
D51V5, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  N0              54               207
  N1              32                81
  N2               6                29
  N3               1                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A  MX
  6P LOSS MUTATED    84   1   1   8
  6P LOSS WILD-TYPE 274   4   0  42
D51V6, multiclass
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  M0               84               274
  M1                1                 4
  M1A               1                 0
  MX                8                42
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V7, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    21  74
  6P LOSS WILD-TYPE  86 239
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     21   74
  6P LOSS WILD-TYPE   86  239
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE              21                86
  MALE                74               239
[1] 2 2
[1] FALSE
D51V8, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  6P LOSS MUTATED                                       2
  6P LOSS WILD-TYPE                                    10
                   vv
clus                LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  6P LOSS MUTATED                                        1
  6P LOSS WILD-TYPE                                      5
                   vv
clus                LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  6P LOSS MUTATED                                         0
  6P LOSS WILD-TYPE                                       1
                   vv
clus                LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  6P LOSS MUTATED                                                            92
  6P LOSS WILD-TYPE                                                         309
D51V9, multiclass
                                                             clus
vv                                                            6P LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     2
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              92
                                                             clus
vv                                                            6P LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      10
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               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"
D51V10, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     2  93
  6P LOSS WILD-TYPE  11 314
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      2   93
  6P LOSS WILD-TYPE   11  314
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  NO                2                11
  YES              93               314
[1] 2 2
[1] FALSE
D51V11, continuous
                   vv
clus                 R0  R1  R2  RX
  6P LOSS MUTATED    80   2   0   7
  6P LOSS WILD-TYPE 262   6   4  11
D51V12, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  R0              80               262
  R1               2                 6
  R2               0                 4
  RX               7                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6P LOSS MUTATED       1                         2    67
  6P LOSS WILD-TYPE     8                        15   231
D51V13, multiclass
                           clus
vv                          6P LOSS MUTATED 6P LOSS WILD-TYPE
  ASIAN                                   1                 8
  BLACK OR AFRICAN AMERICAN               2                15
  WHITE                                  67               231
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V14, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     2  59
  6P LOSS WILD-TYPE   6 208
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      2   59
  6P LOSS WILD-TYPE    6  208
                        clus
vv                       6P LOSS MUTATED 6P LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 6
  NOT HISPANIC OR LATINO              59               208
[1] 2 2
[1] FALSE

Clustering(52) Variable = 6Q LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                 0   1
  6Q LOSS MUTATED    62  28
  6Q LOSS WILD-TYPE 203  95
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               90               298 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               28                95 
$`6Q LOSS MUTATED`
TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 TCGA-18-3415 TCGA-18-3416 TCGA-18-4083 
        2464         1415          345         1810          862          187 
TCGA-18-5592 TCGA-21-1076 TCGA-21-5787 TCGA-22-0940 TCGA-22-4595 TCGA-22-4596 
          92         1852          329          608          734           17 
TCGA-22-4599 TCGA-22-4601 TCGA-22-4607 TCGA-22-5478 TCGA-22-5479 TCGA-22-5492 
        1161         1057          587           24         1651          506 
TCGA-33-4582 TCGA-33-4583 TCGA-34-2596 TCGA-34-2604 TCGA-34-5928 TCGA-37-5819 
        1966         1941           80          958          552          103 
TCGA-39-5016 TCGA-39-5021 TCGA-39-5027 TCGA-39-5034 TCGA-39-5037 TCGA-39-5039 
        2253         1947         1849         1107         1086          544 
TCGA-43-2581 TCGA-43-6143 TCGA-43-8115 TCGA-43-8118 TCGA-46-6025 TCGA-51-4081 
        1176          376          407         1971          324          911 
TCGA-52-7622 TCGA-52-7812 TCGA-56-7582 TCGA-56-7730 TCGA-56-8624 TCGA-56-8625 
         541         1967           26            6           36           63 
TCGA-56-A4BY TCGA-56-A4ZK TCGA-58-A46M TCGA-60-2707 TCGA-60-2722 TCGA-60-2726 
          30            4         1072          661          908          358 
TCGA-63-7020 TCGA-66-2758 TCGA-66-2763 TCGA-66-2773 TCGA-66-2780 TCGA-66-2782 
        1957          639           30         1946         1956         1954 
TCGA-66-2783 TCGA-66-2792 TCGA-66-2795 TCGA-68-7755 TCGA-68-7756 TCGA-68-A59I 
         759          913          122           83          202          121 
TCGA-77-7141 TCGA-77-8007 TCGA-77-8009 TCGA-77-8131 TCGA-77-8140 TCGA-77-8150 
          15         1960         1641         1941         1962         1961 
TCGA-77-A5G8 TCGA-85-6560 TCGA-85-7696 TCGA-85-7698 TCGA-85-7710 TCGA-85-8052 
        1290          364           18           49         1965           16 
TCGA-85-8070 TCGA-85-8072 TCGA-85-8277 TCGA-85-8354 TCGA-85-8479 TCGA-85-A4QQ 
         960          513           11           61           22         1960 
TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 TCGA-85-A5B5 TCGA-90-7767 
          25           19         1973         1967          111           89 
TCGA-92-7341 TCGA-92-8065 TCGA-96-7544 TCGA-96-A4JK TCGA-J1-A4AH TCGA-NC-A5HG 
         106           70         1213          273          222         1548 

$`6Q LOSS WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3414 TCGA-18-3417 
         370          136         2417          146          396          758 
TCGA-18-3419 TCGA-18-3421 TCGA-18-4086 TCGA-18-4721 TCGA-18-5595 TCGA-21-1070 
          50         1331           85         2754          827         3636 
TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 
        1426         3016         2134         1058          474          965 
TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 TCGA-21-5784 
        3724          284         3644          267          962         1268 
TCGA-21-5786 TCGA-21-A5DI TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 
        1032          979          223         1945          131         1952 
TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 TCGA-22-4593 
          53          429          822         1485          623         1067 
TCGA-22-4594 TCGA-22-4604 TCGA-22-4605 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 
        1470          399         1946          358          965         1964 
TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 
        1933          445         1346         1952         1952          357 
TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-A5C4 TCGA-33-4532 
         573          916         1912         1713           29         2524 
TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4586 TCGA-33-4587 
        1940         2979         1311         5287          428         1970 
TCGA-33-4589 TCGA-33-6738 TCGA-34-2600 TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 
        1948          822         1874          881         1000          951 
TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 
        1528         2062         1715          707          365          428 
TCGA-34-5927 TCGA-34-8454 TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 
         941          166          120           13           12          200 
TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-39-5011 
         247          227          238          207           12         1454 
TCGA-39-5019 TCGA-39-5022 TCGA-39-5024 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 
        1361         1996         1964           52          740           59 
TCGA-39-5031 TCGA-39-5035 TCGA-39-5036 TCGA-39-5040 TCGA-43-2576 TCGA-43-2578 
         833          474         1084         1964         1223          684 
TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 TCGA-43-6647 TCGA-43-6770 
         822         1007          349          849          757          310 
TCGA-43-6771 TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 TCGA-43-8116 TCGA-43-A474 
        1936          212          236         1970          358          353 
TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 
         296          432          366          423           12           12 
TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 
        1948          923         1958          881            3          555 
TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 
          62           26           30           13           30           44 
TCGA-56-7580 TCGA-56-7731 TCGA-56-7822 TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 
          40         1961            1           41          178           55 
TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX 
          17           16           34           38            2           46 
TCGA-56-A4ZJ TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 
          25            4            8          378          911         2167 
TCGA-58-8393 TCGA-58-A46J TCGA-58-A46L TCGA-58-A46N TCGA-60-2695 TCGA-60-2696 
        1058         2589         1723          910          642          109 
TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2708 TCGA-60-2709 
         311         1950         1943         1958         1963         1505 
TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2715 
        1963         1260          274         1731         1531         1075 
TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2723 TCGA-60-2724 
        1475         1297           97          983         1092          717 
TCGA-60-2725 TCGA-63-6202 TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 TCGA-66-2727 
         816         1973         1955         1947         1952         1967 
TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 
        1311           61          641           30           31           61 
TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2759 TCGA-66-2765 TCGA-66-2766 
          28           30           30          762           61           31 
TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 TCGA-66-2777 
          61           61         1947          700          578           61 
TCGA-66-2778 TCGA-66-2781 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 
         578          121           60          790         1217          699 
TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 TCGA-66-2793 TCGA-66-2794 TCGA-66-2800 
        1955          699         1977         1952         1645         1492 
TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59J TCGA-77-6842 TCGA-77-6843 
         211          244           96          104         1950         1941 
TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7142 TCGA-77-7335 
        1942         1952         1959         1968         1286         1954 
TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8008 TCGA-77-8128 
        1942         1952         1954          479         1945         1953 
TCGA-77-8130 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8144 
        1945         1941         1947         1946         1951          833 
TCGA-77-8145 TCGA-77-8148 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ 
        1943          293         1684         1092           10         1953 
TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5GA TCGA-77-A5GB 
        1942         1959         1955         1963         1280         1939 
TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6561 TCGA-85-6798 TCGA-85-7697 TCGA-85-7699 
         839          713          395           34           10            1 
TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 TCGA-85-8071 
          35          911           60           26           60          428 
TCGA-85-8276 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 
          13           13           54           60           55           67 
TCGA-85-8353 TCGA-85-8355 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8664 
          54           61           21          445          424            3 
TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 
         475           15         1972         1972         1987           24 
TCGA-85-A53L TCGA-90-6837 TCGA-90-7766 TCGA-90-7769 TCGA-90-7964 TCGA-90-A4ED 
          13          758          289          358          428          244 
TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-8063 TCGA-92-8064 TCGA-94-7033 
         331          269           82          122          160           87 
TCGA-94-7943 TCGA-94-A4VJ TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL 
         356          430         1344          189          211          183 
TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-L3-A4E7 TCGA-L3-A524 
         256          413          224          308           35          449 
TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HE TCGA-NC-A5HI 
          36           83         1722         1135 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                4                 1 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             2464              5287 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            597.5             691.5 
[1] "4.0 - 2464.0 (597.5)" "1.0 - 5287.0 (691.5)"
[1] "hr=" "1"  
D52V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  6Q LOSS MUTATED         0       10       32        0        16        21
  6Q LOSS WILD-TYPE       1       62      105        1        36        50
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  6Q LOSS MUTATED           14          2        2
  6Q LOSS WILD-TYPE         43         18        4
D52V3, multiclass
            clus
vv           6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                10                62
  STAGE IB                32               105
  STAGE II                 0                 1
  STAGE IIA               16                36
  STAGE IIB               21                50
  STAGE IIIA              14                43
  STAGE IIIB               2                18
  STAGE IV                 2                 4
[1] 9 2
[1] 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    17  61  15   4
  6Q LOSS WILD-TYPE  81 193  33  16
D52V4, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T1              17                81
  T2              61               193
  T3              15                33
  T4               4                16
[1] 4 2
[1] 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    57  30   7   1
  6Q LOSS WILD-TYPE 204  83  28   4
D52V5, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  N0              57               204
  N1              30                83
  N2               7                28
  N3               1                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A  MX
  6Q LOSS MUTATED    84   1   1  10
  6Q LOSS WILD-TYPE 274   4   0  40
D52V6, multiclass
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  M0               84               274
  M1                1                 4
  M1A               1                 0
  MX               10                40
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V7, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    24  73
  6Q LOSS WILD-TYPE  83 240
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     24   73
  6Q LOSS WILD-TYPE   83  240
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE              24                83
  MALE                73               240
[1] 2 2
[1] FALSE
D52V8, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  6Q LOSS MUTATED                                       3
  6Q LOSS WILD-TYPE                                     9
                   vv
clus                LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  6Q LOSS MUTATED                                        2
  6Q LOSS WILD-TYPE                                      4
                   vv
clus                LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  6Q LOSS MUTATED                                         0
  6Q LOSS WILD-TYPE                                       1
                   vv
clus                LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  6Q LOSS MUTATED                                                            92
  6Q LOSS WILD-TYPE                                                         309
D52V9, multiclass
                                                             clus
vv                                                            6Q LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     3
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              92
                                                             clus
vv                                                            6Q LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       9
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               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"
D52V10, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED     3  94
  6Q LOSS WILD-TYPE  10 313
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      3   94
  6Q LOSS WILD-TYPE   10  313
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  NO                3                10
  YES              94               313
[1] 2 2
[1] FALSE
D52V11, continuous
                   vv
clus                 R0  R1  R2  RX
  6Q LOSS MUTATED    81   1   1   6
  6Q LOSS WILD-TYPE 261   7   3  12
D52V12, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  R0              81               261
  R1               1                 7
  R2               1                 3
  RX               6                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6Q LOSS MUTATED       2                         2    69
  6Q LOSS WILD-TYPE     7                        15   229
D52V13, multiclass
                           clus
vv                          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  ASIAN                                   2                 7
  BLACK OR AFRICAN AMERICAN               2                15
  WHITE                                  69               229
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V14, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED     3  61
  6Q LOSS WILD-TYPE   5 206
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      3   61
  6Q LOSS WILD-TYPE    5  206
                        clus
vv                       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 5
  NOT HISPANIC OR LATINO              61               206
[1] 2 2
[1] FALSE

Clustering(53) Variable = 7P LOSS MUTATION ANALYSIS
D53V1, survival
                   sevent
clus2                 0   1
  7P LOSS MUTATED    30  16
  7P LOSS WILD-TYPE 235 107
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               46               342 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               16               107 
$`7P LOSS MUTATED`
TCGA-18-3419 TCGA-21-1077 TCGA-21-1083 TCGA-21-5786 TCGA-21-5787 TCGA-21-A5DI 
          50         1058          267         1032          329          979 
TCGA-22-1016 TCGA-22-1017 TCGA-22-4601 TCGA-22-5492 TCGA-33-6738 TCGA-37-3789 
         822         1485         1057          506          822           13 
TCGA-37-4133 TCGA-37-5819 TCGA-39-5029 TCGA-39-5036 TCGA-43-2578 TCGA-43-6770 
         238          103          740         1084          684          310 
TCGA-46-6026 TCGA-56-1622 TCGA-56-5898 TCGA-56-6546 TCGA-56-7580 TCGA-56-8629 
         423          881          555           26           40           34 
TCGA-58-8390 TCGA-60-2695 TCGA-60-2703 TCGA-66-2757 TCGA-66-2773 TCGA-66-2783 
         911          642         1950           30         1946          759 
TCGA-66-2788 TCGA-66-2792 TCGA-66-2793 TCGA-77-7142 TCGA-77-7337 TCGA-77-8144 
         699          913         1952         1286         1942          833 
TCGA-77-A5GH TCGA-85-6560 TCGA-85-7699 TCGA-85-8070 TCGA-85-8277 TCGA-85-8353 
         713          364            1          960           11           54 
TCGA-85-A510 TCGA-85-A512 TCGA-90-7767 TCGA-J1-A4AH 
        1967         1987           89          222 

$`7P LOSS WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 
         370          136         2464         2417          146         1415 
TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-18-3421 
         345          396         1810          862          758         1331 
TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1070 
         187           85         2754           92          827         3636 
TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1078 TCGA-21-1079 
        1426         3016         2134         1852          474          965 
TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 TCGA-21-5782 TCGA-21-5784 TCGA-22-0940 
        3724          284         3644          962         1268          608 
TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 
         223         1945          131         1952           53          429 
TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 
         623         1067         1470          734           17         1161 
TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 
         399         1946          587          358          965         1964 
TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 
        1933          445         1346           24         1651         1952 
TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 
        1952          357          573          916         1912         1713 
TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 
          29         2524         1940         2979         1311         5287 
TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-33-4589 TCGA-34-2596 
        1966         1941          428         1970         1948           80 
TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 
        1874          958          881         1000          951         1528 
TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 
        2062         1715          707          365          428          941 
TCGA-34-5928 TCGA-34-8454 TCGA-37-3783 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 
         552          166          120           12          200          247 
TCGA-37-4132 TCGA-37-4135 TCGA-37-4141 TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 
         227          207           12         1454         2253         1361 
TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5030 
        1947         1996         1964         1849           52           59 
TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5037 TCGA-39-5039 TCGA-39-5040 
         833         1107          474         1086          544         1964 
TCGA-43-2576 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 
        1223         1176          822         1007          349          849 
TCGA-43-6143 TCGA-43-6647 TCGA-43-6771 TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 
         376          757         1936          212          236         1970 
TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U 
         407          358         1971          353          296          432 
TCGA-43-A56V TCGA-46-6025 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 
         366          324           12           12          911          541 
TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 TCGA-56-5897 TCGA-56-6545 
        1948          923         1958         1967            3           62 
TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7582 TCGA-56-7730 
          30           13           30           44           26            6 
TCGA-56-7731 TCGA-56-7822 TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 TCGA-56-8624 
        1961            1           41          178           55           36 
TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX 
          63           17           16           38            2           46 
TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8388 
          30           25            4            4            8          378 
TCGA-58-8391 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N 
        2167         1058         2589         1723         1072          910 
TCGA-60-2696 TCGA-60-2698 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 
         109          311         1943         1958          661         1963 
TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 
        1505         1963         1260          274         1731         1531 
TCGA-60-2715 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 
        1075         1475         1297           97          983          908 
TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 TCGA-63-7020 
        1092          717          816          358         1973         1957 
TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 
        1955         1947         1952         1967         1311           61 
TCGA-66-2742 TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 
         641           30           31           61           28           30 
TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 
         639          762           30           61           31           61 
TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 TCGA-66-2777 TCGA-66-2778 
          61         1947          700          578           61          578 
TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 
        1956          121         1954           60          790         1217 
TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 
        1955          699         1977         1645          122         1492 
TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I 
          83          202          211          244           96          121 
TCGA-68-A59J TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 
         104         1950         1941         1942         1952         1959 
TCGA-77-7139 TCGA-77-7141 TCGA-77-7335 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 
        1968           15         1954         1952         1954          479 
TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 
        1960         1945         1641         1953         1945         1941 
TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8145 
        1941         1947         1946         1951         1962         1943 
TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ 
         293         1961         1684         1092           10         1953 
TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA 
        1942         1959         1955         1963         1290         1280 
TCGA-77-A5GB TCGA-77-A5GF TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 
        1939          839          395           34           18           10 
TCGA-85-7698 TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 
          49         1965           35          911           60           26 
TCGA-85-8049 TCGA-85-8052 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 TCGA-85-8287 
          60           16          428          513           13           13 
TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8354 TCGA-85-8355 
          54           60           55           67           61           61 
TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8664 TCGA-85-8666 
          22           21          445          424            3          475 
TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z 
          15         1972         1960           25           19         1973 
TCGA-85-A511 TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7766 
        1972           24           13          111          758          289 
TCGA-90-7769 TCGA-90-7964 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 
         358          428          244          331          269           82 
TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 TCGA-94-7943 
         106          122          160           70           87          356 
TCGA-94-A4VJ TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK 
         430         1213         1344          189          211          273 
TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-L3-A4E7 
         183          256          413          224          308           35 
TCGA-L3-A524 TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HE TCGA-NC-A5HG TCGA-NC-A5HI 
         449           36           83         1722         1548         1135 

  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                1                 1 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
             1987              5287 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            706.0             615.5 
[1] "1.0 - 1987.0 (706.0)" "1.0 - 5287.0 (615.5)"
[1] "hr=" "1.7"
D53V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  7P LOSS MUTATED         1        5       14        0         6         9
  7P LOSS WILD-TYPE       0       67      123        1        46        62
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  7P LOSS MUTATED           10          3        1
  7P LOSS WILD-TYPE         47         17        5
D53V3, multiclass
            clus
vv           7P LOSS MUTATED 7P LOSS WILD-TYPE
  STAGE I                  1                 0
  STAGE IA                 5                67
  STAGE IB                14               123
  STAGE II                 0                 1
  STAGE IIA                6                46
  STAGE IIB                9                62
  STAGE IIIA              10                47
  STAGE IIIB               3                17
  STAGE IV                 1                 5
[1] 9 2
[1] 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    10  31   4   4
  7P LOSS WILD-TYPE  88 223  44  16
D53V4, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  T1              10                88
  T2              31               223
  T3               4                44
  T4               4                16
[1] 4 2
[1] 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    28  13   6   1
  7P LOSS WILD-TYPE 233 100  29   4
D53V5, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  N0              28               233
  N1              13               100
  N2               6                29
  N3               1                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A  MX
  7P LOSS MUTATED    41   1   0   6
  7P LOSS WILD-TYPE 317   4   1  44
D53V6, multiclass
     clus
vv    7P LOSS MUTATED 7P LOSS WILD-TYPE
  M0               41               317
  M1                1                 4
  M1A               0                 1
  MX                6                44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V7, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     8  41
  7P LOSS WILD-TYPE  99 272
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      8   41
  7P LOSS WILD-TYPE   99  272
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  FEMALE               8                99
  MALE                41               272
[1] 2 2
[1] FALSE
D53V8, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  7P LOSS MUTATED                                       1
  7P LOSS WILD-TYPE                                    11
                   vv
clus                LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  7P LOSS MUTATED                                        0
  7P LOSS WILD-TYPE                                      6
                   vv
clus                LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  7P LOSS MUTATED                                         0
  7P LOSS WILD-TYPE                                       1
                   vv
clus                LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  7P LOSS MUTATED                                                            48
  7P LOSS WILD-TYPE                                                         353
D53V9, multiclass
                                                             clus
vv                                                            7P LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    0
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              48
                                                             clus
vv                                                            7P LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      11
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V10, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     2  47
  7P LOSS WILD-TYPE  11 360
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      2   47
  7P LOSS WILD-TYPE   11  360
     clus
vv    7P LOSS MUTATED 7P LOSS WILD-TYPE
  NO                2                11
  YES              47               360
[1] 2 2
[1] FALSE
D53V11, continuous
                   vv
clus                 R0  R1  R2  RX
  7P LOSS MUTATED    44   0   2   1
  7P LOSS WILD-TYPE 298   8   2  17
D53V12, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  R0              44               298
  R1               0                 8
  R2               2                 2
  RX               1                17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7P LOSS MUTATED       0                         2    35
  7P LOSS WILD-TYPE     9                        15   263
D53V13, multiclass
                           clus
vv                          7P LOSS MUTATED 7P LOSS WILD-TYPE
  ASIAN                                   0                 9
  BLACK OR AFRICAN AMERICAN               2                15
  WHITE                                  35               263
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V14, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     1  31
  7P LOSS WILD-TYPE   7 236
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      1   31
  7P LOSS WILD-TYPE    7  236
                        clus
vv                       7P LOSS MUTATED 7P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 7
  NOT HISPANIC OR LATINO              31               236
[1] 2 2
[1] FALSE

Clustering(54) Variable = 7Q LOSS MUTATION ANALYSIS
D54V1, survival
                   sevent
clus2                 0   1
  7Q LOSS MUTATED    27  15
  7Q LOSS WILD-TYPE 238 108
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               42               346 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               15               108 
$`7Q LOSS MUTATED`
TCGA-18-3419 TCGA-21-1082 TCGA-21-1083 TCGA-21-5786 TCGA-22-1016 TCGA-22-1017 
          50         3644          267         1032          822         1485 
TCGA-22-5481 TCGA-37-3789 TCGA-37-5819 TCGA-39-5029 TCGA-43-2578 TCGA-43-2581 
        1952           13          103          740          684         1176 
TCGA-43-6770 TCGA-43-6771 TCGA-46-6026 TCGA-56-1622 TCGA-56-6546 TCGA-56-7580 
         310         1936          423          881           26           40 
TCGA-56-8629 TCGA-56-A4BW TCGA-60-2695 TCGA-60-2703 TCGA-66-2754 TCGA-66-2773 
          34            2          642         1950           61         1946 
TCGA-66-2788 TCGA-66-2793 TCGA-77-7138 TCGA-77-8136 TCGA-77-8139 TCGA-77-8144 
         699         1952         1959         1947         1951          833 
TCGA-77-A5GB TCGA-77-A5GH TCGA-85-6560 TCGA-85-7699 TCGA-85-8048 TCGA-85-8353 
        1939          713          364            1           26           54 
TCGA-85-A510 TCGA-85-A513 TCGA-85-A53L TCGA-90-7767 TCGA-98-8022 TCGA-J1-A4AH 
        1967           24           13           89          224          222 

$`7Q LOSS WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 
         370          136         2464         2417          146         1415 
TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-18-3421 
         345          396         1810          862          758         1331 
TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1070 
         187           85         2754           92          827         3636 
TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 
        1426         3016         2134         1852         1058          474 
TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 TCGA-21-5782 TCGA-21-5784 TCGA-21-5787 
         965         3724          284          962         1268          329 
TCGA-21-A5DI TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 
         979          608          223         1945          131         1952 
TCGA-22-1011 TCGA-22-1012 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4595 
          53          429          623         1067         1470          734 
TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 
          17         1161         1057          399         1946          587 
TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 
         358          965         1964         1933          445         1346 
TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 
          24         1651         1952          357          573          916 
TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4533 
        1912         1713          506           29         2524         1940 
TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 
        2979         1311         5287         1966         1941          428 
TCGA-33-4587 TCGA-33-4589 TCGA-33-6738 TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 
        1970         1948          822           80         1874          958 
TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 
         881         1000          951         1528         2062         1715 
TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-8454 
         707          365          428          941          552          166 
TCGA-37-3783 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 
         120           12          200          247          227          238 
TCGA-37-4135 TCGA-37-4141 TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 
         207           12         1454         2253         1361         1947 
TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5030 TCGA-39-5031 
        1996         1964         1849           52           59          833 
TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 TCGA-39-5040 
        1107          474         1084         1086          544         1964 
TCGA-43-2576 TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 
        1223          822         1007          349          849          376 
TCGA-43-6647 TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 
         757          212          236         1970          407          358 
TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V TCGA-46-6025 
        1971          353          296          432          366          324 
TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 
          12           12          911          541         1948          923 
TCGA-52-7811 TCGA-52-7812 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-7221 
        1958         1967            3          555           62           30 
TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 
          13           30           44           26            6         1961 
TCGA-56-7822 TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 TCGA-56-8624 TCGA-56-8625 
           1           41          178           55           36           63 
TCGA-56-8626 TCGA-56-8628 TCGA-56-A49D TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ 
          17           16           38           46           30           25 
TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 
           4            4            8          378          911         2167 
TCGA-58-8393 TCGA-58-A46J TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2696 
        1058         2589         1723         1072          910          109 
TCGA-60-2698 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 
         311         1943         1958          661         1963         1505 
TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2715 
        1963         1260          274         1731         1531         1075 
TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 
        1475         1297           97          983          908         1092 
TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 
         717          816          358         1973         1957         1955 
TCGA-63-7022 TCGA-63-7023 TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 
        1947         1952         1967         1311           61          641 
TCGA-66-2744 TCGA-66-2753 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 
          30           31           28           30           30          639 
TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 
         762           30           61           31           61           61 
TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 
        1947          700          578           61          578         1956 
TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 
         121         1954          759           60          790         1217 
TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 TCGA-66-2792 TCGA-66-2794 TCGA-66-2795 
        1955          699         1977          913         1645          122 
TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 
        1492           83          202          211          244           96 
TCGA-68-A59I TCGA-68-A59J TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 
         121          104         1950         1941         1942         1952 
TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 
        1968           15         1286         1954         1942         1952 
TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 
        1954          479         1960         1945         1641         1953 
TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8138 TCGA-77-8140 TCGA-77-8145 
        1945         1941         1941         1946         1962         1943 
TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ 
         293         1961         1684         1092           10         1953 
TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA 
        1942         1959         1955         1963         1290         1280 
TCGA-77-A5GF TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 
         839          395           34           18           10           49 
TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 TCGA-85-8049 TCGA-85-8052 
        1965           35          911           60           60           16 
TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 
         960          428          513           13           11           13 
TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8354 TCGA-85-8355 
          54           60           55           67           61           61 
TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8664 TCGA-85-8666 
          22           21          445          424            3          475 
TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z 
          15         1972         1960           25           19         1973 
TCGA-85-A511 TCGA-85-A512 TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7766 TCGA-90-7769 
        1972         1987          111          758          289          358 
TCGA-90-7964 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 
         428          244          331          269           82          106 
TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 TCGA-94-7943 TCGA-94-A4VJ 
         122          160           70           87          356          430 
TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL 
        1213         1344          189          211          273          183 
TCGA-98-7454 TCGA-98-8021 TCGA-98-8023 TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 
         256          413          308           35          449           36 
TCGA-MF-A522 TCGA-NC-A5HE TCGA-NC-A5HG TCGA-NC-A5HI 
          83         1722         1548         1135 

  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                1                 1 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
             3644              5287 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
              663               640 
[1] "1.0 - 3644.0 (663.0)" "1.0 - 5287.0 (640.0)"
[1] "hr=" "1.4"
D54V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  7Q LOSS MUTATED         0        7       15        0         6         9
  7Q LOSS WILD-TYPE       1       65      122        1        46        62
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  7Q LOSS MUTATED            6          1        0
  7Q LOSS WILD-TYPE         51         19        6
D54V3, multiclass
            clus
vv           7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                 7                65
  STAGE IB                15               122
  STAGE II                 0                 1
  STAGE IIA                6                46
  STAGE IIB                9                62
  STAGE IIIA               6                51
  STAGE IIIB               1                19
  STAGE IV                 0                 6
[1] 9 2
[1] 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     9  29   4   2
  7Q LOSS WILD-TYPE  89 225  44  18
D54V4, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  T1               9                89
  T2              29               225
  T3               4                44
  T4               2                18
[1] 4 2
[1] 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    27  12   3   0
  7Q LOSS WILD-TYPE 234 101  32   5
D54V5, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  N0              27               234
  N1              12               101
  N2               3                32
  N3               0                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A  MX
  7Q LOSS MUTATED    37   0   0   6
  7Q LOSS WILD-TYPE 321   5   1  44
D54V6, multiclass
     clus
vv    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  M0               37               321
  M1                0                 5
  M1A               0                 1
  MX                6                44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V7, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     9  35
  7Q LOSS WILD-TYPE  98 278
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      9   35
  7Q LOSS WILD-TYPE   98  278
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  FEMALE               9                98
  MALE                35               278
[1] 2 2
[1] FALSE
D54V8, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  7Q LOSS MUTATED                                       1
  7Q LOSS WILD-TYPE                                    11
                   vv
clus                LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  7Q LOSS MUTATED                                        0
  7Q LOSS WILD-TYPE                                      6
                   vv
clus                LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  7Q LOSS MUTATED                                         0
  7Q LOSS WILD-TYPE                                       1
                   vv
clus                LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  7Q LOSS MUTATED                                                            43
  7Q LOSS WILD-TYPE                                                         358
D54V9, multiclass
                                                             clus
vv                                                            7Q LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    0
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              43
                                                             clus
vv                                                            7Q LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      11
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               358
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V10, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     1  43
  7Q LOSS WILD-TYPE  12 364
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      1   43
  7Q LOSS WILD-TYPE   12  364
     clus
vv    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  NO                1                12
  YES              43               364
[1] 2 2
[1] FALSE
D54V11, continuous
                   vv
clus                 R0  R1  R2  RX
  7Q LOSS MUTATED    40   0   1   2
  7Q LOSS WILD-TYPE 302   8   3  16
D54V12, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  R0              40               302
  R1               0                 8
  R2               1                 3
  RX               2                16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7Q LOSS MUTATED       2                         1    30
  7Q LOSS WILD-TYPE     7                        16   268
D54V13, multiclass
                           clus
vv                          7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  ASIAN                                   2                 7
  BLACK OR AFRICAN AMERICAN               1                16
  WHITE                                  30               268
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V14, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     1  30
  7Q LOSS WILD-TYPE   7 237
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      1   30
  7Q LOSS WILD-TYPE    7  237
                        clus
vv                       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 7
  NOT HISPANIC OR LATINO              30               237
[1] 2 2
[1] FALSE

Clustering(55) Variable = 8P LOSS MUTATION ANALYSIS
D55V1, survival
                   sevent
clus2                 0   1
  8P LOSS MUTATED   126  63
  8P LOSS WILD-TYPE 139  60
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              189               199 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               63                60 
$`8P LOSS MUTATED`
TCGA-18-3406 TCGA-18-3412 TCGA-18-3415 TCGA-18-3419 TCGA-18-4083 TCGA-18-4721 
         370          345         1810           50          187         2754 
TCGA-18-5592 TCGA-18-5595 TCGA-21-1072 TCGA-21-1076 TCGA-21-1080 TCGA-21-1083 
          92          827         3016         1852         3724          267 
TCGA-21-5782 TCGA-21-5786 TCGA-21-5787 TCGA-22-1000 TCGA-22-1002 TCGA-22-1016 
         962         1032          329         1945          131          822 
TCGA-22-1017 TCGA-22-4591 TCGA-22-4594 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 
        1485          623         1470         1161         1057          399 
TCGA-22-4605 TCGA-22-4613 TCGA-22-5471 TCGA-22-5477 TCGA-22-5478 TCGA-22-5480 
        1946          358          965         1346           24         1952 
TCGA-22-5481 TCGA-22-5483 TCGA-22-5485 TCGA-22-5491 TCGA-22-5492 TCGA-33-4547 
        1952          573          916         1713          506         1311 
TCGA-33-4566 TCGA-33-4582 TCGA-33-4586 TCGA-33-4589 TCGA-33-6738 TCGA-34-2596 
        5287         1966          428         1948          822           80 
TCGA-34-2600 TCGA-34-2609 TCGA-34-5241 TCGA-34-5928 TCGA-34-8454 TCGA-37-3783 
        1874          951          428          552          166          120 
TCGA-37-3789 TCGA-37-3792 TCGA-37-4135 TCGA-37-4141 TCGA-39-5011 TCGA-39-5021 
          13           12          207           12         1454         1947 
TCGA-39-5027 TCGA-39-5031 TCGA-39-5037 TCGA-39-5039 TCGA-43-2576 TCGA-43-2581 
        1849          833         1086          544         1223         1176 
TCGA-43-5668 TCGA-43-6770 TCGA-43-6771 TCGA-43-7657 TCGA-43-8115 TCGA-43-8116 
         349          310         1936          236          407          358 
TCGA-43-8118 TCGA-43-A474 TCGA-46-6025 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 
        1971          353          324           12          911          541 
TCGA-52-7809 TCGA-52-7810 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 
        1948          923         1967          881            3          555 
TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-8504 TCGA-56-8626 
          13           30           44           40          178           17 
TCGA-56-8628 TCGA-56-8629 TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A5DS 
          16           34            2           46           30            8 
TCGA-58-8390 TCGA-58-8393 TCGA-58-A46L TCGA-58-A46M TCGA-60-2698 TCGA-60-2703 
         911         1058         1723         1072          311         1950 
TCGA-60-2711 TCGA-60-2713 TCGA-60-2721 TCGA-60-2723 TCGA-60-2726 TCGA-66-2727 
        1260         1731          983         1092          358         1967 
TCGA-66-2734 TCGA-66-2737 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2757 
        1311           61           31           61           28           30 
TCGA-66-2759 TCGA-66-2766 TCGA-66-2768 TCGA-66-2769 TCGA-66-2780 TCGA-66-2781 
         762           31           61         1947         1956          121 
TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2787 TCGA-66-2790 TCGA-66-2791 
        1954          759           60         1217          699         1977 
TCGA-66-2792 TCGA-66-2795 TCGA-68-7755 TCGA-68-8250 TCGA-68-A59I TCGA-68-A59J 
         913          122           83          244          121          104 
TCGA-77-6842 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7337 TCGA-77-7338 
        1950         1942         1952         1959         1942         1952 
TCGA-77-7465 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8139 
         479         1945         1641         1953         1945         1951 
TCGA-77-8140 TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 TCGA-77-8154 TCGA-77-A5G3 
        1962          833         1943          293         1092         1959 
TCGA-77-A5G6 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GF TCGA-85-6561 TCGA-85-6798 
        1955         1290         1280          839          395           34 
TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 
          18           10           49         1965           35          911 
TCGA-85-7950 TCGA-85-8048 TCGA-85-8070 TCGA-85-8276 TCGA-85-8277 TCGA-85-8350 
          60           26          960           13           11           60 
TCGA-85-8352 TCGA-85-8353 TCGA-85-8354 TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M 
          67           54           61         1960           25           19 
TCGA-85-A50Z TCGA-85-A511 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-7766 TCGA-90-7767 
        1973         1972           13          111          289           89 
TCGA-90-A4ED TCGA-92-7341 TCGA-92-8063 TCGA-94-A4VJ TCGA-96-7544 TCGA-96-8170 
         244          106          122          430         1213          211 
TCGA-96-A4JK TCGA-98-8021 TCGA-98-8022 TCGA-J1-A4AH TCGA-LA-A446 TCGA-MF-A522 
         273          413          224          222           36           83 
TCGA-NC-A5HE TCGA-NC-A5HG TCGA-NC-A5HI 
        1722         1548         1135 

$`8P LOSS WILD-TYPE`
TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 TCGA-18-3414 
         136         2464         2417          146         1415          396 
TCGA-18-3416 TCGA-18-3417 TCGA-18-3421 TCGA-18-4086 TCGA-21-1070 TCGA-21-1071 
         862          758         1331           85         3636         1426 
TCGA-21-1075 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 TCGA-21-1081 TCGA-21-1082 
        2134         1058          474          965          284         3644 
TCGA-21-5784 TCGA-21-A5DI TCGA-22-0940 TCGA-22-0944 TCGA-22-1005 TCGA-22-1011 
        1268          979          608          223         1952           53 
TCGA-22-1012 TCGA-22-4593 TCGA-22-4595 TCGA-22-4596 TCGA-22-4607 TCGA-22-5472 
         429         1067          734           17          587         1964 
TCGA-22-5473 TCGA-22-5474 TCGA-22-5479 TCGA-22-5482 TCGA-22-5489 TCGA-22-A5C4 
        1933          445         1651          357         1912           29 
TCGA-33-4532 TCGA-33-4533 TCGA-33-4538 TCGA-33-4583 TCGA-33-4587 TCGA-34-2604 
        2524         1940         2979         1941         1970          958 
TCGA-34-2605 TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 
         881         1000         1528         2062         1715          707 
TCGA-34-5240 TCGA-34-5927 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 
         365          941          200          247          227          238 
TCGA-37-5819 TCGA-39-5016 TCGA-39-5019 TCGA-39-5022 TCGA-39-5024 TCGA-39-5028 
         103         2253         1361         1996         1964           52 
TCGA-39-5029 TCGA-39-5030 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5040 
         740           59         1107          474         1084         1964 
TCGA-43-2578 TCGA-43-3394 TCGA-43-3920 TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 
         684          822         1007          849          376          757 
TCGA-43-7656 TCGA-43-7658 TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V TCGA-46-6026 
         212         1970          296          432          366          423 
TCGA-51-4079 TCGA-52-7811 TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 TCGA-56-7582 
          12         1958           62           26           30           26 
TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-8503 TCGA-56-8622 TCGA-56-8624 
           6         1961            1           41           55           36 
TCGA-56-8625 TCGA-56-A49D TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR TCGA-58-8388 
          63           38           25            4            4          378 
TCGA-58-8391 TCGA-58-A46J TCGA-58-A46N TCGA-60-2695 TCGA-60-2696 TCGA-60-2704 
        2167         2589          910          642          109         1943 
TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2712 
        1958          661         1963         1505         1963          274 
TCGA-60-2714 TCGA-60-2715 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2722 
        1531         1075         1475         1297           97          908 
TCGA-60-2724 TCGA-60-2725 TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 
         717          816         1973         1957         1955         1947 
TCGA-63-7023 TCGA-66-2742 TCGA-66-2744 TCGA-66-2756 TCGA-66-2758 TCGA-66-2763 
        1952          641           30           30          639           30 
TCGA-66-2765 TCGA-66-2767 TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 
          61           61          700          578         1946           61 
TCGA-66-2778 TCGA-66-2786 TCGA-66-2788 TCGA-66-2789 TCGA-66-2793 TCGA-66-2794 
         578          790          699         1955         1952         1645 
TCGA-66-2800 TCGA-68-7756 TCGA-68-7757 TCGA-68-8251 TCGA-77-6843 TCGA-77-7139 
        1492          202          211           96         1941         1968 
TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7463 TCGA-77-8007 TCGA-77-8131 
          15         1286         1954         1954         1960         1941 
TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8150 TCGA-77-8153 TCGA-77-8156 
        1941         1947         1946         1961         1684           10 
TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G7 TCGA-77-A5GB TCGA-77-A5GH TCGA-85-6560 
        1953         1942         1963         1939          713          364 
TCGA-85-7699 TCGA-85-8049 TCGA-85-8052 TCGA-85-8071 TCGA-85-8072 TCGA-85-8287 
           1           60           16          428          513           13 
TCGA-85-8288 TCGA-85-8351 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 
          54           55           61           22           21          445 
TCGA-85-8582 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A510 
         424            3          475           15         1972         1967 
TCGA-85-A512 TCGA-85-A513 TCGA-90-6837 TCGA-90-7769 TCGA-90-7964 TCGA-90-A4EE 
        1987           24          758          358          428          331 
TCGA-90-A59Q TCGA-92-7340 TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 TCGA-94-7943 
         269           82          160           70           87          356 
TCGA-96-7545 TCGA-96-8169 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8023 TCGA-L3-A4E7 
        1344          189          183          256          308           35 
TCGA-L3-A524 
         449 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                2                 1 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             5287              3644 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              555               684 
[1] "2.0 - 5287.0 (555.0)" "1.0 - 3644.0 (684.0)"
[1] "hr=" "1.3"
D55V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  8P LOSS MUTATED         0       39       62        0        27        38
  8P LOSS WILD-TYPE       1       33       75        1        25        33
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  8P LOSS MUTATED           32          8        1
  8P LOSS WILD-TYPE         25         12        5
D55V3, multiclass
            clus
vv           8P LOSS MUTATED 8P LOSS WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                39                33
  STAGE IB                62                75
  STAGE II                 0                 1
  STAGE IIA               27                25
  STAGE IIB               38                33
  STAGE IIIA              32                25
  STAGE IIIB               8                12
  STAGE IV                 1                 5
[1] 9 2
[1] 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    48 125  28   7
  8P LOSS WILD-TYPE  50 129  20  13
D55V4, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  T1              48                50
  T2             125               129
  T3              28                20
  T4               7                13
[1] 4 2
[1] 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   127  59  19   2
  8P LOSS WILD-TYPE 134  54  16   3
D55V5, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  N0             127               134
  N1              59                54
  N2              19                16
  N3               2                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A  MX
  8P LOSS MUTATED   179   0   1  25
  8P LOSS WILD-TYPE 179   5   0  25
D55V6, multiclass
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  M0              179               179
  M1                0                 5
  M1A               1                 0
  MX               25                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V7, binary
                   cls
clus                  0   1
  8P LOSS MUTATED    48 160
  8P LOSS WILD-TYPE  59 153
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     48  160
  8P LOSS WILD-TYPE   59  153
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE              48                59
  MALE               160               153
[1] 2 2
[1] FALSE
D55V8, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  8P LOSS MUTATED                                       5
  8P LOSS WILD-TYPE                                     7
                   vv
clus                LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  8P LOSS MUTATED                                        1
  8P LOSS WILD-TYPE                                      5
                   vv
clus                LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  8P LOSS MUTATED                                         0
  8P LOSS WILD-TYPE                                       1
                   vv
clus                LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  8P LOSS MUTATED                                                           202
  8P LOSS WILD-TYPE                                                         199
D55V9, multiclass
                                                             clus
vv                                                            8P LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     5
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             202
                                                             clus
vv                                                            8P LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       7
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               199
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V10, binary
                   cls
clus                  0   1
  8P LOSS MUTATED     7 201
  8P LOSS WILD-TYPE   6 206
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      7  201
  8P LOSS WILD-TYPE    6  206
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  NO                7                 6
  YES             201               206
[1] 2 2
[1] FALSE
D55V11, continuous
                   vv
clus                 R0  R1  R2  RX
  8P LOSS MUTATED   170   5   2   8
  8P LOSS WILD-TYPE 172   3   2  10
D55V12, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  R0             170               172
  R1               5                 3
  R2               2                 2
  RX               8                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8P LOSS MUTATED       4                         8   148
  8P LOSS WILD-TYPE     5                         9   150
D55V13, multiclass
                           clus
vv                          8P LOSS MUTATED 8P LOSS WILD-TYPE
  ASIAN                                   4                 5
  BLACK OR AFRICAN AMERICAN               8                 9
  WHITE                                 148               150
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V14, binary
                   cls
clus                  0   1
  8P LOSS MUTATED     3 131
  8P LOSS WILD-TYPE   5 136
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      3  131
  8P LOSS WILD-TYPE    5  136
                        clus
vv                       8P LOSS MUTATED 8P LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 5
  NOT HISPANIC OR LATINO             131               136
[1] 2 2
[1] FALSE

Clustering(56) Variable = 8Q LOSS MUTATION ANALYSIS
D56V1, survival
                   sevent
clus2                 0   1
  8Q LOSS MUTATED    27   7
  8Q LOSS WILD-TYPE 238 116
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               34               354 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                7               116 
$`8Q LOSS MUTATED`
TCGA-21-1072 TCGA-22-5483 TCGA-33-4586 TCGA-33-6738 TCGA-37-3792 TCGA-37-4135 
        3016          573          428          822           12          207 
TCGA-37-4141 TCGA-39-5011 TCGA-39-5037 TCGA-43-6771 TCGA-46-6025 TCGA-52-7622 
          12         1454         1086         1936          324          541 
TCGA-52-7809 TCGA-56-7730 TCGA-56-8629 TCGA-56-A4BW TCGA-66-2727 TCGA-66-2766 
        1948            6           34            2         1967           31 
TCGA-66-2791 TCGA-77-8144 TCGA-77-8154 TCGA-77-A5GF TCGA-85-6561 TCGA-85-7844 
        1977          833         1092          839          395          911 
TCGA-85-8276 TCGA-85-8277 TCGA-85-8352 TCGA-85-A50M TCGA-85-A53L TCGA-90-7766 
          13           11           67           19           13          289 
TCGA-90-A4ED TCGA-MF-A522 TCGA-NC-A5HE TCGA-NC-A5HI 
         244           83         1722         1135 

$`8Q LOSS WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 
         370          136         2464         2417          146         1415 
TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 
         345          396         1810          862          758           50 
TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 
        1331          187           85         2754           92          827 
TCGA-21-1070 TCGA-21-1071 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 
        3636         1426         2134         1852         1058          474 
TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 
         965         3724          284         3644          267          962 
TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-21-A5DI TCGA-22-0940 TCGA-22-0944 
        1268         1032          329          979          608          223 
TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 
        1945          131         1952           53          429          822 
TCGA-22-1017 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4595 TCGA-22-4596 
        1485          623         1067         1470          734           17 
TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-4613 
        1161         1057          399         1946          587          358 
TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 
         965         1964         1933          445         1346           24 
TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 TCGA-22-5485 TCGA-22-5489 
        1651         1952         1952          357          916         1912 
TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4533 TCGA-33-4538 
        1713          506           29         2524         1940         2979 
TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-33-4587 TCGA-33-4589 
        1311         5287         1966         1941         1970         1948 
TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 
          80         1874          958          881         1000          951 
TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 
        1528         2062         1715          707          365          428 
TCGA-34-5927 TCGA-34-5928 TCGA-34-8454 TCGA-37-3783 TCGA-37-3789 TCGA-37-4129 
         941          552          166          120           13          200 
TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-5819 TCGA-39-5016 TCGA-39-5019 
         247          227          238          103         2253         1361 
TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 
        1947         1996         1964         1849           52          740 
TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5039 
          59          833         1107          474         1084          544 
TCGA-39-5040 TCGA-43-2576 TCGA-43-2578 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 
        1964         1223          684         1176          822         1007 
TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-7656 
         349          849          376          757          310          212 
TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 
         236         1970          407          358         1971          353 
TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 
         296          432          366          423           12           12 
TCGA-51-4081 TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 
         911          923         1958         1967          881            3 
TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 
         555           62           26           30           13           30 
TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7731 TCGA-56-7822 TCGA-56-8503 
          44           40           26         1961            1           41 
TCGA-56-8504 TCGA-56-8622 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 
         178           55           36           63           17           16 
TCGA-56-A49D TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR 
          38           46           30           25            4            4 
TCGA-56-A5DS TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-8393 TCGA-58-A46J 
           8          378          911         2167         1058         2589 
TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 TCGA-60-2696 TCGA-60-2698 
        1723         1072          910          642          109          311 
TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 
        1950         1943         1958          661         1963         1505 
TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2715 
        1963         1260          274         1731         1531         1075 
TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 
        1475         1297           97          983          908         1092 
TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 
         717          816          358         1973         1957         1955 
TCGA-63-7022 TCGA-63-7023 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 
        1947         1952         1311           61          641           30 
TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 
          31           61           28           30           30          639 
TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 
         762           30           61           61           61         1947 
TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 
         700          578         1946           61          578         1956 
TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 
         121         1954          759           60          790         1217 
TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 
         699         1955          699          913         1952         1645 
TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 
         122         1492           83          202          211          244 
TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 
          96          121          104         1950         1941         1942 
TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 
        1952         1959         1968           15         1286         1954 
TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 
        1942         1952         1954          479         1960         1945 
TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 
        1641         1953         1945         1941         1941         1947 
TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 
        1946         1951         1962         1943          293         1961 
TCGA-77-8153 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 
        1684           10         1953         1942         1959         1955 
TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GH TCGA-85-6560 
        1963         1290         1280         1939          713          364 
TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 
          34           18           10           49            1         1965 
TCGA-85-7843 TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 
          35           60           26           60           16          960 
TCGA-85-8071 TCGA-85-8072 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 
         428          513           13           54           60           55 
TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 
          54           61           61           22           21          445 
TCGA-85-8582 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A4QQ 
         424            3          475           15         1972         1960 
TCGA-85-A4QR TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 
          25         1973         1967         1972         1987           24 
TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7767 TCGA-90-7769 TCGA-90-7964 TCGA-90-A4EE 
         111          758           89          358          428          331 
TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 
         269           82          106          122          160           70 
TCGA-94-7033 TCGA-94-7943 TCGA-94-A4VJ TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 
          87          356          430         1213         1344          189 
TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 
         211          273          183          256          413          224 
TCGA-98-8023 TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-NC-A5HG 
         308          222           35          449           36         1548 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                2                 1 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             3016              5287 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            411.5             691.5 
[1] "2.0 - 3016.0 (411.5)" "1.0 - 5287.0 (691.5)"
[1] "hr=" "1.2"
D56V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  8Q LOSS MUTATED         0        5       11        0         9         4
  8Q LOSS WILD-TYPE       1       67      126        1        43        67
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  8Q LOSS MUTATED            6          2        0
  8Q LOSS WILD-TYPE         51         18        6
D56V3, multiclass
            clus
vv           8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                 5                67
  STAGE IB                11               126
  STAGE II                 0                 1
  STAGE IIA                9                43
  STAGE IIB                4                67
  STAGE IIIA               6                51
  STAGE IIIB               2                18
  STAGE IV                 0                 6
[1] 9 2
[1] 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     9  26   2   0
  8Q LOSS WILD-TYPE  89 228  46  20
D56V4, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  T1               9                89
  T2              26               228
  T3               2                46
  T4               0                20
[1] 4 2
[1] 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    20  11   4   1
  8Q LOSS WILD-TYPE 241 102  31   4
D56V5, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  N0              20               241
  N1              11               102
  N2               4                31
  N3               1                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A  MX
  8Q LOSS MUTATED    31   0   0   6
  8Q LOSS WILD-TYPE 327   5   1  44
D56V6, multiclass
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  M0               31               327
  M1                0                 5
  M1A               0                 1
  MX                6                44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V7, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     7  30
  8Q LOSS WILD-TYPE 100 283
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      7   30
  8Q LOSS WILD-TYPE  100  283
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE               7               100
  MALE                30               283
[1] 2 2
[1] FALSE
D56V8, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  8Q LOSS MUTATED                                       2
  8Q LOSS WILD-TYPE                                    10
                   vv
clus                LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  8Q LOSS MUTATED                                        0
  8Q LOSS WILD-TYPE                                      6
                   vv
clus                LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  8Q LOSS MUTATED                                         0
  8Q LOSS WILD-TYPE                                       1
                   vv
clus                LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  8Q LOSS MUTATED                                                            35
  8Q LOSS WILD-TYPE                                                         366
D56V9, multiclass
                                                             clus
vv                                                            8Q LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     2
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    0
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              35
                                                             clus
vv                                                            8Q LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      10
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               366
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V10, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     1  36
  8Q LOSS WILD-TYPE  12 371
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      1   36
  8Q LOSS WILD-TYPE   12  371
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  NO                1                12
  YES              36               371
[1] 2 2
[1] FALSE
D56V11, continuous
                   vv
clus                 R0  R1  R2  RX
  8Q LOSS MUTATED    30   1   0   1
  8Q LOSS WILD-TYPE 312   7   4  17
D56V12, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  R0              30               312
  R1               1                 7
  R2               0                 4
  RX               1                17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8Q LOSS MUTATED       2                         0    28
  8Q LOSS WILD-TYPE     7                        17   270
D56V13, multiclass
                           clus
vv                          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  ASIAN                                   2                 7
  BLACK OR AFRICAN AMERICAN               0                17
  WHITE                                  28               270
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V14, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     1  23
  8Q LOSS WILD-TYPE   7 244
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      1   23
  8Q LOSS WILD-TYPE    7  244
                        clus
vv                       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 7
  NOT HISPANIC OR LATINO              23               244
[1] 2 2
[1] FALSE

Clustering(57) Variable = 9P LOSS MUTATION ANALYSIS
D57V1, survival
                   sevent
clus2                 0   1
  9P LOSS MUTATED   169  74
  9P LOSS WILD-TYPE  96  49
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              243               145 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               74                49 
$`9P LOSS MUTATED`
TCGA-18-3406 TCGA-18-3409 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 
         370         2417         1415          345          396         1810 
TCGA-18-3417 TCGA-18-3419 TCGA-18-4083 TCGA-18-4086 TCGA-18-5592 TCGA-21-1070 
         758           50          187           85           92         3636 
TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 TCGA-21-1077 TCGA-21-1080 TCGA-21-1082 
        1426         3016         2134         1058         3724         3644 
TCGA-21-1083 TCGA-21-5786 TCGA-21-5787 TCGA-21-A5DI TCGA-22-1002 TCGA-22-1005 
         267         1032          329          979          131         1952 
TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 
          53          429          822          623         1067         1470 
TCGA-22-4599 TCGA-22-4601 TCGA-22-4607 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 
        1161         1057          587          358          965         1964 
TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 
         445         1346           24          357          573          916 
TCGA-22-5491 TCGA-22-A5C4 TCGA-33-4538 TCGA-33-4547 TCGA-33-4582 TCGA-33-6738 
        1713           29         2979         1311         1966          822 
TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 
          80         1874          958          881         1000          951 
TCGA-34-5231 TCGA-34-5232 TCGA-34-5241 TCGA-34-5927 TCGA-34-8454 TCGA-37-3789 
        1528         2062          428          941          166           13 
TCGA-37-4130 TCGA-37-4135 TCGA-37-4141 TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 
         247          207           12         1454         2253         1361 
TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5031 TCGA-39-5035 TCGA-39-5040 
        1849           52          740          833          474         1964 
TCGA-43-2576 TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 TCGA-43-6647 
        1223          822         1007          349          849          757 
TCGA-43-6770 TCGA-43-6771 TCGA-43-7656 TCGA-43-7657 TCGA-43-8115 TCGA-43-8116 
         310         1936          212          236          407          358 
TCGA-43-8118 TCGA-43-A474 TCGA-43-A56V TCGA-46-6026 TCGA-51-4081 TCGA-52-7809 
        1971          353          366          423          911         1948 
TCGA-52-7810 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 
         923          881            3          555           62           26 
TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 
          30           13           30           44           40           26 
TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-8503 TCGA-56-8622 TCGA-56-8624 
           6         1961            1           41           55           36 
TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW 
          63           17           16           34           38            2 
TCGA-56-A4BX TCGA-56-A4ZJ TCGA-56-A5DS TCGA-58-8390 TCGA-58-8391 TCGA-58-8393 
          46           25            8          911         2167         1058 
TCGA-58-A46J TCGA-58-A46L TCGA-60-2696 TCGA-60-2698 TCGA-60-2703 TCGA-60-2706 
        2589         1723          109          311         1950         1958 
TCGA-60-2707 TCGA-60-2708 TCGA-60-2711 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 
         661         1963         1260         1297           97          983 
TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-7020 TCGA-63-7022 
        1092          717          816          358         1957         1947 
TCGA-63-7023 TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2753 
        1952         1967         1311           61          641           31 
TCGA-66-2755 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2768 
          28          762           30           61           31           61 
TCGA-66-2769 TCGA-66-2771 TCGA-66-2773 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 
        1947          578         1946          578         1956          121 
TCGA-66-2782 TCGA-66-2785 TCGA-66-2786 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 
        1954           60          790          699         1955          699 
TCGA-66-2793 TCGA-68-7757 TCGA-68-8251 TCGA-68-A59I TCGA-77-6843 TCGA-77-6844 
        1952          211           96          121         1941         1942 
TCGA-77-6845 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 
        1952           15         1286         1954         1942         1952 
TCGA-77-7463 TCGA-77-7465 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 
        1954          479         1945         1641         1953         1945 
TCGA-77-8138 TCGA-77-8140 TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 TCGA-77-8153 
        1946         1962          833         1943          293         1684 
TCGA-77-8154 TCGA-77-A5G1 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GH 
        1092         1942         1955         1963         1290          713 
TCGA-85-6560 TCGA-85-7696 TCGA-85-7697 TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 
         364           18           10            1         1965           35 
TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 
         911           60           26           13           54           60 
TCGA-85-8351 TCGA-85-8352 TCGA-85-8479 TCGA-85-8580 TCGA-85-8664 TCGA-85-8666 
          55           67           22          445            3          475 
TCGA-85-A4CL TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 
          15           25           19         1973         1967         1972 
TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-7766 TCGA-90-7767 TCGA-90-7964 
          24           13          111          289           89          428 
TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-92-8065 
         331          269           82          106          122           70 
TCGA-94-7033 TCGA-94-7943 TCGA-94-A4VJ TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 
          87          356          430         1344          189          211 
TCGA-96-A4JK TCGA-96-A4JL TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-L3-A524 
         273          183          413          224          308          449 
TCGA-MF-A522 TCGA-NC-A5HG TCGA-NC-A5HI 
          83         1548         1135 

$`9P LOSS WILD-TYPE`
TCGA-18-3407 TCGA-18-3408 TCGA-18-3410 TCGA-18-3416 TCGA-18-3421 TCGA-18-4721 
         136         2464          146          862         1331         2754 
TCGA-18-5595 TCGA-21-1076 TCGA-21-1078 TCGA-21-1079 TCGA-21-1081 TCGA-21-5782 
         827         1852          474          965          284          962 
TCGA-21-5784 TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1017 TCGA-22-4595 
        1268          608          223         1945         1485          734 
TCGA-22-4596 TCGA-22-4604 TCGA-22-4605 TCGA-22-5473 TCGA-22-5479 TCGA-22-5480 
          17          399         1946         1933         1651         1952 
TCGA-22-5481 TCGA-22-5489 TCGA-22-5492 TCGA-33-4532 TCGA-33-4533 TCGA-33-4566 
        1952         1912          506         2524         1940         5287 
TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-33-4589 TCGA-34-5234 TCGA-34-5239 
        1941          428         1970         1948         1715          707 
TCGA-34-5240 TCGA-34-5928 TCGA-37-3783 TCGA-37-3792 TCGA-37-4129 TCGA-37-4132 
         365          552          120           12          200          227 
TCGA-37-4133 TCGA-37-5819 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5030 
         238          103         1947         1996         1964           59 
TCGA-39-5034 TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 TCGA-43-2578 TCGA-43-2581 
        1107         1084         1086          544          684         1176 
TCGA-43-6143 TCGA-43-7658 TCGA-43-A475 TCGA-43-A56U TCGA-46-6025 TCGA-51-4079 
         376         1970          296          432          324           12 
TCGA-51-4080 TCGA-52-7622 TCGA-52-7811 TCGA-52-7812 TCGA-56-8504 TCGA-56-A4BY 
          12          541         1958         1967          178           30 
TCGA-56-A4ZK TCGA-56-A5DR TCGA-58-8388 TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 
           4            4          378         1072          910          642 
TCGA-60-2704 TCGA-60-2709 TCGA-60-2710 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 
        1943         1505         1963          274         1731         1531 
TCGA-60-2715 TCGA-60-2716 TCGA-60-2722 TCGA-63-6202 TCGA-63-7021 TCGA-66-2744 
        1075         1475          908         1973         1955           30 
TCGA-66-2754 TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 TCGA-66-2767 TCGA-66-2770 
          61           30           30          639           61          700 
TCGA-66-2777 TCGA-66-2783 TCGA-66-2787 TCGA-66-2791 TCGA-66-2792 TCGA-66-2794 
          61          759         1217         1977          913         1645 
TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-8250 TCGA-68-A59J 
         122         1492           83          202          244          104 
TCGA-77-6842 TCGA-77-7138 TCGA-77-7139 TCGA-77-8007 TCGA-77-8131 TCGA-77-8133 
        1950         1959         1968         1960         1941         1941 
TCGA-77-8136 TCGA-77-8139 TCGA-77-8150 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G3 
        1947         1951         1961           10         1953         1959 
TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF TCGA-85-6561 TCGA-85-6798 TCGA-85-7698 
        1280         1939          839          395           34           49 
TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 
          60           16          960          428          513           13 
TCGA-85-8277 TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 TCGA-85-8481 TCGA-85-8582 
          11           54           61           61           21          424 
TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A512 TCGA-90-6837 TCGA-90-7769 TCGA-90-A4ED 
        1972         1960         1987          758          358          244 
TCGA-92-8064 TCGA-96-7544 TCGA-98-7454 TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-LA-A446 
         160         1213          256          222           35           36 
TCGA-NC-A5HE 
        1722 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                1                 4 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             3724              5287 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              573               758 
[1] "1.0 - 3724.0 (573.0)" "4.0 - 5287.0 (758.0)"
[1] "hr=" "1.1"
D57V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  9P LOSS MUTATED         1       51       83        0        37        39
  9P LOSS WILD-TYPE       0       21       54        1        15        32
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  9P LOSS MUTATED           39          8        4
  9P LOSS WILD-TYPE         18         12        2
D57V3, multiclass
            clus
vv           9P LOSS MUTATED 9P LOSS WILD-TYPE
  STAGE I                  1                 0
  STAGE IA                51                21
  STAGE IB                83                54
  STAGE II                 0                 1
  STAGE IIA               37                15
  STAGE IIB               39                32
  STAGE IIIA              39                18
  STAGE IIIB               8                12
  STAGE IV                 4                 2
[1] 9 2
[1] 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    67 159  28  11
  9P LOSS WILD-TYPE  31  95  20   9
D57V4, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  T1              67                31
  T2             159                95
  T3              28                20
  T4              11                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  9P LOSS MUTATED   170  68  23   2
  9P LOSS WILD-TYPE  91  45  12   3
D57V5, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  N0             170                91
  N1              68                45
  N2              23                12
  N3               2                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A  MX
  9P LOSS MUTATED   225   3   1  33
  9P LOSS WILD-TYPE 133   2   0  17
D57V6, multiclass
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  M0              225               133
  M1                3                 2
  M1A               1                 0
  MX               33                17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V7, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    69 196
  9P LOSS WILD-TYPE  38 117
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     69  196
  9P LOSS WILD-TYPE   38  117
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE              69                38
  MALE               196               117
[1] 2 2
[1] FALSE
D57V8, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  9P LOSS MUTATED                                       5
  9P LOSS WILD-TYPE                                     7
                   vv
clus                LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  9P LOSS MUTATED                                        2
  9P LOSS WILD-TYPE                                      4
                   vv
clus                LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  9P LOSS MUTATED                                         0
  9P LOSS WILD-TYPE                                       1
                   vv
clus                LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  9P LOSS MUTATED                                                           258
  9P LOSS WILD-TYPE                                                         143
D57V9, multiclass
                                                             clus
vv                                                            9P LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     5
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             258
                                                             clus
vv                                                            9P LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       7
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               143
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V10, binary
                   cls
clus                  0   1
  9P LOSS MUTATED     8 257
  9P LOSS WILD-TYPE   5 150
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      8  257
  9P LOSS WILD-TYPE    5  150
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  NO                8                 5
  YES             257               150
[1] 2 2
[1] FALSE
D57V11, continuous
                   vv
clus                 R0  R1  R2  RX
  9P LOSS MUTATED   212   5   3  12
  9P LOSS WILD-TYPE 130   3   1   6
D57V12, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  R0             212               130
  R1               5                 3
  R2               3                 1
  RX              12                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9P LOSS MUTATED       6                        12   188
  9P LOSS WILD-TYPE     3                         5   110
D57V13, multiclass
                           clus
vv                          9P LOSS MUTATED 9P LOSS WILD-TYPE
  ASIAN                                   6                 3
  BLACK OR AFRICAN AMERICAN              12                 5
  WHITE                                 188               110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V14, binary
                   cls
clus                  0   1
  9P LOSS MUTATED     4 168
  9P LOSS WILD-TYPE   4  99
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      4  168
  9P LOSS WILD-TYPE    4   99
                        clus
vv                       9P LOSS MUTATED 9P LOSS WILD-TYPE
  HISPANIC OR LATINO                   4                 4
  NOT HISPANIC OR LATINO             168                99
[1] 2 2
[1] FALSE

Clustering(58) Variable = 9Q LOSS MUTATION ANALYSIS
D58V1, survival
                   sevent
clus2                 0   1
  9Q LOSS MUTATED   133  57
  9Q LOSS WILD-TYPE 132  66
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              190               198 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               57                66 
$`9Q LOSS MUTATED`
TCGA-18-3406 TCGA-18-3409 TCGA-18-3414 TCGA-18-3417 TCGA-18-3419 TCGA-18-4083 
         370         2417          396          758           50          187 
TCGA-21-1070 TCGA-21-1075 TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 TCGA-21-5786 
        3636         2134         3644          267          962         1032 
TCGA-21-5787 TCGA-21-A5DI TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 
         329          979          131         1952           53          429 
TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4607 
         822         1485          623         1067         1470          587 
TCGA-22-5474 TCGA-22-5478 TCGA-22-5482 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4547 
         445           24          357           29         2524         1311 
TCGA-33-4582 TCGA-33-4587 TCGA-33-6738 TCGA-34-2600 TCGA-34-2604 TCGA-34-2608 
        1966         1970          822         1874          958         1000 
TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 
         951         1528         2062          428          941          552 
TCGA-34-8454 TCGA-37-4130 TCGA-37-4135 TCGA-37-4141 TCGA-39-5011 TCGA-39-5016 
         166          247          207           12         1454         2253 
TCGA-39-5019 TCGA-39-5024 TCGA-39-5028 TCGA-39-5031 TCGA-39-5035 TCGA-39-5037 
        1361         1964           52          833          474         1086 
TCGA-43-2576 TCGA-43-3920 TCGA-43-5670 TCGA-43-6647 TCGA-43-6771 TCGA-43-7656 
        1223         1007          849          757         1936          212 
TCGA-43-7657 TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 TCGA-43-A56V TCGA-46-6026 
         236          407          358         1971          366          423 
TCGA-51-4081 TCGA-52-7810 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 
         911          923          881            3          555           62 
TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 
          26           30           13           30           44           40 
TCGA-56-7731 TCGA-56-7822 TCGA-56-8503 TCGA-56-8622 TCGA-56-8624 TCGA-56-8626 
        1961            1           41           55           36           17 
TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4ZJ TCGA-56-A5DS TCGA-58-8390 
          16           34           38           25            8          911 
TCGA-58-8393 TCGA-58-A46J TCGA-60-2696 TCGA-60-2698 TCGA-60-2703 TCGA-60-2706 
        1058         2589          109          311         1950         1958 
TCGA-60-2708 TCGA-60-2712 TCGA-60-2714 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 
        1963          274         1531         1297           97          983 
TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-7020 TCGA-63-7022 
        1092          717          816          358         1957         1947 
TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2753 TCGA-66-2755 TCGA-66-2759 
        1311           61          641           31           28          762 
TCGA-66-2763 TCGA-66-2769 TCGA-66-2771 TCGA-66-2773 TCGA-66-2778 TCGA-66-2780 
          30         1947          578         1946          578         1956 
TCGA-66-2781 TCGA-66-2782 TCGA-66-2785 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 
         121         1954           60          699         1955          699 
TCGA-66-2793 TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-77-6842 
        1952          211          244           96          121         1950 
TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7337 TCGA-77-7463 TCGA-77-8007 
        1941         1942         1952         1942         1954         1960 
TCGA-77-8008 TCGA-77-8128 TCGA-77-8130 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 
        1945         1953         1945         1946         1951         1962 
TCGA-77-8145 TCGA-77-8148 TCGA-77-8154 TCGA-77-A5G1 TCGA-77-A5G6 TCGA-77-A5G7 
        1943          293         1092         1942         1955         1963 
TCGA-77-A5G8 TCGA-77-A5GH TCGA-85-6560 TCGA-85-7697 TCGA-85-7843 TCGA-85-8048 
        1290          713          364           10           35           26 
TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8664 
          13           54           60           55           67            3 
TCGA-85-8666 TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 
         475           25           19         1973         1967         1972 
TCGA-85-A513 TCGA-85-A53L TCGA-90-7766 TCGA-90-7767 TCGA-90-7964 TCGA-90-A4EE 
          24           13          289           89          428          331 
TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-92-8065 TCGA-94-7033 TCGA-94-7943 
         269           82          106           70           87          356 
TCGA-94-A4VJ TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 TCGA-98-8021 TCGA-98-8022 
         430         1213          189          211          413          224 
TCGA-98-8023 TCGA-L3-A4E7 TCGA-NC-A5HG TCGA-NC-A5HI 
         308           35         1548         1135 

$`9Q LOSS WILD-TYPE`
TCGA-18-3407 TCGA-18-3408 TCGA-18-3410 TCGA-18-3411 TCGA-18-3412 TCGA-18-3415 
         136         2464          146         1415          345         1810 
TCGA-18-3416 TCGA-18-3421 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 
         862         1331           85         2754           92          827 
TCGA-21-1071 TCGA-21-1072 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 
        1426         3016         1852         1058          474          965 
TCGA-21-1080 TCGA-21-1081 TCGA-21-5784 TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 
        3724          284         1268          608          223         1945 
TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 
         734           17         1161         1057          399         1946 
TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 TCGA-22-5477 TCGA-22-5479 
         358          965         1964         1933         1346         1651 
TCGA-22-5480 TCGA-22-5481 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 
        1952         1952          573          916         1912         1713 
TCGA-22-5492 TCGA-33-4533 TCGA-33-4538 TCGA-33-4566 TCGA-33-4583 TCGA-33-4586 
         506         1940         2979         5287         1941          428 
TCGA-33-4589 TCGA-34-2596 TCGA-34-2605 TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 
        1948           80          881         1715          707          365 
TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-37-4132 TCGA-37-4133 
         120           13           12          200          227          238 
TCGA-37-5819 TCGA-39-5021 TCGA-39-5022 TCGA-39-5027 TCGA-39-5029 TCGA-39-5030 
         103         1947         1996         1849          740           59 
TCGA-39-5034 TCGA-39-5036 TCGA-39-5039 TCGA-39-5040 TCGA-43-2578 TCGA-43-2581 
        1107         1084          544         1964          684         1176 
TCGA-43-3394 TCGA-43-5668 TCGA-43-6143 TCGA-43-6770 TCGA-43-7658 TCGA-43-A474 
         822          349          376          310         1970          353 
TCGA-43-A475 TCGA-43-A56U TCGA-46-6025 TCGA-51-4079 TCGA-51-4080 TCGA-52-7622 
         296          432          324           12           12          541 
TCGA-52-7809 TCGA-52-7811 TCGA-52-7812 TCGA-56-7582 TCGA-56-7730 TCGA-56-8504 
        1948         1958         1967           26            6          178 
TCGA-56-8625 TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZK TCGA-56-A5DR 
          63            2           46           30            4            4 
TCGA-58-8388 TCGA-58-8391 TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 
         378         2167         1723         1072          910          642 
TCGA-60-2704 TCGA-60-2707 TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 TCGA-60-2713 
        1943          661         1505         1963         1260         1731 
TCGA-60-2715 TCGA-60-2716 TCGA-60-2722 TCGA-63-6202 TCGA-63-7021 TCGA-63-7023 
        1075         1475          908         1973         1955         1952 
TCGA-66-2727 TCGA-66-2744 TCGA-66-2754 TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 
        1967           30           61           30           30          639 
TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2770 TCGA-66-2777 
          61           31           61           61          700           61 
TCGA-66-2783 TCGA-66-2786 TCGA-66-2787 TCGA-66-2791 TCGA-66-2792 TCGA-66-2794 
         759          790         1217         1977          913         1645 
TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-A59J TCGA-77-7138 
         122         1492           83          202          104         1959 
TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7338 TCGA-77-7465 
        1968           15         1286         1954         1952          479 
TCGA-77-8009 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 TCGA-77-8144 TCGA-77-8150 
        1641         1941         1941         1947          833         1961 
TCGA-77-8153 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G3 TCGA-77-A5GA TCGA-77-A5GB 
        1684           10         1953         1959         1280         1939 
TCGA-77-A5GF TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7698 TCGA-85-7699 
         839          395           34           18           49            1 
TCGA-85-7710 TCGA-85-7844 TCGA-85-7950 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 
        1965          911           60           60           16          960 
TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8353 TCGA-85-8354 
         428          513           13           11           54           61 
TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-A4CL 
          61           22           21          445          424           15 
TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A512 TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7769 
        1972         1960         1987          111          758          358 
TCGA-90-A4ED TCGA-92-8063 TCGA-92-8064 TCGA-96-7545 TCGA-96-A4JK TCGA-96-A4JL 
         244          122          160         1344          273          183 
TCGA-98-7454 TCGA-J1-A4AH TCGA-L3-A524 TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HE 
         256          222          449           36           83         1722 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                1                 1 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             3644              5287 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            578.0             703.5 
[1] "1.0 - 3644.0 (578.0)" "1.0 - 5287.0 (703.5)"
[1] "hr=" "1.1"
D58V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  9Q LOSS MUTATED         1       41       57        0        27        38
  9Q LOSS WILD-TYPE       0       31       80        1        25        33
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  9Q LOSS MUTATED           27          6        4
  9Q LOSS WILD-TYPE         30         14        2
D58V3, multiclass
            clus
vv           9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  STAGE I                  1                 0
  STAGE IA                41                31
  STAGE IB                57                80
  STAGE II                 0                 1
  STAGE IIA               27                25
  STAGE IIB               38                33
  STAGE IIIA              27                30
  STAGE IIIB               6                14
  STAGE IV                 4                 2
[1] 9 2
[1] 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    53 121  24   6
  9Q LOSS WILD-TYPE  45 133  24  14
D58V4, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T1              53                45
  T2             121               133
  T3              24                24
  T4               6                14
[1] 4 2
[1] 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   126  59  15   2
  9Q LOSS WILD-TYPE 135  54  20   3
D58V5, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  N0             126               135
  N1              59                54
  N2              15                20
  N3               2                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A  MX
  9Q LOSS MUTATED   168   3   1  30
  9Q LOSS WILD-TYPE 190   2   0  20
D58V6, multiclass
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  M0              168               190
  M1                3                 2
  M1A               1                 0
  MX               30                20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V7, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    55 149
  9Q LOSS WILD-TYPE  52 164
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     55  149
  9Q LOSS WILD-TYPE   52  164
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE              55                52
  MALE               149               164
[1] 2 2
[1] FALSE
D58V8, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  9Q LOSS MUTATED                                       3
  9Q LOSS WILD-TYPE                                     9
                   vv
clus                LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  9Q LOSS MUTATED                                        1
  9Q LOSS WILD-TYPE                                      5
                   vv
clus                LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  9Q LOSS MUTATED                                         1
  9Q LOSS WILD-TYPE                                       0
                   vv
clus                LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  9Q LOSS MUTATED                                                           199
  9Q LOSS WILD-TYPE                                                         202
D58V9, multiclass
                                                             clus
vv                                                            9Q LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     3
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)             199
                                                             clus
vv                                                            9Q LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       9
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               202
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V10, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED     4 200
  9Q LOSS WILD-TYPE   9 207
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      4  200
  9Q LOSS WILD-TYPE    9  207
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  NO                4                 9
  YES             200               207
[1] 2 2
[1] FALSE
D58V11, continuous
                   vv
clus                 R0  R1  R2  RX
  9Q LOSS MUTATED   162   3   2   6
  9Q LOSS WILD-TYPE 180   5   2  12
D58V12, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  R0             162               180
  R1               3                 5
  R2               2                 2
  RX               6                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9Q LOSS MUTATED       5                        11   143
  9Q LOSS WILD-TYPE     4                         6   155
D58V13, multiclass
                           clus
vv                          9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  ASIAN                                   5                 4
  BLACK OR AFRICAN AMERICAN              11                 6
  WHITE                                 143               155
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V14, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED     1 136
  9Q LOSS WILD-TYPE   7 131
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      1  136
  9Q LOSS WILD-TYPE    7  131
                        clus
vv                       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 7
  NOT HISPANIC OR LATINO             136               131
[1] 2 2
[1] FALSE

Clustering(59) Variable = 10P LOSS MUTATION ANALYSIS
D59V1, survival
                    sevent
clus2                  0   1
  10P LOSS MUTATED   112  53
  10P LOSS WILD-TYPE 153  70
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               165                223 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                53                 70 
$`10P LOSS MUTATED`
TCGA-18-3406 TCGA-18-3411 TCGA-18-3412 TCGA-18-3421 TCGA-18-4083 TCGA-18-5592 
         370         1415          345         1331          187           92 
TCGA-18-5595 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 
         827         1426         3016         2134         1852         1058 
TCGA-21-1079 TCGA-21-1080 TCGA-21-1082 TCGA-21-5786 TCGA-21-A5DI TCGA-22-0940 
         965         3724         3644         1032          979          608 
TCGA-22-1000 TCGA-22-1005 TCGA-22-1011 TCGA-22-1016 TCGA-22-4591 TCGA-22-4593 
        1945         1952           53          822          623         1067 
TCGA-22-4595 TCGA-22-4599 TCGA-22-4613 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 
         734         1161          358          445         1346           24 
TCGA-22-5479 TCGA-22-5482 TCGA-22-5483 TCGA-22-5491 TCGA-33-4533 TCGA-33-4538 
        1651          357          573         1713         1940         2979 
TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-34-2596 TCGA-34-2605 TCGA-34-5927 
        1966         1941          428           80          881          941 
TCGA-37-3789 TCGA-37-3792 TCGA-37-4135 TCGA-37-5819 TCGA-39-5019 TCGA-39-5021 
          13           12          207          103         1361         1947 
TCGA-39-5027 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5036 TCGA-39-5039 
        1849          740           59          833         1084          544 
TCGA-43-2576 TCGA-43-2578 TCGA-43-3920 TCGA-43-6143 TCGA-43-6770 TCGA-43-8118 
        1223          684         1007          376          310         1971 
TCGA-43-A56U TCGA-43-A56V TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 
         432          366           12          911          541         1948 
TCGA-52-7810 TCGA-56-1622 TCGA-56-5898 TCGA-56-7223 TCGA-56-7580 TCGA-56-7582 
         923          881          555           30           40           26 
TCGA-56-7730 TCGA-56-8503 TCGA-56-8622 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 
           6           41           55           17           16           34 
TCGA-56-A49D TCGA-56-A4BY TCGA-56-A4ZK TCGA-58-8391 TCGA-58-8393 TCGA-58-A46J 
          38           30            4         2167         1058         2589 
TCGA-58-A46M TCGA-60-2695 TCGA-60-2703 TCGA-60-2704 TCGA-60-2708 TCGA-60-2709 
        1072          642         1950         1943         1963         1505 
TCGA-60-2710 TCGA-60-2715 TCGA-60-2719 TCGA-60-2722 TCGA-60-2723 TCGA-60-2725 
        1963         1075         1297          908         1092          816 
TCGA-63-7020 TCGA-63-7021 TCGA-66-2727 TCGA-66-2737 TCGA-66-2753 TCGA-66-2754 
        1957         1955         1967           61           31           61 
TCGA-66-2755 TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 TCGA-66-2770 TCGA-66-2777 
          28           30          639          762          700           61 
TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2791 TCGA-66-2793 
         790         1217          699         1955         1977         1952 
TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59J 
        1492           83          202          244           96          104 
TCGA-77-6842 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7465 TCGA-77-8009 
        1950         1952         1959         1968          479         1641 
TCGA-77-8130 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 
        1945         1941         1947         1946         1951         1962 
TCGA-77-8144 TCGA-77-8153 TCGA-77-8156 TCGA-77-A5GB TCGA-77-A5GF TCGA-85-6798 
         833         1684           10         1939          839           34 
TCGA-85-7696 TCGA-85-7699 TCGA-85-7844 TCGA-85-7950 TCGA-85-8052 TCGA-85-8070 
          18            1          911           60           16          960 
TCGA-85-8071 TCGA-85-8277 TCGA-85-8351 TCGA-85-8353 TCGA-85-8354 TCGA-85-8479 
         428           11           55           54           61           22 
TCGA-85-8580 TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A5B5 TCGA-90-A4EE TCGA-92-8064 
         445         1960           25          111          331          160 
TCGA-94-7033 TCGA-96-8170 TCGA-96-A4JK TCGA-98-8021 TCGA-98-8023 TCGA-J1-A4AH 
          87          211          273          413          308          222 
TCGA-L3-A524 TCGA-LA-A446 TCGA-MF-A522 
         449           36           83 

$`10P LOSS WILD-TYPE`
TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3414 TCGA-18-3415 
         136         2464         2417          146          396         1810 
TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 TCGA-18-4086 TCGA-18-4721 TCGA-21-1070 
         862          758           50           85         2754         3636 
TCGA-21-1078 TCGA-21-1081 TCGA-21-1083 TCGA-21-5782 TCGA-21-5784 TCGA-21-5787 
         474          284          267          962         1268          329 
TCGA-22-0944 TCGA-22-1002 TCGA-22-1012 TCGA-22-1017 TCGA-22-4594 TCGA-22-4596 
         223          131          429         1485         1470           17 
TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-5471 TCGA-22-5472 
        1057          399         1946          587          965         1964 
TCGA-22-5473 TCGA-22-5480 TCGA-22-5481 TCGA-22-5485 TCGA-22-5489 TCGA-22-5492 
        1933         1952         1952          916         1912          506 
TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4547 TCGA-33-4566 TCGA-33-4587 TCGA-33-4589 
          29         2524         1311         5287         1970         1948 
TCGA-33-6738 TCGA-34-2600 TCGA-34-2604 TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 
         822         1874          958         1000          951         1528 
TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5928 
        2062         1715          707          365          428          552 
TCGA-34-8454 TCGA-37-3783 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 
         166          120          200          247          227          238 
TCGA-37-4141 TCGA-39-5011 TCGA-39-5016 TCGA-39-5022 TCGA-39-5024 TCGA-39-5028 
          12         1454         2253         1996         1964           52 
TCGA-39-5034 TCGA-39-5035 TCGA-39-5037 TCGA-39-5040 TCGA-43-2581 TCGA-43-3394 
        1107          474         1086         1964         1176          822 
TCGA-43-5668 TCGA-43-5670 TCGA-43-6647 TCGA-43-6771 TCGA-43-7656 TCGA-43-7657 
         349          849          757         1936          212          236 
TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 TCGA-43-A474 TCGA-43-A475 TCGA-46-6025 
        1970          407          358          353          296          324 
TCGA-46-6026 TCGA-51-4079 TCGA-52-7811 TCGA-52-7812 TCGA-56-5897 TCGA-56-6545 
         423           12         1958         1967            3           62 
TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 TCGA-56-7579 TCGA-56-7731 TCGA-56-7822 
          26           30           13           44         1961            1 
TCGA-56-8504 TCGA-56-8624 TCGA-56-8625 TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4ZJ 
         178           36           63            2           46           25 
TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8388 TCGA-58-8390 TCGA-58-A46L TCGA-58-A46N 
           4            8          378          911         1723          910 
TCGA-60-2696 TCGA-60-2698 TCGA-60-2706 TCGA-60-2707 TCGA-60-2711 TCGA-60-2712 
         109          311         1958          661         1260          274 
TCGA-60-2713 TCGA-60-2714 TCGA-60-2716 TCGA-60-2720 TCGA-60-2721 TCGA-60-2724 
        1731         1531         1475           97          983          717 
TCGA-60-2726 TCGA-63-6202 TCGA-63-7022 TCGA-63-7023 TCGA-66-2734 TCGA-66-2742 
         358         1973         1947         1952         1311          641 
TCGA-66-2744 TCGA-66-2756 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 
          30           30           30           61           31           61 
TCGA-66-2768 TCGA-66-2769 TCGA-66-2771 TCGA-66-2773 TCGA-66-2778 TCGA-66-2780 
          61         1947          578         1946          578         1956 
TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2790 TCGA-66-2792 
         121         1954          759           60          699          913 
TCGA-66-2794 TCGA-66-2795 TCGA-68-7757 TCGA-68-A59I TCGA-77-6843 TCGA-77-6844 
        1645          122          211          121         1941         1942 
TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 
          15         1286         1954         1942         1952         1954 
TCGA-77-8007 TCGA-77-8008 TCGA-77-8128 TCGA-77-8131 TCGA-77-8145 TCGA-77-8148 
        1960         1945         1953         1941         1943          293 
TCGA-77-8150 TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 
        1961         1092         1953         1942         1959         1955 
TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GH TCGA-85-6560 TCGA-85-6561 
        1963         1290         1280          713          364          395 
TCGA-85-7697 TCGA-85-7698 TCGA-85-7710 TCGA-85-7843 TCGA-85-8048 TCGA-85-8049 
          10           49         1965           35           26           60 
TCGA-85-8072 TCGA-85-8276 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8352 
         513           13           13           54           60           67 
TCGA-85-8355 TCGA-85-8481 TCGA-85-8582 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL 
          61           21          424            3          475           15 
TCGA-85-A4PA TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A512 
        1972           19         1973         1967         1972         1987 
TCGA-85-A513 TCGA-85-A53L TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 
          24           13          758          289           89          358 
TCGA-90-7964 TCGA-90-A4ED TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 
         428          244          269           82          106          122 
TCGA-92-8065 TCGA-94-7943 TCGA-94-A4VJ TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 
          70          356          430         1213         1344          189 
TCGA-96-A4JL TCGA-98-7454 TCGA-98-8022 TCGA-L3-A4E7 TCGA-NC-A5HE TCGA-NC-A5HG 
         183          256          224           35         1722         1548 
TCGA-NC-A5HI 
        1135 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 1                  1 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              3724               5287 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               734                552 
[1] "1.0 - 3724.0 (734.0)" "1.0 - 5287.0 (552.0)"
[1] "hr=" "1.1"
D59V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  10P LOSS MUTATED         1       30       69        0        18        27
  10P LOSS WILD-TYPE       0       42       68        1        34        44
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  10P LOSS MUTATED           24          8        1
  10P LOSS WILD-TYPE         33         12        5
D59V3, multiclass
            clus
vv           10P LOSS MUTATED 10P LOSS WILD-TYPE
  STAGE I                   1                  0
  STAGE IA                 30                 42
  STAGE IB                 69                 68
  STAGE II                  0                  1
  STAGE IIA                18                 34
  STAGE IIB                27                 44
  STAGE IIIA               24                 33
  STAGE IIIB                8                 12
  STAGE IV                  1                  5
[1] 9 2
[1] 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    41 112  18   7
  10P LOSS WILD-TYPE  57 142  30  13
D59V4, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  T1               41                 57
  T2              112                142
  T3               18                 30
  T4                7                 13
[1] 4 2
[1] 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   118  40  16   2
  10P LOSS WILD-TYPE 143  73  19   3
D59V5, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  N0              118                143
  N1               40                 73
  N2               16                 19
  N3                2                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A  MX
  10P LOSS MUTATED   156   1   0  18
  10P LOSS WILD-TYPE 202   4   1  32
D59V6, multiclass
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  M0               156                202
  M1                 1                  4
  M1A                0                  1
  MX                18                 32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V7, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    39 139
  10P LOSS WILD-TYPE  68 174
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     39  139
  10P LOSS WILD-TYPE   68  174
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE               39                 68
  MALE                139                174
[1] 2 2
[1] FALSE
D59V8, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  10P LOSS MUTATED                                       5
  10P LOSS WILD-TYPE                                     7
                    vv
clus                 LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  10P LOSS MUTATED                                        2
  10P LOSS WILD-TYPE                                      4
                    vv
clus                 LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  10P LOSS MUTATED                                         0
  10P LOSS WILD-TYPE                                       1
                    vv
clus                 LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  10P LOSS MUTATED                                                           171
  10P LOSS WILD-TYPE                                                         230
D59V9, multiclass
                                                             clus
vv                                                            10P LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      5
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              171
                                                             clus
vv                                                            10P LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                        7
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                230
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V10, binary
                    cls
clus                   0   1
  10P LOSS MUTATED     4 174
  10P LOSS WILD-TYPE   9 233
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      4  174
  10P LOSS WILD-TYPE    9  233
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  NO                 4                  9
  YES              174                233
[1] 2 2
[1] FALSE
D59V11, continuous
                    vv
clus                  R0  R1  R2  RX
  10P LOSS MUTATED   151   3   0   8
  10P LOSS WILD-TYPE 191   5   4  10
D59V12, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  R0              151                191
  R1                3                  5
  R2                0                  4
  RX                8                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10P LOSS MUTATED       2                         8   128
  10P LOSS WILD-TYPE     7                         9   170
D59V13, multiclass
                           clus
vv                          10P LOSS MUTATED 10P LOSS WILD-TYPE
  ASIAN                                    2                  7
  BLACK OR AFRICAN AMERICAN                8                  9
  WHITE                                  128                170
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V14, binary
                    cls
clus                   0   1
  10P LOSS MUTATED     4 113
  10P LOSS WILD-TYPE   4 154
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      4  113
  10P LOSS WILD-TYPE    4  154
                        clus
vv                       10P LOSS MUTATED 10P LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  4
  NOT HISPANIC OR LATINO              113                154
[1] 2 2
[1] FALSE

Clustering(60) Variable = 10Q LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                  0   1
  10Q LOSS MUTATED   119  53
  10Q LOSS WILD-TYPE 146  70
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               172                216 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                53                 70 
$`10Q LOSS MUTATED`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3411 TCGA-18-3412 TCGA-18-4083 TCGA-18-4721 
         370          136         1415          345          187         2754 
TCGA-18-5592 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 
          92         1426         3016         2134         1852         1058 
TCGA-21-1082 TCGA-21-A5DI TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1005 
        3644          979          608          223         1945         1952 
TCGA-22-1011 TCGA-22-4593 TCGA-22-4595 TCGA-22-4599 TCGA-22-5474 TCGA-22-5477 
          53         1067          734         1161          445         1346 
TCGA-22-5478 TCGA-22-5479 TCGA-22-5482 TCGA-22-5483 TCGA-22-5491 TCGA-33-4533 
          24         1651          357          573         1713         1940 
TCGA-33-4538 TCGA-33-4583 TCGA-33-4586 TCGA-33-6738 TCGA-34-2596 TCGA-34-2605 
        2979         1941          428          822           80          881 
TCGA-34-5927 TCGA-37-3792 TCGA-37-4135 TCGA-37-5819 TCGA-39-5016 TCGA-39-5019 
         941           12          207          103         2253         1361 
TCGA-39-5021 TCGA-39-5027 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5036 
        1947         1849          740           59          833         1084 
TCGA-39-5039 TCGA-43-2576 TCGA-43-2578 TCGA-43-3394 TCGA-43-3920 TCGA-43-6770 
         544         1223          684          822         1007          310 
TCGA-43-7658 TCGA-43-A474 TCGA-43-A56U TCGA-43-A56V TCGA-46-6025 TCGA-51-4079 
        1970          353          432          366          324           12 
TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 TCGA-56-1622 
          12          911          541         1948          923          881 
TCGA-56-5898 TCGA-56-7221 TCGA-56-7223 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 
         555           30           30           40           26            6 
TCGA-56-8503 TCGA-56-8622 TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BX 
          41           55           16           34           38           46 
TCGA-56-A4BY TCGA-56-A4ZK TCGA-58-8388 TCGA-58-8391 TCGA-58-8393 TCGA-58-A46J 
          30            4          378         2167         1058         2589 
TCGA-58-A46M TCGA-60-2695 TCGA-60-2704 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 
        1072          642         1943         1963         1505         1963 
TCGA-60-2712 TCGA-60-2715 TCGA-60-2719 TCGA-60-2722 TCGA-60-2723 TCGA-60-2725 
         274         1075         1297          908         1092          816 
TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-66-2727 TCGA-66-2737 TCGA-66-2753 
        1957         1955         1947         1967           61           31 
TCGA-66-2754 TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 TCGA-66-2770 TCGA-66-2773 
          61           30          639          762          700         1946 
TCGA-66-2782 TCGA-66-2785 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2791 
        1954           60         1217          699         1955         1977 
TCGA-66-2792 TCGA-66-2793 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 
         913         1952         1492           83          202          211 
TCGA-68-8251 TCGA-68-A59J TCGA-77-6842 TCGA-77-7138 TCGA-77-7139 TCGA-77-7463 
          96          104         1950         1959         1968         1954 
TCGA-77-7465 TCGA-77-8009 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 
         479         1641         1941         1947         1946         1951 
TCGA-77-8140 TCGA-77-8144 TCGA-77-8148 TCGA-77-8153 TCGA-77-8156 TCGA-77-A5G3 
        1962          833          293         1684           10         1959 
TCGA-77-A5GB TCGA-77-A5GF TCGA-85-6560 TCGA-85-6798 TCGA-85-7696 TCGA-85-7698 
        1939          839          364           34           18           49 
TCGA-85-7699 TCGA-85-7844 TCGA-85-7950 TCGA-85-8052 TCGA-85-8070 TCGA-85-8277 
           1          911           60           16          960           11 
TCGA-85-8351 TCGA-85-8353 TCGA-85-8354 TCGA-85-8479 TCGA-85-8580 TCGA-85-A4QQ 
          55           54           61           22          445         1960 
TCGA-85-A4QR TCGA-85-A5B5 TCGA-90-A4EE TCGA-92-8064 TCGA-94-7033 TCGA-96-7545 
          25          111          331          160           87         1344 
TCGA-96-8170 TCGA-96-A4JK TCGA-98-8021 TCGA-98-8023 TCGA-J1-A4AH TCGA-L3-A4E7 
         211          273          413          308          222           35 
TCGA-L3-A524 TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HI 
         449           36           83         1135 

$`10Q LOSS WILD-TYPE`
TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3414 TCGA-18-3415 TCGA-18-3416 
        2464         2417          146          396         1810          862 
TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4086 TCGA-18-5595 TCGA-21-1070 
         758           50         1331           85          827         3636 
TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 TCGA-21-1083 TCGA-21-5782 
         474          965         3724          284          267          962 
TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-22-1002 TCGA-22-1012 TCGA-22-1016 
        1268         1032          329          131          429          822 
TCGA-22-1017 TCGA-22-4591 TCGA-22-4594 TCGA-22-4596 TCGA-22-4601 TCGA-22-4604 
        1485          623         1470           17         1057          399 
TCGA-22-4605 TCGA-22-4607 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 
        1946          587          358          965         1964         1933 
TCGA-22-5480 TCGA-22-5481 TCGA-22-5485 TCGA-22-5489 TCGA-22-5492 TCGA-22-A5C4 
        1952         1952          916         1912          506           29 
TCGA-33-4532 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4587 TCGA-33-4589 
        2524         1311         5287         1966         1970         1948 
TCGA-34-2600 TCGA-34-2604 TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 
        1874          958         1000          951         1528         2062 
TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5928 TCGA-34-8454 
        1715          707          365          428          552          166 
TCGA-37-3783 TCGA-37-3789 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 
         120           13          200          247          227          238 
TCGA-37-4141 TCGA-39-5011 TCGA-39-5022 TCGA-39-5024 TCGA-39-5028 TCGA-39-5034 
          12         1454         1996         1964           52         1107 
TCGA-39-5035 TCGA-39-5037 TCGA-39-5040 TCGA-43-2581 TCGA-43-5668 TCGA-43-5670 
         474         1086         1964         1176          349          849 
TCGA-43-6143 TCGA-43-6647 TCGA-43-6771 TCGA-43-7656 TCGA-43-7657 TCGA-43-8115 
         376          757         1936          212          236          407 
TCGA-43-8116 TCGA-43-8118 TCGA-43-A475 TCGA-46-6026 TCGA-52-7811 TCGA-52-7812 
         358         1971          296          423         1958         1967 
TCGA-56-5897 TCGA-56-6545 TCGA-56-6546 TCGA-56-7222 TCGA-56-7579 TCGA-56-7731 
           3           62           26           13           44         1961 
TCGA-56-7822 TCGA-56-8504 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-A4BW 
           1          178           36           63           17            2 
TCGA-56-A4ZJ TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8390 TCGA-58-A46L TCGA-58-A46N 
          25            4            8          911         1723          910 
TCGA-60-2696 TCGA-60-2698 TCGA-60-2703 TCGA-60-2706 TCGA-60-2707 TCGA-60-2711 
         109          311         1950         1958          661         1260 
TCGA-60-2713 TCGA-60-2714 TCGA-60-2716 TCGA-60-2720 TCGA-60-2721 TCGA-60-2724 
        1731         1531         1475           97          983          717 
TCGA-60-2726 TCGA-63-6202 TCGA-63-7023 TCGA-66-2734 TCGA-66-2742 TCGA-66-2744 
         358         1973         1952         1311          641           30 
TCGA-66-2755 TCGA-66-2756 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 
          28           30           30           61           31           61 
TCGA-66-2768 TCGA-66-2769 TCGA-66-2771 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 
          61         1947          578           61          578         1956 
TCGA-66-2781 TCGA-66-2783 TCGA-66-2786 TCGA-66-2790 TCGA-66-2794 TCGA-66-2795 
         121          759          790          699         1645          122 
TCGA-68-8250 TCGA-68-A59I TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7141 
         244          121         1941         1942         1952           15 
TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-8007 TCGA-77-8008 
        1286         1954         1942         1952         1960         1945 
TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8145 TCGA-77-8150 TCGA-77-8154 
        1953         1945         1941         1943         1961         1092 
TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA 
        1953         1942         1955         1963         1290         1280 
TCGA-77-A5GH TCGA-85-6561 TCGA-85-7697 TCGA-85-7710 TCGA-85-7843 TCGA-85-8048 
         713          395           10         1965           35           26 
TCGA-85-8049 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 TCGA-85-8287 TCGA-85-8288 
          60          428          513           13           13           54 
TCGA-85-8350 TCGA-85-8352 TCGA-85-8355 TCGA-85-8481 TCGA-85-8582 TCGA-85-8664 
          60           67           61           21          424            3 
TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 
         475           15         1972           19         1973         1967 
TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L TCGA-90-6837 TCGA-90-7766 
        1972         1987           24           13          758          289 
TCGA-90-7767 TCGA-90-7769 TCGA-90-7964 TCGA-90-A4ED TCGA-90-A59Q TCGA-92-7340 
          89          358          428          244          269           82 
TCGA-92-7341 TCGA-92-8063 TCGA-92-8065 TCGA-94-7943 TCGA-94-A4VJ TCGA-96-7544 
         106          122           70          356          430         1213 
TCGA-96-8169 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8022 TCGA-NC-A5HE TCGA-NC-A5HG 
         189          183          256          224         1722         1548 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 1                  1 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              3644               5287 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             691.5              605.0 
[1] "1.0 - 3644.0 (691.5)" "1.0 - 5287.0 (605.0)"
[1] "hr=" "1"  
D60V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  10Q LOSS MUTATED         1       28       73        0        22        28
  10Q LOSS WILD-TYPE       0       44       64        1        30        43
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  10Q LOSS MUTATED           25          8        1
  10Q LOSS WILD-TYPE         32         12        5
D60V3, multiclass
            clus
vv           10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  STAGE I                   1                  0
  STAGE IA                 28                 44
  STAGE IB                 73                 64
  STAGE II                  0                  1
  STAGE IIA                22                 30
  STAGE IIB                28                 43
  STAGE IIIA               25                 32
  STAGE IIIB                8                 12
  STAGE IV                  1                  5
[1] 9 2
[1] 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    42 121  18   6
  10Q LOSS WILD-TYPE  56 133  30  14
D60V4, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T1               42                 56
  T2              121                133
  T3               18                 30
  T4                6                 14
[1] 4 2
[1] 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   122  45  16   2
  10Q LOSS WILD-TYPE 139  68  19   3
D60V5, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  N0              122                139
  N1               45                 68
  N2               16                 19
  N3                2                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A  MX
  10Q LOSS MUTATED   162   1   0  20
  10Q LOSS WILD-TYPE 196   4   1  30
D60V6, multiclass
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  M0               162                196
  M1                 1                  4
  M1A                0                  1
  MX                20                 30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V7, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    41 146
  10Q LOSS WILD-TYPE  66 167
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     41  146
  10Q LOSS WILD-TYPE   66  167
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE               41                 66
  MALE                146                167
[1] 2 2
[1] FALSE
D60V8, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  10Q LOSS MUTATED                                       6
  10Q LOSS WILD-TYPE                                     6
                    vv
clus                 LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  10Q LOSS MUTATED                                        2
  10Q LOSS WILD-TYPE                                      4
                    vv
clus                 LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  10Q LOSS MUTATED                                         0
  10Q LOSS WILD-TYPE                                       1
                    vv
clus                 LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  10Q LOSS MUTATED                                                           179
  10Q LOSS WILD-TYPE                                                         222
D60V9, multiclass
                                                             clus
vv                                                            10Q LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      6
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              179
                                                             clus
vv                                                            10Q LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                        6
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                222
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V10, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     4 183
  10Q LOSS WILD-TYPE   9 224
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      4  183
  10Q LOSS WILD-TYPE    9  224
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  NO                 4                  9
  YES              183                224
[1] 2 2
[1] FALSE
D60V11, continuous
                    vv
clus                  R0  R1  R2  RX
  10Q LOSS MUTATED   158   2   0   7
  10Q LOSS WILD-TYPE 184   6   4  11
D60V12, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  R0              158                184
  R1                2                  6
  R2                0                  4
  RX                7                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10Q LOSS MUTATED       3                         8   132
  10Q LOSS WILD-TYPE     6                         9   166
D60V13, multiclass
                           clus
vv                          10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  ASIAN                                    3                  6
  BLACK OR AFRICAN AMERICAN                8                  9
  WHITE                                  132                166
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V14, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     4 115
  10Q LOSS WILD-TYPE   4 152
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      4  115
  10Q LOSS WILD-TYPE    4  152
                        clus
vv                       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  4
  NOT HISPANIC OR LATINO              115                152
[1] 2 2
[1] FALSE

Clustering(61) Variable = 11P LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                  0   1
  11P LOSS MUTATED    94  43
  11P LOSS WILD-TYPE 171  80
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               137                251 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                43                 80 
$`11P LOSS MUTATED`
TCGA-18-3406 TCGA-18-3409 TCGA-18-3412 TCGA-18-3414 TCGA-18-3417 TCGA-18-3421 
         370         2417          345          396          758         1331 
TCGA-21-1071 TCGA-21-1076 TCGA-21-1080 TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 
        1426         1852         3724         3644          267          962 
TCGA-21-5786 TCGA-21-5787 TCGA-22-1002 TCGA-22-1017 TCGA-22-4593 TCGA-22-4596 
        1032          329          131         1485         1067           17 
TCGA-22-4601 TCGA-22-5471 TCGA-22-5473 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 
        1057          965         1933         1346           24         1651 
TCGA-22-5481 TCGA-22-5483 TCGA-22-A5C4 TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 
        1952          573           29         1940         2979         1311 
TCGA-33-4587 TCGA-34-2596 TCGA-34-2600 TCGA-34-2605 TCGA-34-5231 TCGA-34-5232 
        1970           80         1874          881         1528         2062 
TCGA-34-5928 TCGA-37-3789 TCGA-37-4130 TCGA-37-4132 TCGA-37-4135 TCGA-37-4141 
         552           13          247          227          207           12 
TCGA-39-5011 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5031 TCGA-39-5035 
        1454         1361         1947         1996          833          474 
TCGA-39-5037 TCGA-43-2581 TCGA-43-3920 TCGA-43-6143 TCGA-43-7657 TCGA-43-7658 
        1086         1176         1007          376          236         1970 
TCGA-43-A56V TCGA-46-6025 TCGA-51-4079 TCGA-56-7221 TCGA-56-7222 TCGA-56-7579 
         366          324           12           30           13           44 
TCGA-56-7580 TCGA-56-7822 TCGA-56-8503 TCGA-56-8504 TCGA-56-8624 TCGA-56-8628 
          40            1           41          178           36           16 
TCGA-56-8629 TCGA-56-A4BW TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR TCGA-58-8390 
          34            2           25            4            4          911 
TCGA-60-2695 TCGA-60-2698 TCGA-60-2708 TCGA-60-2712 TCGA-60-2714 TCGA-60-2720 
         642          311         1963          274         1531           97 
TCGA-60-2721 TCGA-60-2723 TCGA-60-2724 TCGA-60-2726 TCGA-63-6202 TCGA-66-2742 
         983         1092          717          358         1973          641 
TCGA-66-2758 TCGA-66-2759 TCGA-66-2767 TCGA-66-2768 TCGA-66-2771 TCGA-66-2773 
         639          762           61           61          578         1946 
TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2793 TCGA-68-7757 TCGA-68-8250 
        1956          121         1954         1952          211          244 
TCGA-68-8251 TCGA-68-A59J TCGA-77-6844 TCGA-77-7139 TCGA-77-7141 TCGA-77-7338 
          96          104         1942         1968           15         1952 
TCGA-77-7465 TCGA-77-8008 TCGA-77-8009 TCGA-77-8133 TCGA-77-8138 TCGA-77-8140 
         479         1945         1641         1941         1946         1962 
TCGA-77-8144 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-A5G6 TCGA-77-A5G8 
         833          293         1961         1684         1955         1290 
TCGA-77-A5GA TCGA-77-A5GF TCGA-85-6561 TCGA-85-7696 TCGA-85-7699 TCGA-85-7843 
        1280          839          395           18            1           35 
TCGA-85-8048 TCGA-85-8277 TCGA-85-8288 TCGA-85-8352 TCGA-85-8353 TCGA-85-8479 
          26           11           54           67           54           22 
TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A510 TCGA-85-A5B5 TCGA-90-7964 TCGA-90-A59Q 
        1960           25         1967          111          428          269 
TCGA-96-7545 TCGA-98-8023 TCGA-MF-A522 TCGA-NC-A5HE TCGA-NC-A5HG 
        1344          308           83         1722         1548 

$`11P LOSS WILD-TYPE`
TCGA-18-3407 TCGA-18-3408 TCGA-18-3410 TCGA-18-3411 TCGA-18-3415 TCGA-18-3416 
         136         2464          146         1415         1810          862 
TCGA-18-3419 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 
          50          187           85         2754           92          827 
TCGA-21-1070 TCGA-21-1072 TCGA-21-1075 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 
        3636         3016         2134         1058          474          965 
TCGA-21-1081 TCGA-21-5784 TCGA-21-A5DI TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 
         284         1268          979          608          223         1945 
TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-4591 TCGA-22-4594 
        1952           53          429          822          623         1470 
TCGA-22-4595 TCGA-22-4599 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-4613 
         734         1161          399         1946          587          358 
TCGA-22-5472 TCGA-22-5474 TCGA-22-5480 TCGA-22-5482 TCGA-22-5485 TCGA-22-5489 
        1964          445         1952          357          916         1912 
TCGA-22-5491 TCGA-22-5492 TCGA-33-4532 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 
        1713          506         2524         5287         1966         1941 
TCGA-33-4586 TCGA-33-4589 TCGA-33-6738 TCGA-34-2604 TCGA-34-2608 TCGA-34-2609 
         428         1948          822          958         1000          951 
TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-8454 
        1715          707          365          428          941          166 
TCGA-37-3783 TCGA-37-3792 TCGA-37-4129 TCGA-37-4133 TCGA-37-5819 TCGA-39-5016 
         120           12          200          238          103         2253 
TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5034 
        1964         1849           52          740           59         1107 
TCGA-39-5036 TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 TCGA-43-2578 TCGA-43-3394 
        1084          544         1964         1223          684          822 
TCGA-43-5668 TCGA-43-5670 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-7656 
         349          849          757          310         1936          212 
TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U 
         407          358         1971          353          296          432 
TCGA-46-6026 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 
         423           12          911          541         1948          923 
TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 
        1958         1967          881            3          555           62 
TCGA-56-6546 TCGA-56-7223 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-8622 
          26           30           26            6         1961           55 
TCGA-56-8625 TCGA-56-8626 TCGA-56-A49D TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A5DS 
          63           17           38           46           30            8 
TCGA-58-8388 TCGA-58-8391 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46L TCGA-58-A46M 
         378         2167         1058         2589         1723         1072 
TCGA-58-A46N TCGA-60-2696 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 
         910          109         1950         1943         1958          661 
TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 TCGA-60-2713 TCGA-60-2715 TCGA-60-2716 
        1505         1963         1260         1731         1075         1475 
TCGA-60-2719 TCGA-60-2722 TCGA-60-2725 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 
        1297          908          816         1957         1955         1947 
TCGA-63-7023 TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2744 TCGA-66-2753 
        1952         1967         1311           61           30           31 
TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2763 TCGA-66-2765 
          61           28           30           30           30           61 
TCGA-66-2766 TCGA-66-2769 TCGA-66-2770 TCGA-66-2777 TCGA-66-2778 TCGA-66-2783 
          31         1947          700           61          578          759 
TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 
          60          790         1217          699         1955          699 
TCGA-66-2791 TCGA-66-2792 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 
        1977          913         1645          122         1492           83 
TCGA-68-7756 TCGA-68-A59I TCGA-77-6842 TCGA-77-6843 TCGA-77-6845 TCGA-77-7138 
         202          121         1950         1941         1952         1959 
TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7463 TCGA-77-8007 TCGA-77-8128 
        1286         1954         1942         1954         1960         1953 
TCGA-77-8130 TCGA-77-8131 TCGA-77-8136 TCGA-77-8139 TCGA-77-8145 TCGA-77-8154 
        1945         1941         1947         1951         1943         1092 
TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G7 TCGA-77-A5GB 
          10         1953         1942         1959         1963         1939 
TCGA-77-A5GH TCGA-85-6560 TCGA-85-6798 TCGA-85-7697 TCGA-85-7698 TCGA-85-7710 
         713          364           34           10           49         1965 
TCGA-85-7844 TCGA-85-7950 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 
         911           60           60           16          960          428 
TCGA-85-8072 TCGA-85-8276 TCGA-85-8287 TCGA-85-8350 TCGA-85-8351 TCGA-85-8354 
         513           13           13           60           55           61 
TCGA-85-8355 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8664 TCGA-85-8666 
          61           21          445          424            3          475 
TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A50M TCGA-85-A50Z TCGA-85-A511 TCGA-85-A512 
          15         1972           19         1973         1972         1987 
TCGA-85-A513 TCGA-85-A53L TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 
          24           13          758          289           89          358 
TCGA-90-A4ED TCGA-90-A4EE TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 
         244          331           82          106          122          160 
TCGA-92-8065 TCGA-94-7033 TCGA-94-7943 TCGA-94-A4VJ TCGA-96-7544 TCGA-96-8169 
          70           87          356          430         1213          189 
TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 
         211          273          183          256          413          224 
TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-NC-A5HI 
         222           35          449           36         1135 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 1                  3 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              3724               5287 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               639                684 
[1] "1.0 - 3724.0 (639.0)" "3.0 - 5287.0 (684.0)"
[1] "hr=" "1.1"
D61V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  11P LOSS MUTATED         0       22       51        0        18        22
  11P LOSS WILD-TYPE       1       50       86        1        34        49
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  11P LOSS MUTATED           22          4        4
  11P LOSS WILD-TYPE         35         16        2
D61V3, multiclass
            clus
vv           11P LOSS MUTATED 11P LOSS WILD-TYPE
  STAGE I                   0                  1
  STAGE IA                 22                 50
  STAGE IB                 51                 86
  STAGE II                  0                  1
  STAGE IIA                18                 34
  STAGE IIB                22                 49
  STAGE IIIA               22                 35
  STAGE IIIB                4                 16
  STAGE IV                  4                  2
[1] 9 2
[1] 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    31  93  17   5
  11P LOSS WILD-TYPE  67 161  31  15
D61V4, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  T1               31                 67
  T2               93                161
  T3               17                 31
  T4                5                 15
[1] 4 2
[1] 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    91  44   9   1
  11P LOSS WILD-TYPE 170  69  26   4
D61V5, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  N0               91                170
  N1               44                 69
  N2                9                 26
  N3                1                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A  MX
  11P LOSS MUTATED   124   4   0  14
  11P LOSS WILD-TYPE 234   1   1  36
D61V6, multiclass
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  M0               124                234
  M1                 4                  1
  M1A                0                  1
  MX                14                 36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V7, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    36 110
  11P LOSS WILD-TYPE  71 203
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     36  110
  11P LOSS WILD-TYPE   71  203
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE               36                 71
  MALE                110                203
[1] 2 2
[1] FALSE
D61V8, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  11P LOSS MUTATED                                       4
  11P LOSS WILD-TYPE                                     8
                    vv
clus                 LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  11P LOSS MUTATED                                        1
  11P LOSS WILD-TYPE                                      5
                    vv
clus                 LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  11P LOSS MUTATED                                         1
  11P LOSS WILD-TYPE                                       0
                    vv
clus                 LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  11P LOSS MUTATED                                                           140
  11P LOSS WILD-TYPE                                                         261
D61V9, multiclass
                                                             clus
vv                                                            11P LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      4
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              140
                                                             clus
vv                                                            11P LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                        8
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                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"
D61V10, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     5 141
  11P LOSS WILD-TYPE   8 266
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      5  141
  11P LOSS WILD-TYPE    8  266
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  NO                 5                  8
  YES              141                266
[1] 2 2
[1] FALSE
D61V11, continuous
                    vv
clus                  R0  R1  R2  RX
  11P LOSS MUTATED   124   2   1   3
  11P LOSS WILD-TYPE 218   6   3  15
D61V12, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  R0              124                218
  R1                2                  6
  R2                1                  3
  RX                3                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11P LOSS MUTATED       1                         8   106
  11P LOSS WILD-TYPE     8                         9   192
D61V13, multiclass
                           clus
vv                          11P LOSS MUTATED 11P LOSS WILD-TYPE
  ASIAN                                    1                  8
  BLACK OR AFRICAN AMERICAN                8                  9
  WHITE                                  106                192
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V14, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     2  94
  11P LOSS WILD-TYPE   6 173
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      2   94
  11P LOSS WILD-TYPE    6  173
                        clus
vv                       11P LOSS MUTATED 11P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  6
  NOT HISPANIC OR LATINO               94                173
[1] 2 2
[1] FALSE

Clustering(62) Variable = 11Q LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                  0   1
  11Q LOSS MUTATED    80  33
  11Q LOSS WILD-TYPE 185  90
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               113                275 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                33                 90 
$`11Q LOSS MUTATED`
TCGA-18-3406 TCGA-18-3409 TCGA-18-3412 TCGA-18-3414 TCGA-18-3417 TCGA-18-3421 
         370         2417          345          396          758         1331 
TCGA-21-1076 TCGA-21-1080 TCGA-21-1083 TCGA-21-5787 TCGA-22-1002 TCGA-22-1011 
        1852         3724          267          329          131           53 
TCGA-22-4593 TCGA-22-4601 TCGA-22-5473 TCGA-22-5477 TCGA-22-5478 TCGA-33-4533 
        1067         1057         1933         1346           24         1940 
TCGA-33-4589 TCGA-34-2596 TCGA-34-2600 TCGA-34-2605 TCGA-34-5232 TCGA-34-5928 
        1948           80         1874          881         2062          552 
TCGA-37-3789 TCGA-37-4130 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 
          13          247         2253         1361         1947         1996 
TCGA-39-5027 TCGA-39-5031 TCGA-39-5037 TCGA-43-2581 TCGA-43-3920 TCGA-43-7657 
        1849          833         1086         1176         1007          236 
TCGA-43-7658 TCGA-43-8116 TCGA-43-A474 TCGA-43-A56V TCGA-46-6025 TCGA-46-6026 
        1970          358          353          366          324          423 
TCGA-51-4079 TCGA-52-7809 TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 TCGA-56-7580 
          12         1948           30           13           30           40 
TCGA-56-7822 TCGA-56-8504 TCGA-56-8624 TCGA-56-8629 TCGA-56-A4BW TCGA-56-A4BX 
           1          178           36           34            2           46 
TCGA-56-A4ZK TCGA-58-8390 TCGA-60-2695 TCGA-60-2698 TCGA-60-2708 TCGA-60-2712 
           4          911          642          311         1963          274 
TCGA-60-2714 TCGA-60-2722 TCGA-60-2723 TCGA-60-2725 TCGA-60-2726 TCGA-66-2758 
        1531          908         1092          816          358          639 
TCGA-66-2767 TCGA-66-2768 TCGA-66-2790 TCGA-66-2793 TCGA-68-8250 TCGA-68-8251 
          61           61          699         1952          244           96 
TCGA-68-A59J TCGA-77-7139 TCGA-77-7338 TCGA-77-7465 TCGA-77-8008 TCGA-77-8009 
         104         1968         1952          479         1945         1641 
TCGA-77-8130 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8144 TCGA-77-8148 
        1945         1941         1947         1946          833          293 
TCGA-77-8150 TCGA-77-8153 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5GF TCGA-85-6561 
        1961         1684         1959         1955          839          395 
TCGA-85-6798 TCGA-85-7696 TCGA-85-7699 TCGA-85-8048 TCGA-85-8072 TCGA-85-8277 
          34           18            1           26          513           11 
TCGA-85-8352 TCGA-85-8479 TCGA-85-8664 TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A511 
          67           22            3         1960           25         1972 
TCGA-85-A5B5 TCGA-90-7766 TCGA-90-7964 TCGA-90-A59Q TCGA-92-7341 TCGA-96-7545 
         111          289          428          269          106         1344 
TCGA-96-A4JL TCGA-98-8023 TCGA-MF-A522 TCGA-NC-A5HE TCGA-NC-A5HG 
         183          308           83         1722         1548 

$`11Q LOSS WILD-TYPE`
TCGA-18-3407 TCGA-18-3408 TCGA-18-3410 TCGA-18-3411 TCGA-18-3415 TCGA-18-3416 
         136         2464          146         1415         1810          862 
TCGA-18-3419 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 
          50          187           85         2754           92          827 
TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 TCGA-21-1077 TCGA-21-1078 
        3636         1426         3016         2134         1058          474 
TCGA-21-1079 TCGA-21-1081 TCGA-21-1082 TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 
         965          284         3644          962         1268         1032 
TCGA-21-A5DI TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1005 TCGA-22-1012 
         979          608          223         1945         1952          429 
TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 TCGA-22-4594 TCGA-22-4595 TCGA-22-4596 
         822         1485          623         1470          734           17 
TCGA-22-4599 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-4613 TCGA-22-5471 
        1161          399         1946          587          358          965 
TCGA-22-5472 TCGA-22-5474 TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 
        1964          445         1651         1952         1952          357 
TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 
         573          916         1912         1713          506           29 
TCGA-33-4532 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 
        2524         2979         1311         5287         1966         1941 
TCGA-33-4586 TCGA-33-4587 TCGA-33-6738 TCGA-34-2604 TCGA-34-2608 TCGA-34-2609 
         428         1970          822          958         1000          951 
TCGA-34-5231 TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 
        1528         1715          707          365          428          941 
TCGA-34-8454 TCGA-37-3783 TCGA-37-3792 TCGA-37-4129 TCGA-37-4132 TCGA-37-4133 
         166          120           12          200          227          238 
TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5011 TCGA-39-5024 TCGA-39-5028 
         207           12          103         1454         1964           52 
TCGA-39-5029 TCGA-39-5030 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5039 
         740           59         1107          474         1084          544 
TCGA-39-5040 TCGA-43-2576 TCGA-43-2578 TCGA-43-3394 TCGA-43-5668 TCGA-43-5670 
        1964         1223          684          822          349          849 
TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-7656 TCGA-43-8115 
         376          757          310         1936          212          407 
TCGA-43-8118 TCGA-43-A475 TCGA-43-A56U TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 
        1971          296          432           12          911          541 
TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 
         923         1958         1967          881            3          555 
TCGA-56-6545 TCGA-56-6546 TCGA-56-7579 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 
          62           26           44           26            6         1961 
TCGA-56-8503 TCGA-56-8622 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-A49D 
          41           55           63           17           16           38 
TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8388 TCGA-58-8391 
          30           25            4            8          378         2167 
TCGA-58-8393 TCGA-58-A46J TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2696 
        1058         2589         1723         1072          910          109 
TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2709 TCGA-60-2710 
        1950         1943         1958          661         1505         1963 
TCGA-60-2711 TCGA-60-2713 TCGA-60-2715 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 
        1260         1731         1075         1475         1297           97 
TCGA-60-2721 TCGA-60-2724 TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 
         983          717         1973         1957         1955         1947 
TCGA-63-7023 TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 
        1952         1967         1311           61          641           30 
TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2759 
          31           61           28           30           30          762 
TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 
          30           61           31         1947          700          578 
TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 
        1946           61          578         1956          121         1954 
TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 
         759           60          790         1217          699         1955 
TCGA-66-2791 TCGA-66-2792 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 
        1977          913         1645          122         1492           83 
TCGA-68-7756 TCGA-68-7757 TCGA-68-A59I TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 
         202          211          121         1950         1941         1942 
TCGA-77-6845 TCGA-77-7138 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 
        1952         1959           15         1286         1954         1942 
TCGA-77-7463 TCGA-77-8007 TCGA-77-8128 TCGA-77-8131 TCGA-77-8139 TCGA-77-8140 
        1954         1960         1953         1941         1951         1962 
TCGA-77-8145 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G7 
        1943         1092           10         1953         1942         1963 
TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GH TCGA-85-6560 TCGA-85-7697 
        1290         1280         1939          713          364           10 
TCGA-85-7698 TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 TCGA-85-8049 
          49         1965           35          911           60           60 
TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8276 TCGA-85-8287 TCGA-85-8288 
          16          960          428           13           13           54 
TCGA-85-8350 TCGA-85-8351 TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 TCGA-85-8481 
          60           55           54           61           61           21 
TCGA-85-8580 TCGA-85-8582 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A50M 
         445          424          475           15         1972           19 
TCGA-85-A50Z TCGA-85-A510 TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L TCGA-90-6837 
        1973         1967         1987           24           13          758 
TCGA-90-7767 TCGA-90-7769 TCGA-90-A4ED TCGA-90-A4EE TCGA-92-7340 TCGA-92-8063 
          89          358          244          331           82          122 
TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 TCGA-94-7943 TCGA-94-A4VJ TCGA-96-7544 
         160           70           87          356          430         1213 
TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 
         189          211          273          256          413          224 
TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-NC-A5HI 
         222           35          449           36         1135 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 1                  3 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              3724               5287 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               479                700 
[1] "1.0 - 3724.0 (479.0)" "3.0 - 5287.0 (700.0)"
[1] "hr=" "1"  
D62V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  11Q LOSS MUTATED         0       16       39        0        17        23
  11Q LOSS WILD-TYPE       1       56       98        1        35        48
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  11Q LOSS MUTATED           17          4        2
  11Q LOSS WILD-TYPE         40         16        4
D62V3, multiclass
            clus
vv           11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  STAGE I                   0                  1
  STAGE IA                 16                 56
  STAGE IB                 39                 98
  STAGE II                  0                  1
  STAGE IIA                17                 35
  STAGE IIB                23                 48
  STAGE IIIA               17                 40
  STAGE IIIB                4                 16
  STAGE IV                  2                  4
[1] 9 2
[1] 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    22  82  12   5
  11Q LOSS WILD-TYPE  76 172  36  15
D62V4, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T1               22                 76
  T2               82                172
  T3               12                 36
  T4                5                 15
[1] 4 2
[1] 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    68  44   7   1
  11Q LOSS WILD-TYPE 193  69  28   4
D62V5, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  N0               68                193
  N1               44                 69
  N2                7                 28
  N3                1                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A  MX
  11Q LOSS MUTATED   101   2   0  14
  11Q LOSS WILD-TYPE 257   3   1  36
D62V6, multiclass
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  M0               101                257
  M1                 2                  3
  M1A                0                  1
  MX                14                 36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V7, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    25  96
  11Q LOSS WILD-TYPE  82 217
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     25   96
  11Q LOSS WILD-TYPE   82  217
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE               25                 82
  MALE                 96                217
[1] 2 2
[1] FALSE
D62V8, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  11Q LOSS MUTATED                                       5
  11Q LOSS WILD-TYPE                                     7
                    vv
clus                 LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  11Q LOSS MUTATED                                        1
  11Q LOSS WILD-TYPE                                      5
                    vv
clus                 LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  11Q LOSS MUTATED                                         0
  11Q LOSS WILD-TYPE                                       1
                    vv
clus                 LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  11Q LOSS MUTATED                                                           115
  11Q LOSS WILD-TYPE                                                         286
D62V9, multiclass
                                                             clus
vv                                                            11Q LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      5
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              115
                                                             clus
vv                                                            11Q LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                        7
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                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"
D62V10, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     4 117
  11Q LOSS WILD-TYPE   9 290
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      4  117
  11Q LOSS WILD-TYPE    9  290
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  NO                 4                  9
  YES              117                290
[1] 2 2
[1] FALSE
D62V11, continuous
                    vv
clus                  R0  R1  R2  RX
  11Q LOSS MUTATED   102   2   1   1
  11Q LOSS WILD-TYPE 240   6   3  17
D62V12, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  R0              102                240
  R1                2                  6
  R2                1                  3
  RX                1                 17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11Q LOSS MUTATED       2                         8    88
  11Q LOSS WILD-TYPE     7                         9   210
D62V13, multiclass
                           clus
vv                          11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  ASIAN                                    2                  7
  BLACK OR AFRICAN AMERICAN                8                  9
  WHITE                                   88                210
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V14, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     2  82
  11Q LOSS WILD-TYPE   6 185
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      2   82
  11Q LOSS WILD-TYPE    6  185
                        clus
vv                       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  6
  NOT HISPANIC OR LATINO               82                185
[1] 2 2
[1] FALSE

Clustering(63) Variable = 12P LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                  0   1
  12P LOSS MUTATED    21  11
  12P LOSS WILD-TYPE 244 112
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                32                356 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                11                112 
$`12P LOSS MUTATED`
TCGA-18-3407 TCGA-22-1016 TCGA-22-5478 TCGA-33-4533 TCGA-33-4587 TCGA-34-2604 
         136          822           24         1940         1970          958 
TCGA-37-4129 TCGA-37-4130 TCGA-37-4141 TCGA-39-5011 TCGA-43-2581 TCGA-43-5668 
         200          247           12         1454         1176          349 
TCGA-43-6143 TCGA-43-8118 TCGA-56-5898 TCGA-56-7579 TCGA-56-8624 TCGA-56-A49D 
         376         1971          555           44           36           38 
TCGA-56-A4ZK TCGA-60-2722 TCGA-66-2773 TCGA-77-7138 TCGA-77-8008 TCGA-77-8150 
           4          908         1946         1959         1945         1961 
TCGA-77-8153 TCGA-77-A5GA TCGA-85-6798 TCGA-85-8353 TCGA-85-8479 TCGA-85-A50M 
        1684         1280           34           54           22           19 
TCGA-85-A5B5 TCGA-90-A4ED 
         111          244 

$`12P LOSS WILD-TYPE`
TCGA-18-3406 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 TCGA-18-3412 
         370         2464         2417          146         1415          345 
TCGA-18-3414 TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 
         396         1810          862          758           50         1331 
TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1070 
         187           85         2754           92          827         3636 
TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 
        1426         3016         2134         1852         1058          474 
TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 
         965         3724          284         3644          267          962 
TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-21-A5DI TCGA-22-0940 TCGA-22-0944 
        1268         1032          329          979          608          223 
TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1017 
        1945          131         1952           53          429         1485 
TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 
         623         1067         1470          734           17         1161 
TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-4613 TCGA-22-5471 
        1057          399         1946          587          358          965 
TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5479 TCGA-22-5480 
        1964         1933          445         1346         1651         1952 
TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 
        1952          357          573          916         1912         1713 
TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 
         506           29         2524         2979         1311         5287 
TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-4589 TCGA-33-6738 TCGA-34-2596 
        1966         1941          428         1948          822           80 
TCGA-34-2600 TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 
        1874          881         1000          951         1528         2062 
TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 
        1715          707          365          428          941          552 
TCGA-34-8454 TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4132 TCGA-37-4133 
         166          120           13           12          227          238 
TCGA-37-4135 TCGA-37-5819 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 
         207          103         2253         1361         1947         1996 
TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 
        1964         1849           52          740           59          833 
TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 TCGA-39-5040 
        1107          474         1084         1086          544         1964 
TCGA-43-2576 TCGA-43-2578 TCGA-43-3394 TCGA-43-3920 TCGA-43-5670 TCGA-43-6647 
        1223          684          822         1007          849          757 
TCGA-43-6770 TCGA-43-6771 TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 
         310         1936          212          236         1970          407 
TCGA-43-8116 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V TCGA-46-6025 
         358          353          296          432          366          324 
TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 
         423           12           12          911          541         1948 
TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-6545 
         923         1958         1967          881            3           62 
TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 TCGA-56-7580 TCGA-56-7582 
          26           30           13           30           40           26 
TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 
           6         1961            1           41          178           55 
TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A4BW TCGA-56-A4BX 
          63           17           16           34            2           46 
TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8388 TCGA-58-8390 
          30           25            4            8          378          911 
TCGA-58-8391 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N 
        2167         1058         2589         1723         1072          910 
TCGA-60-2695 TCGA-60-2696 TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 
         642          109          311         1950         1943         1958 
TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 
         661         1963         1505         1963         1260          274 
TCGA-60-2713 TCGA-60-2714 TCGA-60-2715 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 
        1731         1531         1075         1475         1297           97 
TCGA-60-2721 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 
         983         1092          717          816          358         1973 
TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 TCGA-66-2727 TCGA-66-2734 
        1957         1955         1947         1952         1967         1311 
TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 
          61          641           30           31           61           28 
TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 
          30           30          639          762           30           61 
TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 
          31           61           61         1947          700          578 
TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 
          61          578         1956          121         1954          759 
TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 
          60          790         1217          699         1955          699 
TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 
        1977          913         1952         1645          122         1492 
TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I 
          83          202          211          244           96          121 
TCGA-68-A59J TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7139 
         104         1950         1941         1942         1952         1968 
TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 
          15         1286         1954         1942         1952         1954 
TCGA-77-7465 TCGA-77-8007 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 
         479         1960         1641         1953         1945         1941 
TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8144 
        1941         1947         1946         1951         1962          833 
TCGA-77-8145 TCGA-77-8148 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 
        1943          293         1092           10         1953         1942 
TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GB TCGA-77-A5GF 
        1959         1955         1963         1290         1939          839 
TCGA-77-A5GH TCGA-85-6560 TCGA-85-6561 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 
         713          364          395           18           10           49 
TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 
           1         1965           35          911           60           26 
TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 
          60           16          960          428          513           13 
TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 
          11           13           54           60           55           67 
TCGA-85-8354 TCGA-85-8355 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8664 
          61           61           21          445          424            3 
TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50Z 
         475           15         1972         1960           25         1973 
TCGA-85-A510 TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L TCGA-90-6837 
        1967         1972         1987           24           13          758 
TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 TCGA-90-7964 TCGA-90-A4EE TCGA-90-A59Q 
         289           89          358          428          331          269 
TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 
          82          106          122          160           70           87 
TCGA-94-7943 TCGA-94-A4VJ TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 
         356          430         1213         1344          189          211 
TCGA-96-A4JK TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 
         273          183          256          413          224          308 
TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HE 
         222           35          449           36           83         1722 
TCGA-NC-A5HG TCGA-NC-A5HI 
        1548         1135 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 4                  1 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              1971               5287 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             362.5              672.5 
[1] "4.0 - 1971.0 (362.5)" "1.0 - 5287.0 (672.5)"
[1] "hr=" "1.3"
D63V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  12P LOSS MUTATED         0        6       16        0         2         3
  12P LOSS WILD-TYPE       1       66      121        1        50        68
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  12P LOSS MUTATED            5          1        0
  12P LOSS WILD-TYPE         52         19        6
D63V3, multiclass
            clus
vv           12P LOSS MUTATED 12P LOSS WILD-TYPE
  STAGE I                   0                  1
  STAGE IA                  6                 66
  STAGE IB                 16                121
  STAGE II                  0                  1
  STAGE IIA                 2                 50
  STAGE IIB                 3                 68
  STAGE IIIA                5                 52
  STAGE IIIB                1                 19
  STAGE IV                  0                  6
[1] 9 2
[1] 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     9  17   7   0
  12P LOSS WILD-TYPE  89 237  41  20
D63V4, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  T1                9                 89
  T2               17                237
  T3                7                 41
  T4                0                 20
[1] 4 2
[1] 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    25   7   1   0
  12P LOSS WILD-TYPE 236 106  34   5
D63V5, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  N0               25                236
  N1                7                106
  N2                1                 34
  N3                0                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A  MX
  12P LOSS MUTATED    29   0   0   4
  12P LOSS WILD-TYPE 329   5   1  46
D63V6, multiclass
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  M0                29                329
  M1                 0                  5
  M1A                0                  1
  MX                 4                 46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V7, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    10  23
  12P LOSS WILD-TYPE  97 290
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     10   23
  12P LOSS WILD-TYPE   97  290
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE               10                 97
  MALE                 23                290
[1] 2 2
[1] FALSE
D63V8, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  12P LOSS MUTATED                                       1
  12P LOSS WILD-TYPE                                    11
                    vv
clus                 LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  12P LOSS MUTATED                                        1
  12P LOSS WILD-TYPE                                      5
                    vv
clus                 LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  12P LOSS MUTATED                                         1
  12P LOSS WILD-TYPE                                       0
                    vv
clus                 LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  12P LOSS MUTATED                                                            30
  12P LOSS WILD-TYPE                                                         371
D63V9, multiclass
                                                             clus
vv                                                            12P LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               30
                                                             clus
vv                                                            12P LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       11
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                371
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V10, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     0  33
  12P LOSS WILD-TYPE  13 374
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      0   33
  12P LOSS WILD-TYPE   13  374
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  NO                 0                 13
  YES               33                374
[1] 2 2
[1] FALSE
D63V11, continuous
                    vv
clus                  R0  R1  R2  RX
  12P LOSS MUTATED    28   1   0   1
  12P LOSS WILD-TYPE 314   7   4  17
D63V12, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  R0               28                314
  R1                1                  7
  R2                0                  4
  RX                1                 17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12P LOSS MUTATED       2                         1    23
  12P LOSS WILD-TYPE     7                        16   275
D63V13, multiclass
                           clus
vv                          12P LOSS MUTATED 12P LOSS WILD-TYPE
  ASIAN                                    2                  7
  BLACK OR AFRICAN AMERICAN                1                 16
  WHITE                                   23                275
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V14, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     0  25
  12P LOSS WILD-TYPE   8 242
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      0   25
  12P LOSS WILD-TYPE    8  242
                        clus
vv                       12P LOSS MUTATED 12P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  8
  NOT HISPANIC OR LATINO               25                242
[1] 2 2
[1] FALSE

Clustering(64) Variable = 12Q LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                  0   1
  12Q LOSS MUTATED    26  13
  12Q LOSS WILD-TYPE 239 110
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                39                349 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                13                110 
$`12Q LOSS MUTATED`
TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-22-4595 TCGA-22-5478 TCGA-33-4533 
         136         2464         2417          734           24         1940 
TCGA-33-4587 TCGA-34-2604 TCGA-37-4129 TCGA-37-4141 TCGA-43-2581 TCGA-43-5668 
        1970          958          200           12         1176          349 
TCGA-43-6143 TCGA-43-8118 TCGA-43-A56V TCGA-51-4081 TCGA-52-7810 TCGA-56-5898 
         376         1971          366          911          923          555 
TCGA-56-8624 TCGA-56-A49D TCGA-60-2703 TCGA-60-2722 TCGA-60-2723 TCGA-66-2773 
          36           38         1950          908         1092         1946 
TCGA-68-8250 TCGA-77-7138 TCGA-77-8007 TCGA-77-8008 TCGA-77-8131 TCGA-77-8153 
         244         1959         1960         1945         1941         1684 
TCGA-77-A5GA TCGA-85-6560 TCGA-85-6798 TCGA-85-7696 TCGA-85-8479 TCGA-85-A50M 
        1280          364           34           18           22           19 
TCGA-90-A4ED TCGA-94-A4VJ TCGA-MF-A522 
         244          430           83 

$`12Q LOSS WILD-TYPE`
TCGA-18-3406 TCGA-18-3410 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 
         370          146         1415          345          396         1810 
TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 
         862          758           50         1331          187           85 
TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 
        2754           92          827         3636         1426         3016 
TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 
        2134         1852         1058          474          965         3724 
TCGA-21-1081 TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 
         284         3644          267          962         1268         1032 
TCGA-21-5787 TCGA-21-A5DI TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 
         329          979          608          223         1945          131 
TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 
        1952           53          429          822         1485          623 
TCGA-22-4593 TCGA-22-4594 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 
        1067         1470           17         1161         1057          399 
TCGA-22-4605 TCGA-22-4607 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 
        1946          587          358          965         1964         1933 
TCGA-22-5474 TCGA-22-5477 TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 
         445         1346         1651         1952         1952          357 
TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 
         573          916         1912         1713          506           29 
TCGA-33-4532 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 
        2524         2979         1311         5287         1966         1941 
TCGA-33-4586 TCGA-33-4589 TCGA-33-6738 TCGA-34-2596 TCGA-34-2600 TCGA-34-2605 
         428         1948          822           80         1874          881 
TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 
        1000          951         1528         2062         1715          707 
TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-8454 TCGA-37-3783 
         365          428          941          552          166          120 
TCGA-37-3789 TCGA-37-3792 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 
          13           12          247          227          238          207 
TCGA-37-5819 TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 
         103         1454         2253         1361         1947         1996 
TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 
        1964         1849           52          740           59          833 
TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 TCGA-39-5040 
        1107          474         1084         1086          544         1964 
TCGA-43-2576 TCGA-43-2578 TCGA-43-3394 TCGA-43-3920 TCGA-43-5670 TCGA-43-6647 
        1223          684          822         1007          849          757 
TCGA-43-6770 TCGA-43-6771 TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 
         310         1936          212          236         1970          407 
TCGA-43-8116 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U TCGA-46-6025 TCGA-46-6026 
         358          353          296          432          324          423 
TCGA-51-4079 TCGA-51-4080 TCGA-52-7622 TCGA-52-7809 TCGA-52-7811 TCGA-52-7812 
          12           12          541         1948         1958         1967 
TCGA-56-1622 TCGA-56-5897 TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 
         881            3           62           26           30           13 
TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 
          30           44           40           26            6         1961 
TCGA-56-7822 TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 TCGA-56-8625 TCGA-56-8626 
           1           41          178           55           63           17 
TCGA-56-8628 TCGA-56-8629 TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ 
          16           34            2           46           30           25 
TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 
           4            4            8          378          911         2167 
TCGA-58-8393 TCGA-58-A46J TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 
        1058         2589         1723         1072          910          642 
TCGA-60-2696 TCGA-60-2698 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 
         109          311         1943         1958          661         1963 
TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 
        1505         1963         1260          274         1731         1531 
TCGA-60-2715 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2724 
        1075         1475         1297           97          983          717 
TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 
         816          358         1973         1957         1955         1947 
TCGA-63-7023 TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 
        1952         1967         1311           61          641           30 
TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 
          31           61           28           30           30          639 
TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 
         762           30           61           31           61           61 
TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 
        1947          700          578           61          578         1956 
TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 
         121         1954          759           60          790         1217 
TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 
         699         1955          699         1977          913         1952 
TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 
        1645          122         1492           83          202          211 
TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 
          96          121          104         1950         1941         1942 
TCGA-77-6845 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 
        1952         1968           15         1286         1954         1942 
TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 
        1952         1954          479         1641         1953         1945 
TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8144 
        1941         1947         1946         1951         1962          833 
TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ 
        1943          293         1961         1092           10         1953 
TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GB 
        1942         1959         1955         1963         1290         1939 
TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6561 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 
         839          713          395           10           49            1 
TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 
        1965           35          911           60           26           60 
TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 
          16          960          428          513           13           11 
TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 
          13           54           60           55           67           54 
TCGA-85-8354 TCGA-85-8355 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8664 
          61           61           21          445          424            3 
TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50Z 
         475           15         1972         1960           25         1973 
TCGA-85-A510 TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 
        1967         1972         1987           24           13          111 
TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 TCGA-90-7964 TCGA-90-A4EE 
         758          289           89          358          428          331 
TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 
         269           82          106          122          160           70 
TCGA-94-7033 TCGA-94-7943 TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 
          87          356         1213         1344          189          211 
TCGA-96-A4JK TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 
         273          183          256          413          224          308 
TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-NC-A5HE TCGA-NC-A5HG 
         222           35          449           36         1722         1548 
TCGA-NC-A5HI 
        1135 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                12                  1 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
              2464               5287 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
               734                641 
[1] "12.0 - 2464.0 (734.0)" "1.0 - 5287.0 (641.0)" 
[1] "hr=" "1"  
D64V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  12Q LOSS MUTATED         0        6       18        0         3         7
  12Q LOSS WILD-TYPE       1       66      119        1        49        64
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  12Q LOSS MUTATED            4          1        0
  12Q LOSS WILD-TYPE         53         19        6
D64V3, multiclass
            clus
vv           12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  STAGE I                   0                  1
  STAGE IA                  6                 66
  STAGE IB                 18                119
  STAGE II                  0                  1
  STAGE IIA                 3                 49
  STAGE IIB                 7                 64
  STAGE IIIA                4                 53
  STAGE IIIB                1                 19
  STAGE IV                  0                  6
[1] 9 2
[1] 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    11  23   6   0
  12Q LOSS WILD-TYPE  87 231  42  20
D64V4, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  T1               11                 87
  T2               23                231
  T3                6                 42
  T4                0                 20
[1] 4 2
[1] 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    28   8   3   0
  12Q LOSS WILD-TYPE 233 105  32   5
D64V5, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  N0               28                233
  N1                8                105
  N2                3                 32
  N3                0                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A  MX
  12Q LOSS MUTATED    33   0   0   6
  12Q LOSS WILD-TYPE 325   5   1  44
D64V6, multiclass
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  M0                33                325
  M1                 0                  5
  M1A                0                  1
  MX                 6                 44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V7, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    12  28
  12Q LOSS WILD-TYPE  95 285
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     12   28
  12Q LOSS WILD-TYPE   95  285
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE               12                 95
  MALE                 28                285
[1] 2 2
[1] FALSE
D64V8, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  12Q LOSS MUTATED                                       2
  12Q LOSS WILD-TYPE                                    10
                    vv
clus                 LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  12Q LOSS MUTATED                                        1
  12Q LOSS WILD-TYPE                                      5
                    vv
clus                 LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  12Q LOSS MUTATED                                         1
  12Q LOSS WILD-TYPE                                       0
                    vv
clus                 LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  12Q LOSS MUTATED                                                            36
  12Q LOSS WILD-TYPE                                                         365
D64V9, multiclass
                                                             clus
vv                                                            12Q LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      2
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               36
                                                             clus
vv                                                            12Q LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       10
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                365
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V10, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     1  39
  12Q LOSS WILD-TYPE  12 368
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      1   39
  12Q LOSS WILD-TYPE   12  368
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  NO                 1                 12
  YES               39                368
[1] 2 2
[1] FALSE
D64V11, continuous
                    vv
clus                  R0  R1  R2  RX
  12Q LOSS MUTATED    31   0   0   1
  12Q LOSS WILD-TYPE 311   8   4  17
D64V12, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  R0               31                311
  R1                0                  8
  R2                0                  4
  RX                1                 17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12Q LOSS MUTATED       2                         3    26
  12Q LOSS WILD-TYPE     7                        14   272
D64V13, multiclass
                           clus
vv                          12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  ASIAN                                    2                  7
  BLACK OR AFRICAN AMERICAN                3                 14
  WHITE                                   26                272
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V14, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     0  28
  12Q LOSS WILD-TYPE   8 239
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      0   28
  12Q LOSS WILD-TYPE    8  239
                        clus
vv                       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  8
  NOT HISPANIC OR LATINO               28                239
[1] 2 2
[1] FALSE

Clustering(65) Variable = 13Q LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                  0   1
  13Q LOSS MUTATED   162  75
  13Q LOSS WILD-TYPE 103  48
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               237                151 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                75                 48 
$`13Q LOSS MUTATED`
TCGA-18-3409 TCGA-18-3410 TCGA-18-3415 TCGA-18-3416 TCGA-18-3419 TCGA-18-3421 
        2417          146         1810          862           50         1331 
TCGA-18-4083 TCGA-18-4721 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 
         187         2754         3636         1426         3016         2134 
TCGA-21-1076 TCGA-21-1080 TCGA-21-1083 TCGA-21-5786 TCGA-21-5787 TCGA-21-A5DI 
        1852         3724          267         1032          329          979 
TCGA-22-0940 TCGA-22-1002 TCGA-22-1011 TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 
         608          131           53          822         1485          623 
TCGA-22-4593 TCGA-22-4596 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 
        1067           17         1057          399         1946          587 
TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 TCGA-22-5477 TCGA-22-5478 
         358          965         1964         1933         1346           24 
TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5491 TCGA-22-5492 
        1952          357          573          916         1713          506 
TCGA-22-A5C4 TCGA-33-4538 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 
          29         2979         1966         1941          428         1970 
TCGA-33-4589 TCGA-33-6738 TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 
        1948          822           80         1874          958          881 
TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 TCGA-34-5928 TCGA-37-3792 
        1000          951         1528         2062          552           12 
TCGA-37-4129 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-5819 TCGA-39-5011 
         200          227          238          207          103         1454 
TCGA-39-5016 TCGA-39-5022 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 
        2253         1996           52          740           59          833 
TCGA-39-5036 TCGA-43-2578 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 
        1084          684         1176          822         1007          349 
TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-7656 TCGA-43-7658 TCGA-43-8115 
         376          757          310          212         1970          407 
TCGA-43-8116 TCGA-43-A474 TCGA-46-6025 TCGA-51-4079 TCGA-52-7622 TCGA-52-7809 
         358          353          324           12          541         1948 
TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-6546 TCGA-56-7222 TCGA-56-7579 
        1958         1967          881           26           13           44 
TCGA-56-7582 TCGA-56-7730 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 
          26            6           36           63           17           16 
TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BY TCGA-58-8390 TCGA-58-8391 TCGA-58-8393 
          34           38           30          911         2167         1058 
TCGA-58-A46J TCGA-58-A46M TCGA-60-2696 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 
        2589         1072          109         1950         1943         1958 
TCGA-60-2707 TCGA-60-2708 TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 
         661         1963         1963         1260          274         1731 
TCGA-60-2714 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 
        1531         1297           97          983          908         1092 
TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 
         717          816          358         1973         1957         1955 
TCGA-63-7022 TCGA-66-2727 TCGA-66-2734 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 
        1947         1967         1311           31           61           28 
TCGA-66-2756 TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2767 TCGA-66-2768 
          30          639          762           30           61           61 
TCGA-66-2771 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 
         578           61          578         1956          121         1954 
TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2790 
         759           60          790         1217          699          699 
TCGA-66-2792 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 
         913         1492           83          202          211          244 
TCGA-68-8251 TCGA-68-A59I TCGA-77-6842 TCGA-77-6844 TCGA-77-7139 TCGA-77-7141 
          96          121         1950         1942         1968           15 
TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 
        1954         1942         1952         1954          479         1960 
TCGA-77-8009 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8138 TCGA-77-8139 
        1641         1945         1941         1941         1946         1951 
TCGA-77-8144 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-A5G1 
         833          293         1961         1684         1092         1942 
TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GF 
        1959         1955         1963         1290         1280          839 
TCGA-85-6561 TCGA-85-7697 TCGA-85-7698 TCGA-85-7844 TCGA-85-7950 TCGA-85-8049 
         395           10           49          911           60           60 
TCGA-85-8070 TCGA-85-8071 TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 TCGA-85-8351 
         960          428           11           13           54           55 
TCGA-85-8352 TCGA-85-8353 TCGA-85-8580 TCGA-85-8664 TCGA-85-A4QR TCGA-85-A50Z 
          67           54          445            3           25         1973 
TCGA-85-A510 TCGA-85-A512 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-7766 TCGA-90-7767 
        1967         1987           13          111          289           89 
TCGA-90-7769 TCGA-90-7964 TCGA-90-A4EE TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 
         358          428          331           82          106          122 
TCGA-92-8064 TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 TCGA-96-A4JK TCGA-98-7454 
         160         1213         1344          189          273          256 
TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 
         413          224          308          222           35          449 
TCGA-NC-A5HE TCGA-NC-A5HG TCGA-NC-A5HI 
        1722         1548         1135 

$`13Q LOSS WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 
         370          136         2464         1415          345          396 
TCGA-18-3417 TCGA-18-4086 TCGA-18-5592 TCGA-18-5595 TCGA-21-1077 TCGA-21-1078 
         758           85           92          827         1058          474 
TCGA-21-1079 TCGA-21-1081 TCGA-21-1082 TCGA-21-5782 TCGA-21-5784 TCGA-22-0944 
         965          284         3644          962         1268          223 
TCGA-22-1000 TCGA-22-1005 TCGA-22-1012 TCGA-22-4594 TCGA-22-4595 TCGA-22-4599 
        1945         1952          429         1470          734         1161 
TCGA-22-5474 TCGA-22-5479 TCGA-22-5480 TCGA-22-5489 TCGA-33-4532 TCGA-33-4533 
         445         1651         1952         1912         2524         1940 
TCGA-33-4547 TCGA-33-4566 TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 
        1311         5287         1715          707          365          428 
TCGA-34-5927 TCGA-34-8454 TCGA-37-3783 TCGA-37-3789 TCGA-37-4130 TCGA-37-4141 
         941          166          120           13          247           12 
TCGA-39-5019 TCGA-39-5021 TCGA-39-5024 TCGA-39-5027 TCGA-39-5034 TCGA-39-5035 
        1361         1947         1964         1849         1107          474 
TCGA-39-5037 TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 TCGA-43-5670 TCGA-43-6771 
        1086          544         1964         1223          849         1936 
TCGA-43-7657 TCGA-43-8118 TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V TCGA-46-6026 
         236         1971          296          432          366          423 
TCGA-51-4080 TCGA-51-4081 TCGA-52-7810 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 
          12          911          923            3          555           62 
TCGA-56-7221 TCGA-56-7223 TCGA-56-7580 TCGA-56-7731 TCGA-56-7822 TCGA-56-8503 
          30           30           40         1961            1           41 
TCGA-56-8504 TCGA-56-8622 TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4ZJ TCGA-56-A4ZK 
         178           55            2           46           25            4 
TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8388 TCGA-58-A46L TCGA-58-A46N TCGA-60-2695 
           4            8          378         1723          910          642 
TCGA-60-2698 TCGA-60-2709 TCGA-60-2715 TCGA-60-2716 TCGA-63-7023 TCGA-66-2737 
         311         1505         1075         1475         1952           61 
TCGA-66-2742 TCGA-66-2744 TCGA-66-2757 TCGA-66-2765 TCGA-66-2766 TCGA-66-2769 
         641           30           30           61           31         1947 
TCGA-66-2770 TCGA-66-2773 TCGA-66-2789 TCGA-66-2791 TCGA-66-2793 TCGA-66-2794 
         700         1946         1955         1977         1952         1645 
TCGA-66-2795 TCGA-68-A59J TCGA-77-6843 TCGA-77-6845 TCGA-77-7138 TCGA-77-7142 
         122          104         1941         1952         1959         1286 
TCGA-77-8008 TCGA-77-8128 TCGA-77-8136 TCGA-77-8140 TCGA-77-8145 TCGA-77-8156 
        1945         1953         1947         1962         1943           10 
TCGA-77-A5FZ TCGA-77-A5GB TCGA-77-A5GH TCGA-85-6560 TCGA-85-6798 TCGA-85-7696 
        1953         1939          713          364           34           18 
TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 TCGA-85-8048 TCGA-85-8052 TCGA-85-8072 
           1         1965           35           26           16          513 
TCGA-85-8276 TCGA-85-8350 TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 
          13           60           61           61           22           21 
TCGA-85-8582 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50M 
         424          475           15         1972         1960           19 
TCGA-85-A511 TCGA-85-A513 TCGA-90-6837 TCGA-90-A4ED TCGA-90-A59Q TCGA-92-8065 
        1972           24          758          244          269           70 
TCGA-94-7033 TCGA-94-7943 TCGA-94-A4VJ TCGA-96-8170 TCGA-96-A4JL TCGA-LA-A446 
          87          356          430          211          183           36 
TCGA-MF-A522 
          83 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 3                  1 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              3724               5287 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               757                474 
[1] "3.0 - 3724.0 (757.0)" "1.0 - 5287.0 (474.0)"
[1] "hr=" "1.1"
D65V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  13Q LOSS MUTATED         1       42       80        1        34        46
  13Q LOSS WILD-TYPE       0       30       57        0        18        25
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  13Q LOSS MUTATED           37          9        2
  13Q LOSS WILD-TYPE         20         11        4
D65V3, multiclass
            clus
vv           13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  STAGE I                   1                  0
  STAGE IA                 42                 30
  STAGE IB                 80                 57
  STAGE II                  1                  0
  STAGE IIA                34                 18
  STAGE IIB                46                 25
  STAGE IIIA               37                 20
  STAGE IIIB                9                 11
  STAGE IV                  2                  4
[1] 9 2
[1] 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    59 160  26   9
  13Q LOSS WILD-TYPE  39  94  22  11
D65V4, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T1               59                 39
  T2              160                 94
  T3               26                 22
  T4                9                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  13Q LOSS MUTATED   153  74  21   3
  13Q LOSS WILD-TYPE 108  39  14   2
D65V5, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  N0              153                108
  N1               74                 39
  N2               21                 14
  N3                3                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A  MX
  13Q LOSS MUTATED   221   2   0  29
  13Q LOSS WILD-TYPE 137   3   1  21
D65V6, multiclass
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  M0               221                137
  M1                 2                  3
  M1A                0                  1
  MX                29                 21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V7, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    64 190
  13Q LOSS WILD-TYPE  43 123
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     64  190
  13Q LOSS WILD-TYPE   43  123
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE               64                 43
  MALE                190                123
[1] 2 2
[1] FALSE
D65V8, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  13Q LOSS MUTATED                                       6
  13Q LOSS WILD-TYPE                                     6
                    vv
clus                 LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  13Q LOSS MUTATED                                        0
  13Q LOSS WILD-TYPE                                      6
                    vv
clus                 LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  13Q LOSS MUTATED                                         1
  13Q LOSS WILD-TYPE                                       0
                    vv
clus                 LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  13Q LOSS MUTATED                                                           247
  13Q LOSS WILD-TYPE                                                         154
D65V9, multiclass
                                                             clus
vv                                                            13Q LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      6
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     0
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              247
                                                             clus
vv                                                            13Q LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                        6
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                154
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V10, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     8 246
  13Q LOSS WILD-TYPE   5 161
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      8  246
  13Q LOSS WILD-TYPE    5  161
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO                 8                  5
  YES              246                161
[1] 2 2
[1] FALSE
D65V11, continuous
                    vv
clus                  R0  R1  R2  RX
  13Q LOSS MUTATED   208   3   3  11
  13Q LOSS WILD-TYPE 134   5   1   7
D65V12, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  R0              208                134
  R1                3                  5
  R2                3                  1
  RX               11                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  13Q LOSS MUTATED       2                        11   179
  13Q LOSS WILD-TYPE     7                         6   119
D65V13, multiclass
                           clus
vv                          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  ASIAN                                    2                  7
  BLACK OR AFRICAN AMERICAN               11                  6
  WHITE                                  179                119
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V14, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     8 152
  13Q LOSS WILD-TYPE   0 115
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      8  152
  13Q LOSS WILD-TYPE    0  115
                        clus
vv                       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    8                  0
  NOT HISPANIC OR LATINO              152                115
[1] 2 2
[1] FALSE

Clustering(66) Variable = 14Q LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                  0   1
  14Q LOSS MUTATED    88  43
  14Q LOSS WILD-TYPE 177  80
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               131                257 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                43                 80 
$`14Q LOSS MUTATED`
TCGA-18-3410 TCGA-18-4083 TCGA-18-4086 TCGA-21-1071 TCGA-21-1083 TCGA-21-5784 
         146          187           85         1426          267         1268 
TCGA-22-0940 TCGA-22-1012 TCGA-22-1016 TCGA-22-4596 TCGA-22-4613 TCGA-22-5473 
         608          429          822           17          358         1933 
TCGA-22-5474 TCGA-22-5477 TCGA-22-5480 TCGA-22-5481 TCGA-22-5483 TCGA-22-5491 
         445         1346         1952         1952          573         1713 
TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 
        1941          428         1970           80         1874          958 
TCGA-34-2605 TCGA-34-5927 TCGA-34-5928 TCGA-37-4130 TCGA-37-4133 TCGA-37-4135 
         881          941          552          247          238          207 
TCGA-39-5016 TCGA-39-5021 TCGA-39-5024 TCGA-39-5030 TCGA-39-5035 TCGA-39-5040 
        2253         1947         1964           59          474         1964 
TCGA-43-3394 TCGA-43-6770 TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 TCGA-43-8116 
         822          310          212          236         1970          358 
TCGA-43-A475 TCGA-46-6026 TCGA-51-4079 TCGA-52-7809 TCGA-56-5897 TCGA-56-7582 
         296          423           12         1948            3           26 
TCGA-56-8503 TCGA-56-A4BY TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-A46J 
          41           30          378          911         2167         2589 
TCGA-60-2695 TCGA-60-2704 TCGA-60-2709 TCGA-60-2710 TCGA-60-2712 TCGA-60-2713 
         642         1943         1505         1963          274         1731 
TCGA-60-2714 TCGA-60-2723 TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 TCGA-63-7023 
        1531         1092          816          358         1973         1952 
TCGA-66-2727 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2757 TCGA-66-2758 
        1967           31           61           28           30          639 
TCGA-66-2769 TCGA-66-2770 TCGA-66-2773 TCGA-66-2786 TCGA-66-2787 TCGA-66-2795 
        1947          700         1946          790         1217          122 
TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59J TCGA-77-6842 TCGA-77-6843 
         211          244           96          104         1950         1941 
TCGA-77-7139 TCGA-77-7141 TCGA-77-7338 TCGA-77-7465 TCGA-77-8008 TCGA-77-8009 
        1968           15         1952          479         1945         1641 
TCGA-77-8140 TCGA-77-8156 TCGA-77-A5G7 TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6560 
        1962           10         1963          839          713          364 
TCGA-85-6798 TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 
          34           35          911           60           26           60 
TCGA-85-8052 TCGA-85-8070 TCGA-85-8072 TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 
          16          960          513           11           13           54 
TCGA-85-8352 TCGA-85-8580 TCGA-85-8664 TCGA-85-A4CL TCGA-85-A510 TCGA-85-A511 
          67          445            3           15         1967         1972 
TCGA-85-A512 TCGA-85-A513 TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 TCGA-90-A4ED 
        1987           24          289           89          358          244 
TCGA-90-A4EE TCGA-90-A59Q TCGA-94-7943 TCGA-96-7545 TCGA-96-A4JL TCGA-98-7454 
         331          269          356         1344          183          256 
TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-LA-A446 TCGA-NC-A5HE 
         413          224          308           36         1722 

$`14Q LOSS WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3411 TCGA-18-3412 
         370          136         2464         2417         1415          345 
TCGA-18-3414 TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 
         396         1810          862          758           50         1331 
TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1070 TCGA-21-1072 TCGA-21-1075 
        2754           92          827         3636         3016         2134 
TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 
        1852         1058          474          965         3724          284 
TCGA-21-1082 TCGA-21-5782 TCGA-21-5786 TCGA-21-5787 TCGA-21-A5DI TCGA-22-0944 
        3644          962         1032          329          979          223 
TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1017 TCGA-22-4591 
        1945          131         1952           53         1485          623 
TCGA-22-4593 TCGA-22-4594 TCGA-22-4595 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 
        1067         1470          734         1161         1057          399 
TCGA-22-4605 TCGA-22-4607 TCGA-22-5471 TCGA-22-5472 TCGA-22-5478 TCGA-22-5479 
        1946          587          965         1964           24         1651 
TCGA-22-5482 TCGA-22-5485 TCGA-22-5489 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4532 
         357          916         1912          506           29         2524 
TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4589 
        1940         2979         1311         5287         1966         1948 
TCGA-33-6738 TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 
         822         1000          951         1528         2062         1715 
TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-8454 TCGA-37-3783 TCGA-37-3789 
         707          365          428          166          120           13 
TCGA-37-3792 TCGA-37-4129 TCGA-37-4132 TCGA-37-4141 TCGA-37-5819 TCGA-39-5011 
          12          200          227           12          103         1454 
TCGA-39-5019 TCGA-39-5022 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5031 
        1361         1996         1849           52          740          833 
TCGA-39-5034 TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 TCGA-43-2576 TCGA-43-2578 
        1107         1084         1086          544         1223          684 
TCGA-43-2581 TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 
        1176         1007          349          849          376          757 
TCGA-43-6771 TCGA-43-8115 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56U TCGA-43-A56V 
        1936          407         1971          353          432          366 
TCGA-46-6025 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7810 TCGA-52-7811 
         324           12          911          541          923         1958 
TCGA-52-7812 TCGA-56-1622 TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 
        1967          881          555           62           26           30 
TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-7730 TCGA-56-7731 
          13           30           44           40            6         1961 
TCGA-56-7822 TCGA-56-8504 TCGA-56-8622 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 
           1          178           55           36           63           17 
TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4ZJ 
          16           34           38            2           46           25 
TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8393 TCGA-58-A46L TCGA-58-A46M 
           4            4            8         1058         1723         1072 
TCGA-58-A46N TCGA-60-2696 TCGA-60-2698 TCGA-60-2703 TCGA-60-2706 TCGA-60-2707 
         910          109          311         1950         1958          661 
TCGA-60-2708 TCGA-60-2711 TCGA-60-2715 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 
        1963         1260         1075         1475         1297           97 
TCGA-60-2721 TCGA-60-2722 TCGA-60-2724 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 
         983          908          717         1957         1955         1947 
TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 TCGA-66-2756 TCGA-66-2759 
        1311           61          641           30           30          762 
TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2771 
          30           61           31           61           61          578 
TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 
          61          578         1956          121         1954          759 
TCGA-66-2785 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 TCGA-66-2792 
          60          699         1955          699         1977          913 
TCGA-66-2793 TCGA-66-2794 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-A59I 
        1952         1645         1492           83          202          121 
TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 
        1942         1952         1959         1286         1954         1942 
TCGA-77-7463 TCGA-77-8007 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 
        1954         1960         1953         1945         1941         1941 
TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 
        1947         1946         1951          833         1943          293 
TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 
        1961         1684         1092         1953         1942         1959 
TCGA-77-A5G6 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB TCGA-85-6561 TCGA-85-7696 
        1955         1290         1280         1939          395           18 
TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-8071 TCGA-85-8276 
          10           49            1         1965          428           13 
TCGA-85-8350 TCGA-85-8351 TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 
          60           55           54           61           61           22 
TCGA-85-8481 TCGA-85-8582 TCGA-85-8666 TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR 
          21          424          475         1972         1960           25 
TCGA-85-A50M TCGA-85-A50Z TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7964 
          19         1973           13          111          758          428 
TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 
          82          106          122          160           70           87 
TCGA-94-A4VJ TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK TCGA-J1-A4AH 
         430         1213          189          211          273          222 
TCGA-L3-A4E7 TCGA-L3-A524 TCGA-MF-A522 TCGA-NC-A5HG TCGA-NC-A5HI 
          35          449           83         1548         1135 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                 3                  1 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              2589               5287 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               445                757 
[1] "3.0 - 2589.0 (445.0)" "1.0 - 5287.0 (757.0)"
[1] "hr=" "1.2"
D66V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  14Q LOSS MUTATED         0       31       47        0        20        23
  14Q LOSS WILD-TYPE       1       41       90        1        32        48
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  14Q LOSS MUTATED           13          6        0
  14Q LOSS WILD-TYPE         44         14        6
D66V3, multiclass
            clus
vv           14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  STAGE I                   0                  1
  STAGE IA                 31                 41
  STAGE IB                 47                 90
  STAGE II                  0                  1
  STAGE IIA                20                 32
  STAGE IIB                23                 48
  STAGE IIIA               13                 44
  STAGE IIIB                6                 14
  STAGE IV                  0                  6
[1] 9 2
[1] 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    41  85  10   4
  14Q LOSS WILD-TYPE  57 169  38  16
D66V4, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  T1               41                 57
  T2               85                169
  T3               10                 38
  T4                4                 16
[1] 4 2
[1] 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    87  44   7   0
  14Q LOSS WILD-TYPE 174  69  28   5
D66V5, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  N0               87                174
  N1               44                 69
  N2                7                 28
  N3                0                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A  MX
  14Q LOSS MUTATED   120   0   0  19
  14Q LOSS WILD-TYPE 238   5   1  31
D66V6, multiclass
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  M0               120                238
  M1                 0                  5
  M1A                0                  1
  MX                19                 31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V7, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    40 100
  14Q LOSS WILD-TYPE  67 213
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     40  100
  14Q LOSS WILD-TYPE   67  213
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE               40                 67
  MALE                100                213
[1] 2 2
[1] FALSE
D66V8, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  14Q LOSS MUTATED                                       5
  14Q LOSS WILD-TYPE                                     7
                    vv
clus                 LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  14Q LOSS MUTATED                                        0
  14Q LOSS WILD-TYPE                                      6
                    vv
clus                 LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  14Q LOSS MUTATED                                         1
  14Q LOSS WILD-TYPE                                       0
                    vv
clus                 LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  14Q LOSS MUTATED                                                           134
  14Q LOSS WILD-TYPE                                                         267
D66V9, multiclass
                                                             clus
vv                                                            14Q LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      5
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     0
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              134
                                                             clus
vv                                                            14Q LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                        7
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                267
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V10, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED     4 136
  14Q LOSS WILD-TYPE   9 271
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      4  136
  14Q LOSS WILD-TYPE    9  271
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  NO                 4                  9
  YES              136                271
[1] 2 2
[1] FALSE
D66V11, continuous
                    vv
clus                  R0  R1  R2  RX
  14Q LOSS MUTATED   116   3   1   3
  14Q LOSS WILD-TYPE 226   5   3  15
D66V12, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  R0              116                226
  R1                3                  5
  R2                1                  3
  RX                3                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  14Q LOSS MUTATED       3                         6   106
  14Q LOSS WILD-TYPE     6                        11   192
D66V13, multiclass
                           clus
vv                          14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  ASIAN                                    3                  6
  BLACK OR AFRICAN AMERICAN                6                 11
  WHITE                                  106                192
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V14, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED     1  96
  14Q LOSS WILD-TYPE   7 171
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      1   96
  14Q LOSS WILD-TYPE    7  171
                        clus
vv                       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  7
  NOT HISPANIC OR LATINO               96                171
[1] 2 2
[1] FALSE

Clustering(67) Variable = 15Q LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                  0   1
  15Q LOSS MUTATED    67  38
  15Q LOSS WILD-TYPE 198  85
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               105                283 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                38                 85 
$`15Q LOSS MUTATED`
TCGA-18-3406 TCGA-18-3412 TCGA-18-3416 TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 
         370          345          862           92         3636         1426 
TCGA-21-1072 TCGA-21-1080 TCGA-21-5787 TCGA-22-0944 TCGA-22-1000 TCGA-22-1012 
        3016         3724          329          223         1945          429 
TCGA-22-1016 TCGA-22-1017 TCGA-22-4594 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 
         822         1485         1470          734           17         1161 
TCGA-22-5471 TCGA-22-5480 TCGA-33-4533 TCGA-33-4582 TCGA-33-4587 TCGA-33-4589 
         965         1952         1940         1966         1970         1948 
TCGA-34-2600 TCGA-37-3783 TCGA-37-4130 TCGA-37-4133 TCGA-37-4141 TCGA-37-5819 
        1874          120          247          238           12          103 
TCGA-39-5011 TCGA-39-5016 TCGA-39-5021 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 
        1454         2253         1947           52          740           59 
TCGA-39-5031 TCGA-39-5034 TCGA-39-5040 TCGA-43-2578 TCGA-43-2581 TCGA-43-5668 
         833         1107         1964          684         1176          349 
TCGA-43-5670 TCGA-43-A56V TCGA-46-6025 TCGA-46-6026 TCGA-52-7810 TCGA-56-7223 
         849          366          324          423          923           30 
TCGA-56-7580 TCGA-56-7822 TCGA-56-8503 TCGA-56-A49D TCGA-56-A4BW TCGA-60-2698 
          40            1           41           38            2          311 
TCGA-60-2703 TCGA-60-2708 TCGA-60-2712 TCGA-60-2714 TCGA-60-2720 TCGA-60-2723 
        1950         1963          274         1531           97         1092 
TCGA-60-2726 TCGA-63-7022 TCGA-66-2737 TCGA-66-2742 TCGA-66-2756 TCGA-66-2791 
         358         1947           61          641           30         1977 
TCGA-66-2793 TCGA-66-2794 TCGA-66-2800 TCGA-68-8250 TCGA-68-A59I TCGA-68-A59J 
        1952         1645         1492          244          121          104 
TCGA-77-6842 TCGA-77-7139 TCGA-77-7337 TCGA-77-8007 TCGA-77-8009 TCGA-77-8128 
        1950         1968         1942         1960         1641         1953 
TCGA-77-8130 TCGA-77-8145 TCGA-77-8153 TCGA-77-8156 TCGA-77-A5G6 TCGA-77-A5GH 
        1945         1943         1684           10         1955          713 
TCGA-85-6560 TCGA-85-7696 TCGA-85-7843 TCGA-85-8072 TCGA-85-8288 TCGA-85-8479 
         364           18           35          513           54           22 
TCGA-85-8666 TCGA-85-A4QQ TCGA-85-A50M TCGA-85-A511 TCGA-85-A53L TCGA-85-A5B5 
         475         1960           19         1972           13          111 
TCGA-90-7767 TCGA-90-A4ED TCGA-90-A4EE TCGA-92-8064 TCGA-92-8065 TCGA-96-A4JK 
          89          244          331          160           70          273 
TCGA-MF-A522 TCGA-NC-A5HG TCGA-NC-A5HI 
          83         1548         1135 

$`15Q LOSS WILD-TYPE`
TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 TCGA-18-3414 
         136         2464         2417          146         1415          396 
TCGA-18-3415 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 
        1810          758           50         1331          187           85 
TCGA-18-4721 TCGA-18-5595 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 
        2754          827         2134         1852         1058          474 
TCGA-21-1079 TCGA-21-1081 TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 TCGA-21-5784 
         965          284         3644          267          962         1268 
TCGA-21-5786 TCGA-21-A5DI TCGA-22-0940 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 
        1032          979          608          131         1952           53 
TCGA-22-4591 TCGA-22-4593 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 
         623         1067         1057          399         1946          587 
TCGA-22-4613 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 
         358         1964         1933          445         1346           24 
TCGA-22-5479 TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 
        1651         1952          357          573          916         1912 
TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4538 TCGA-33-4547 
        1713          506           29         2524         2979         1311 
TCGA-33-4566 TCGA-33-4583 TCGA-33-4586 TCGA-33-6738 TCGA-34-2596 TCGA-34-2604 
        5287         1941          428          822           80          958 
TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 
         881         1000          951         1528         2062         1715 
TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-8454 
         707          365          428          941          552          166 
TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-37-4132 TCGA-37-4135 TCGA-39-5019 
          13           12          200          227          207         1361 
TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 
        1996         1964         1849          474         1084         1086 
TCGA-39-5039 TCGA-43-2576 TCGA-43-3394 TCGA-43-3920 TCGA-43-6143 TCGA-43-6647 
         544         1223          822         1007          376          757 
TCGA-43-6770 TCGA-43-6771 TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 
         310         1936          212          236         1970          407 
TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U TCGA-51-4079 
         358         1971          353          296          432           12 
TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 TCGA-52-7811 TCGA-52-7812 
          12          911          541         1948         1958         1967 
TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 
         881            3          555           62           26           30 
TCGA-56-7222 TCGA-56-7579 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-8504 
          13           44           26            6         1961          178 
TCGA-56-8622 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 
          55           36           63           17           16           34 
TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS 
          46           30           25            4            4            8 
TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46L 
         378          911         2167         1058         2589         1723 
TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 TCGA-60-2696 TCGA-60-2704 TCGA-60-2706 
        1072          910          642          109         1943         1958 
TCGA-60-2707 TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 TCGA-60-2713 TCGA-60-2715 
         661         1505         1963         1260         1731         1075 
TCGA-60-2716 TCGA-60-2719 TCGA-60-2721 TCGA-60-2722 TCGA-60-2724 TCGA-60-2725 
        1475         1297          983          908          717          816 
TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 TCGA-63-7023 TCGA-66-2727 TCGA-66-2734 
        1973         1957         1955         1952         1967         1311 
TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2757 TCGA-66-2758 
          30           31           61           28           30          639 
TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 
         762           30           61           31           61           61 
TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 
        1947          700          578         1946           61          578 
TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 
        1956          121         1954          759           60          790 
TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2792 TCGA-66-2795 
        1217          699         1955          699          913          122 
TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-8251 TCGA-77-6843 TCGA-77-6844 
          83          202          211           96         1941         1942 
TCGA-77-6845 TCGA-77-7138 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7338 
        1952         1959           15         1286         1954         1952 
TCGA-77-7463 TCGA-77-7465 TCGA-77-8008 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 
        1954          479         1945         1941         1941         1947 
TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8144 TCGA-77-8148 TCGA-77-8150 
        1946         1951         1962          833          293         1961 
TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G7 TCGA-77-A5G8 
        1092         1953         1942         1959         1963         1290 
TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF TCGA-85-6561 TCGA-85-6798 TCGA-85-7697 
        1280         1939          839          395           34           10 
TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 
          49            1         1965          911           60           26 
TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8276 TCGA-85-8277 
          60           16          960          428           13           11 
TCGA-85-8287 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 TCGA-85-8354 
          13           60           55           67           54           61 
TCGA-85-8355 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8664 TCGA-85-A4CL 
          61           21          445          424            3           15 
TCGA-85-A4PA TCGA-85-A4QR TCGA-85-A50Z TCGA-85-A510 TCGA-85-A512 TCGA-85-A513 
        1972           25         1973         1967         1987           24 
TCGA-90-6837 TCGA-90-7766 TCGA-90-7769 TCGA-90-7964 TCGA-90-A59Q TCGA-92-7340 
         758          289          358          428          269           82 
TCGA-92-7341 TCGA-92-8063 TCGA-94-7033 TCGA-94-7943 TCGA-94-A4VJ TCGA-96-7544 
         106          122           87          356          430         1213 
TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 
        1344          189          211          183          256          413 
TCGA-98-8022 TCGA-98-8023 TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 
         224          308          222           35          449           36 
TCGA-NC-A5HE 
        1722 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 1                  1 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              3724               5287 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               684                639 
[1] "1.0 - 3724.0 (684.0)" "1.0 - 5287.0 (639.0)"
[1] "hr=" "1.1"
D67V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  15Q LOSS MUTATED         0       14       30        0        12        26
  15Q LOSS WILD-TYPE       1       58      107        1        40        45
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  15Q LOSS MUTATED           20          7        2
  15Q LOSS WILD-TYPE         37         13        4
D67V3, multiclass
            clus
vv           15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  STAGE I                   0                  1
  STAGE IA                 14                 58
  STAGE IB                 30                107
  STAGE II                  0                  1
  STAGE IIA                12                 40
  STAGE IIB                26                 45
  STAGE IIIA               20                 37
  STAGE IIIB                7                 13
  STAGE IV                  2                  4
[1] 9 2
[1] 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    21  67  16   7
  15Q LOSS WILD-TYPE  77 187  32  13
D67V4, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T1               21                 77
  T2               67                187
  T3               16                 32
  T4                7                 13
[1] 4 2
[1] 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    57  38  14   1
  15Q LOSS WILD-TYPE 204  75  21   4
D67V5, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  N0               57                204
  N1               38                 75
  N2               14                 21
  N3                1                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A  MX
  15Q LOSS MUTATED    97   2   0  11
  15Q LOSS WILD-TYPE 261   3   1  39
D67V6, multiclass
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  M0                97                261
  M1                 2                  3
  M1A                0                  1
  MX                11                 39
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V7, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED    32  79
  15Q LOSS WILD-TYPE  75 234
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     32   79
  15Q LOSS WILD-TYPE   75  234
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE               32                 75
  MALE                 79                234
[1] 2 2
[1] FALSE
D67V8, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  15Q LOSS MUTATED                                       2
  15Q LOSS WILD-TYPE                                    10
                    vv
clus                 LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  15Q LOSS MUTATED                                        1
  15Q LOSS WILD-TYPE                                      5
                    vv
clus                 LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  15Q LOSS MUTATED                                         1
  15Q LOSS WILD-TYPE                                       0
                    vv
clus                 LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  15Q LOSS MUTATED                                                           107
  15Q LOSS WILD-TYPE                                                         294
D67V9, multiclass
                                                             clus
vv                                                            15Q LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      2
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              107
                                                             clus
vv                                                            15Q LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       10
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                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"
D67V10, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     6 105
  15Q LOSS WILD-TYPE   7 302
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      6  105
  15Q LOSS WILD-TYPE    7  302
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  NO                 6                  7
  YES              105                302
[1] 2 2
[1] FALSE
D67V11, continuous
                    vv
clus                  R0  R1  R2  RX
  15Q LOSS MUTATED    92   2   2   4
  15Q LOSS WILD-TYPE 250   6   2  14
D67V12, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  R0               92                250
  R1                2                  6
  R2                2                  2
  RX                4                 14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  15Q LOSS MUTATED       4                         7    77
  15Q LOSS WILD-TYPE     5                        10   221
D67V13, multiclass
                           clus
vv                          15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  ASIAN                                    4                  5
  BLACK OR AFRICAN AMERICAN                7                 10
  WHITE                                   77                221
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V14, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     2  72
  15Q LOSS WILD-TYPE   6 195
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      2   72
  15Q LOSS WILD-TYPE    6  195
                        clus
vv                       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  6
  NOT HISPANIC OR LATINO               72                195
[1] 2 2
[1] FALSE

Clustering(68) Variable = 16P LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                  0   1
  16P LOSS MUTATED    90  28
  16P LOSS WILD-TYPE 175  95
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
               118                270 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                28                 95 
$`16P LOSS MUTATED`
TCGA-18-3410 TCGA-18-3415 TCGA-18-4083 TCGA-18-5592 TCGA-21-1070 TCGA-21-1076 
         146         1810          187           92         3636         1852 
TCGA-21-1080 TCGA-21-5786 TCGA-22-0940 TCGA-22-1002 TCGA-22-1012 TCGA-22-4594 
        3724         1032          608          131          429         1470 
TCGA-22-4595 TCGA-22-4599 TCGA-22-4604 TCGA-22-4613 TCGA-22-5478 TCGA-22-5480 
         734         1161          399          358           24         1952 
TCGA-22-5482 TCGA-33-4533 TCGA-34-2596 TCGA-34-2609 TCGA-34-5239 TCGA-34-5927 
         357         1940           80          951          707          941 
TCGA-34-5928 TCGA-39-5011 TCGA-39-5016 TCGA-39-5021 TCGA-39-5027 TCGA-39-5028 
         552         1454         2253         1947         1849           52 
TCGA-39-5040 TCGA-43-3394 TCGA-43-5670 TCGA-43-6143 TCGA-43-7656 TCGA-43-7657 
        1964          822          849          376          212          236 
TCGA-43-7658 TCGA-43-8116 TCGA-43-A56U TCGA-46-6025 TCGA-52-7622 TCGA-52-7809 
        1970          358          432          324          541         1948 
TCGA-52-7810 TCGA-56-7580 TCGA-56-7822 TCGA-56-8503 TCGA-56-8629 TCGA-56-A49D 
         923           40            1           41           34           38 
TCGA-56-A4BX TCGA-56-A4BY TCGA-58-8391 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46L 
          46           30         2167         1058         2589         1723 
TCGA-60-2695 TCGA-60-2708 TCGA-60-2714 TCGA-60-2719 TCGA-60-2720 TCGA-60-2723 
         642         1963         1531         1297           97         1092 
TCGA-60-2724 TCGA-63-6202 TCGA-66-2727 TCGA-66-2734 TCGA-66-2753 TCGA-66-2755 
         717         1973         1967         1311           31           28 
TCGA-66-2757 TCGA-66-2758 TCGA-66-2763 TCGA-66-2769 TCGA-66-2781 TCGA-66-2782 
          30          639           30         1947          121         1954 
TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2790 TCGA-66-2792 TCGA-66-2800 
          60          790         1217          699          913         1492 
TCGA-68-7756 TCGA-68-8251 TCGA-77-6842 TCGA-77-7139 TCGA-77-7142 TCGA-77-7463 
         202           96         1950         1968         1286         1954 
TCGA-77-8130 TCGA-77-8136 TCGA-77-8140 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5G7 
        1945         1947         1962         1092           10         1963 
TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6798 TCGA-85-7698 TCGA-85-7699 TCGA-85-7950 
         839          713           34           49            1           60 
TCGA-85-8052 TCGA-85-8070 TCGA-85-8277 TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 
          16          960           11           55           67           54 
TCGA-85-8355 TCGA-85-8580 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4QR TCGA-85-A53L 
          61          445            3          475           25           13 
TCGA-85-A5B5 TCGA-90-7767 TCGA-90-A4EE TCGA-92-8064 TCGA-96-7544 TCGA-96-8169 
         111           89          331          160         1213          189 
TCGA-96-A4JK TCGA-L3-A4E7 TCGA-L3-A524 TCGA-NC-A5HG 
         273           35          449         1548 

$`16P LOSS WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3411 TCGA-18-3412 
         370          136         2464         2417         1415          345 
TCGA-18-3414 TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4086 
         396          862          758           50         1331           85 
TCGA-18-4721 TCGA-18-5595 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 TCGA-21-1077 
        2754          827         1426         3016         2134         1058 
TCGA-21-1078 TCGA-21-1079 TCGA-21-1081 TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 
         474          965          284         3644          267          962 
TCGA-21-5784 TCGA-21-5787 TCGA-21-A5DI TCGA-22-0944 TCGA-22-1000 TCGA-22-1005 
        1268          329          979          223         1945         1952 
TCGA-22-1011 TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 TCGA-22-4593 TCGA-22-4596 
          53          822         1485          623         1067           17 
TCGA-22-4601 TCGA-22-4605 TCGA-22-4607 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 
        1057         1946          587          965         1964         1933 
TCGA-22-5474 TCGA-22-5477 TCGA-22-5479 TCGA-22-5481 TCGA-22-5483 TCGA-22-5485 
         445         1346         1651         1952          573          916 
TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4538 
        1912         1713          506           29         2524         2979 
TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 
        1311         5287         1966         1941          428         1970 
TCGA-33-4589 TCGA-33-6738 TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 
        1948          822         1874          958          881         1000 
TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5240 TCGA-34-5241 TCGA-34-8454 
        1528         2062         1715          365          428          166 
TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 
         120           13           12          200          247          227 
TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5019 TCGA-39-5022 
         238          207           12          103         1361         1996 
TCGA-39-5024 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 
        1964          740           59          833         1107          474 
TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 TCGA-43-2576 TCGA-43-2578 TCGA-43-2581 
        1084         1086          544         1223          684         1176 
TCGA-43-3920 TCGA-43-5668 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-8115 
        1007          349          757          310         1936          407 
TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56V TCGA-46-6026 TCGA-51-4079 
        1971          353          296          366          423           12 
TCGA-51-4080 TCGA-51-4081 TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 
          12          911         1958         1967          881            3 
TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 
         555           62           26           30           13           30 
TCGA-56-7579 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-8504 TCGA-56-8622 
          44           26            6         1961          178           55 
TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-A4BW TCGA-56-A4ZJ 
          36           63           17           16            2           25 
TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8388 TCGA-58-8390 TCGA-58-A46M 
           4            4            8          378          911         1072 
TCGA-58-A46N TCGA-60-2696 TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 
         910          109          311         1950         1943         1958 
TCGA-60-2707 TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 
         661         1505         1963         1260          274         1731 
TCGA-60-2715 TCGA-60-2716 TCGA-60-2721 TCGA-60-2722 TCGA-60-2725 TCGA-60-2726 
        1075         1475          983          908          816          358 
TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 TCGA-66-2737 TCGA-66-2742 
        1957         1955         1947         1952           61          641 
TCGA-66-2744 TCGA-66-2754 TCGA-66-2756 TCGA-66-2759 TCGA-66-2765 TCGA-66-2766 
          30           61           30          762           61           31 
TCGA-66-2767 TCGA-66-2768 TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 
          61           61          700          578         1946           61 
TCGA-66-2778 TCGA-66-2780 TCGA-66-2783 TCGA-66-2788 TCGA-66-2789 TCGA-66-2791 
         578         1956          759          699         1955         1977 
TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 TCGA-68-7755 TCGA-68-7757 TCGA-68-8250 
        1952         1645          122           83          211          244 
TCGA-68-A59I TCGA-68-A59J TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 
         121          104         1941         1942         1952         1959 
TCGA-77-7141 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7465 TCGA-77-8007 
          15         1954         1942         1952          479         1960 
TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8131 TCGA-77-8133 TCGA-77-8138 
        1945         1641         1953         1941         1941         1946 
TCGA-77-8139 TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 
        1951          833         1943          293         1961         1684 
TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G8 TCGA-77-A5GA 
        1953         1942         1959         1955         1290         1280 
TCGA-77-A5GB TCGA-85-6560 TCGA-85-6561 TCGA-85-7696 TCGA-85-7697 TCGA-85-7710 
        1939          364          395           18           10         1965 
TCGA-85-7843 TCGA-85-7844 TCGA-85-8048 TCGA-85-8049 TCGA-85-8071 TCGA-85-8072 
          35          911           26           60          428          513 
TCGA-85-8276 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8354 TCGA-85-8479 
          13           13           54           60           61           22 
TCGA-85-8481 TCGA-85-8582 TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50M 
          21          424           15         1972         1960           19 
TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 TCGA-90-6837 
        1973         1967         1972         1987           24          758 
TCGA-90-7766 TCGA-90-7769 TCGA-90-7964 TCGA-90-A4ED TCGA-90-A59Q TCGA-92-7340 
         289          358          428          244          269           82 
TCGA-92-7341 TCGA-92-8063 TCGA-92-8065 TCGA-94-7033 TCGA-94-7943 TCGA-94-A4VJ 
         106          122           70           87          356          430 
TCGA-96-7545 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 
        1344          211          183          256          413          224 
TCGA-98-8023 TCGA-J1-A4AH TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HE TCGA-NC-A5HI 
         308          222           36           83         1722         1135 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 1                  2 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              3724               5287 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             580.0              691.5 
[1] "1.0 - 3724.0 (580.0)" "2.0 - 5287.0 (691.5)"
[1] "hr=" "1.3"
D68V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  16P LOSS MUTATED         0       20       45        0        13        27
  16P LOSS WILD-TYPE       1       52       92        1        39        44
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  16P LOSS MUTATED           20          4        2
  16P LOSS WILD-TYPE         37         16        4
D68V3, multiclass
            clus
vv           16P LOSS MUTATED 16P LOSS WILD-TYPE
  STAGE I                   0                  1
  STAGE IA                 20                 52
  STAGE IB                 45                 92
  STAGE II                  0                  1
  STAGE IIA                13                 39
  STAGE IIB                27                 44
  STAGE IIIA               20                 37
  STAGE IIIB                4                 16
  STAGE IV                  2                  4
[1] 9 2
[1] 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    23  84  17   7
  16P LOSS WILD-TYPE  75 170  31  13
D68V4, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  T1               23                 75
  T2               84                170
  T3               17                 31
  T4                7                 13
[1] 4 2
[1] 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    85  35  10   0
  16P LOSS WILD-TYPE 176  78  25   5
D68V5, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  N0               85                176
  N1               35                 78
  N2               10                 25
  N3                0                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A  MX
  16P LOSS MUTATED   116   1   1  12
  16P LOSS WILD-TYPE 242   4   0  38
D68V6, multiclass
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  M0               116                242
  M1                 1                  4
  M1A                1                  0
  MX                12                 38
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V7, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    38  93
  16P LOSS WILD-TYPE  69 220
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     38   93
  16P LOSS WILD-TYPE   69  220
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE               38                 69
  MALE                 93                220
[1] 2 2
[1] FALSE
D68V8, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  16P LOSS MUTATED                                       7
  16P LOSS WILD-TYPE                                     5
                    vv
clus                 LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  16P LOSS MUTATED                                        0
  16P LOSS WILD-TYPE                                      6
                    vv
clus                 LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  16P LOSS MUTATED                                         0
  16P LOSS WILD-TYPE                                       1
                    vv
clus                 LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  16P LOSS MUTATED                                                           124
  16P LOSS WILD-TYPE                                                         277
D68V9, multiclass
                                                             clus
vv                                                            16P LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      7
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     0
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              124
                                                             clus
vv                                                            16P LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                        5
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                277
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V10, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     4 127
  16P LOSS WILD-TYPE   9 280
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      4  127
  16P LOSS WILD-TYPE    9  280
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  NO                 4                  9
  YES              127                280
[1] 2 2
[1] FALSE
D68V11, continuous
                    vv
clus                  R0  R1  R2  RX
  16P LOSS MUTATED   109   1   0   4
  16P LOSS WILD-TYPE 233   7   4  14
D68V12, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  R0              109                233
  R1                1                  7
  R2                0                  4
  RX                4                 14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16P LOSS MUTATED       1                         6    90
  16P LOSS WILD-TYPE     8                        11   208
D68V13, multiclass
                           clus
vv                          16P LOSS MUTATED 16P LOSS WILD-TYPE
  ASIAN                                    1                  8
  BLACK OR AFRICAN AMERICAN                6                 11
  WHITE                                   90                208
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V14, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     2  80
  16P LOSS WILD-TYPE   6 187
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      2   80
  16P LOSS WILD-TYPE    6  187
                        clus
vv                       16P LOSS MUTATED 16P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  6
  NOT HISPANIC OR LATINO               80                187
[1] 2 2
[1] FALSE

Clustering(69) Variable = 16Q LOSS MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                  0   1
  16Q LOSS MUTATED    97  36
  16Q LOSS WILD-TYPE 168  87
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               133                255 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                36                 87 
$`16Q LOSS MUTATED`
TCGA-18-3410 TCGA-18-3415 TCGA-18-3419 TCGA-18-4083 TCGA-18-5592 TCGA-21-1070 
         146         1810           50          187           92         3636 
TCGA-21-1076 TCGA-21-1080 TCGA-21-1083 TCGA-22-0940 TCGA-22-1002 TCGA-22-1012 
        1852         3724          267          608          131          429 
TCGA-22-4594 TCGA-22-4595 TCGA-22-4599 TCGA-22-4604 TCGA-22-5473 TCGA-22-5478 
        1470          734         1161          399         1933           24 
TCGA-22-5480 TCGA-22-5481 TCGA-22-5489 TCGA-33-4533 TCGA-33-4586 TCGA-34-2596 
        1952         1952         1912         1940          428           80 
TCGA-34-2604 TCGA-34-2609 TCGA-34-5231 TCGA-34-5239 TCGA-34-5927 TCGA-34-5928 
         958          951         1528          707          941          552 
TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5027 TCGA-39-5028 TCGA-39-5030 
        1454         2253         1361         1849           52           59 
TCGA-39-5040 TCGA-43-2578 TCGA-43-3394 TCGA-43-3920 TCGA-43-5670 TCGA-43-7657 
        1964          684          822         1007          849          236 
TCGA-43-7658 TCGA-43-8116 TCGA-43-A56U TCGA-46-6025 TCGA-46-6026 TCGA-52-7622 
        1970          358          432          324          423          541 
TCGA-52-7809 TCGA-52-7810 TCGA-56-7221 TCGA-56-7222 TCGA-56-7580 TCGA-56-7730 
        1948          923           30           13           40            6 
TCGA-56-7822 TCGA-56-8503 TCGA-56-8626 TCGA-56-A49D TCGA-56-A4BX TCGA-56-A4BY 
           1           41           17           38           46           30 
TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46L 
         378          911         2167         1058         2589         1723 
TCGA-58-A46M TCGA-60-2695 TCGA-60-2710 TCGA-60-2711 TCGA-60-2713 TCGA-60-2714 
        1072          642         1963         1260         1731         1531 
TCGA-60-2719 TCGA-60-2720 TCGA-60-2723 TCGA-63-6202 TCGA-63-7023 TCGA-66-2727 
        1297           97         1092         1973         1952         1967 
TCGA-66-2734 TCGA-66-2753 TCGA-66-2755 TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 
        1311           31           28           30          639          762 
TCGA-66-2763 TCGA-66-2767 TCGA-66-2769 TCGA-66-2770 TCGA-66-2778 TCGA-66-2782 
          30           61         1947          700          578         1954 
TCGA-66-2787 TCGA-66-2789 TCGA-66-2790 TCGA-66-2792 TCGA-66-2793 TCGA-66-2800 
        1217         1955          699          913         1952         1492 
TCGA-68-7756 TCGA-68-8251 TCGA-68-A59J TCGA-77-6842 TCGA-77-7139 TCGA-77-7142 
         202           96          104         1950         1968         1286 
TCGA-77-7463 TCGA-77-8136 TCGA-77-8139 TCGA-77-8140 TCGA-77-8150 TCGA-77-8153 
        1954         1947         1951         1962         1961         1684 
TCGA-77-8156 TCGA-77-A5GH TCGA-85-6561 TCGA-85-6798 TCGA-85-7698 TCGA-85-7699 
          10          713          395           34           49            1 
TCGA-85-7950 TCGA-85-8071 TCGA-85-8353 TCGA-85-8355 TCGA-85-8580 TCGA-85-8664 
          60          428           54           61          445            3 
TCGA-85-8666 TCGA-85-A4QR TCGA-85-A512 TCGA-85-A5B5 TCGA-90-7767 TCGA-90-A4ED 
         475           25         1987          111           89          244 
TCGA-90-A4EE TCGA-92-8064 TCGA-92-8065 TCGA-94-A4VJ TCGA-96-8169 TCGA-96-A4JK 
         331          160           70          430          189          273 
TCGA-NC-A5HG 
        1548 

$`16Q LOSS WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3411 TCGA-18-3412 
         370          136         2464         2417         1415          345 
TCGA-18-3414 TCGA-18-3416 TCGA-18-3417 TCGA-18-3421 TCGA-18-4086 TCGA-18-4721 
         396          862          758         1331           85         2754 
TCGA-18-5595 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 TCGA-21-1077 TCGA-21-1078 
         827         1426         3016         2134         1058          474 
TCGA-21-1079 TCGA-21-1081 TCGA-21-1082 TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 
         965          284         3644          962         1268         1032 
TCGA-21-5787 TCGA-21-A5DI TCGA-22-0944 TCGA-22-1000 TCGA-22-1005 TCGA-22-1011 
         329          979          223         1945         1952           53 
TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 TCGA-22-4593 TCGA-22-4596 TCGA-22-4601 
         822         1485          623         1067           17         1057 
TCGA-22-4605 TCGA-22-4607 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5474 
        1946          587          358          965         1964          445 
TCGA-22-5477 TCGA-22-5479 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5491 
        1346         1651          357          573          916         1713 
TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 
         506           29         2524         2979         1311         5287 
TCGA-33-4582 TCGA-33-4583 TCGA-33-4587 TCGA-33-4589 TCGA-33-6738 TCGA-34-2600 
        1966         1941         1970         1948          822         1874 
TCGA-34-2605 TCGA-34-2608 TCGA-34-5232 TCGA-34-5234 TCGA-34-5240 TCGA-34-5241 
         881         1000         2062         1715          365          428 
TCGA-34-8454 TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 
         166          120           13           12          200          247 
TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5021 
         227          238          207           12          103         1947 
TCGA-39-5022 TCGA-39-5024 TCGA-39-5029 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 
        1996         1964          740          833         1107          474 
TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 TCGA-43-2576 TCGA-43-2581 TCGA-43-5668 
        1084         1086          544         1223         1176          349 
TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-7656 TCGA-43-8115 
         376          757          310         1936          212          407 
TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56V TCGA-51-4079 TCGA-51-4080 
        1971          353          296          366           12           12 
TCGA-51-4081 TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 
         911         1958         1967          881            3          555 
TCGA-56-6545 TCGA-56-6546 TCGA-56-7223 TCGA-56-7579 TCGA-56-7582 TCGA-56-7731 
          62           26           30           44           26         1961 
TCGA-56-8504 TCGA-56-8622 TCGA-56-8624 TCGA-56-8625 TCGA-56-8628 TCGA-56-8629 
         178           55           36           63           16           34 
TCGA-56-A4BW TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS TCGA-58-A46N 
           2           25            4            4            8          910 
TCGA-60-2696 TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 
         109          311         1950         1943         1958          661 
TCGA-60-2708 TCGA-60-2709 TCGA-60-2712 TCGA-60-2715 TCGA-60-2716 TCGA-60-2721 
        1963         1505          274         1075         1475          983 
TCGA-60-2722 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-7020 TCGA-63-7021 
         908          717          816          358         1957         1955 
TCGA-63-7022 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 TCGA-66-2754 TCGA-66-2756 
        1947           61          641           30           61           30 
TCGA-66-2765 TCGA-66-2766 TCGA-66-2768 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 
          61           31           61          578         1946           61 
TCGA-66-2780 TCGA-66-2781 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2788 
        1956          121          759           60          790          699 
TCGA-66-2791 TCGA-66-2794 TCGA-66-2795 TCGA-68-7755 TCGA-68-7757 TCGA-68-8250 
        1977         1645          122           83          211          244 
TCGA-68-A59I TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7141 
         121         1941         1942         1952         1959           15 
TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 
        1954         1942         1952          479         1960         1945 
TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8138 
        1641         1953         1945         1941         1941         1946 
TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G1 
         833         1943          293         1092         1953         1942 
TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB 
        1959         1955         1963         1290         1280         1939 
TCGA-77-A5GF TCGA-85-6560 TCGA-85-7696 TCGA-85-7697 TCGA-85-7710 TCGA-85-7843 
         839          364           18           10         1965           35 
TCGA-85-7844 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8072 
         911           26           60           16          960          513 
TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 
          13           11           13           54           60           55 
TCGA-85-8352 TCGA-85-8354 TCGA-85-8479 TCGA-85-8481 TCGA-85-8582 TCGA-85-A4CL 
          67           61           22           21          424           15 
TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 
        1972         1960           19         1973         1967         1972 
TCGA-85-A513 TCGA-85-A53L TCGA-90-6837 TCGA-90-7766 TCGA-90-7769 TCGA-90-7964 
          24           13          758          289          358          428 
TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-94-7033 TCGA-94-7943 
         269           82          106          122           87          356 
TCGA-96-7544 TCGA-96-7545 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 
        1213         1344          211          183          256          413 
TCGA-98-8022 TCGA-98-8023 TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 
         224          308          222           35          449           36 
TCGA-MF-A522 TCGA-NC-A5HE TCGA-NC-A5HI 
          83         1722         1135 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 1                  2 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              3724               5287 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               684                623 
[1] "1.0 - 3724.0 (684.0)" "2.0 - 5287.0 (623.0)"
[1] "hr=" "1.2"
D69V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  16Q LOSS MUTATED         0       22       50        0        15        29
  16Q LOSS WILD-TYPE       1       50       87        1        37        42
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  16Q LOSS MUTATED           20          8        2
  16Q LOSS WILD-TYPE         37         12        4
D69V3, multiclass
            clus
vv           16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  STAGE I                   0                  1
  STAGE IA                 22                 50
  STAGE IB                 50                 87
  STAGE II                  0                  1
  STAGE IIA                15                 37
  STAGE IIB                29                 42
  STAGE IIIA               20                 37
  STAGE IIIB                8                 12
  STAGE IV                  2                  4
[1] 9 2
[1] 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    29  93  18   8
  16Q LOSS WILD-TYPE  69 161  30  12
D69V4, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  T1               29                 69
  T2               93                161
  T3               18                 30
  T4                8                 12
[1] 4 2
[1] 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    94  37  12   3
  16Q LOSS WILD-TYPE 167  76  23   2
D69V5, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  N0               94                167
  N1               37                 76
  N2               12                 23
  N3                3                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A  MX
  16Q LOSS MUTATED   130   1   1  13
  16Q LOSS WILD-TYPE 228   4   0  37
D69V6, multiclass
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  M0               130                228
  M1                 1                  4
  M1A                1                  0
  MX                13                 37
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V7, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    46 102
  16Q LOSS WILD-TYPE  61 211
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     46  102
  16Q LOSS WILD-TYPE   61  211
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE               46                 61
  MALE                102                211
[1] 2 2
[1] FALSE
D69V8, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  16Q LOSS MUTATED                                       6
  16Q LOSS WILD-TYPE                                     6
                    vv
clus                 LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  16Q LOSS MUTATED                                        0
  16Q LOSS WILD-TYPE                                      6
                    vv
clus                 LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  16Q LOSS MUTATED                                         0
  16Q LOSS WILD-TYPE                                       1
                    vv
clus                 LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  16Q LOSS MUTATED                                                           142
  16Q LOSS WILD-TYPE                                                         259
D69V9, multiclass
                                                             clus
vv                                                            16Q LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      6
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     0
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              142
                                                             clus
vv                                                            16Q LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                        6
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                259
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V10, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED     7 141
  16Q LOSS WILD-TYPE   6 266
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      7  141
  16Q LOSS WILD-TYPE    6  266
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  NO                 7                  6
  YES              141                266
[1] 2 2
[1] FALSE
D69V11, continuous
                    vv
clus                  R0  R1  R2  RX
  16Q LOSS MUTATED   117   1   2   4
  16Q LOSS WILD-TYPE 225   7   2  14
D69V12, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  R0              117                225
  R1                1                  7
  R2                2                  2
  RX                4                 14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16Q LOSS MUTATED       1                         6   103
  16Q LOSS WILD-TYPE     8                        11   195
D69V13, multiclass
                           clus
vv                          16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  ASIAN                                    1                  8
  BLACK OR AFRICAN AMERICAN                6                 11
  WHITE                                  103                195
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V14, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED     2  91
  16Q LOSS WILD-TYPE   6 176
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      2   91
  16Q LOSS WILD-TYPE    6  176
                        clus
vv                       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  6
  NOT HISPANIC OR LATINO               91                176
[1] 2 2
[1] FALSE

Clustering(70) Variable = 17P LOSS MUTATION ANALYSIS
D70V1, survival
                    sevent
clus2                  0   1
  17P LOSS MUTATED   152  78
  17P LOSS WILD-TYPE 113  45
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               230                158 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                78                 45 
$`17P LOSS MUTATED`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3410 TCGA-18-3411 TCGA-18-3414 TCGA-18-3415 
         370          136          146         1415          396         1810 
TCGA-18-3416 TCGA-18-3419 TCGA-18-3421 TCGA-18-4721 TCGA-21-1070 TCGA-21-1075 
         862           50         1331         2754         3636         2134 
TCGA-21-1077 TCGA-21-1080 TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 TCGA-21-5786 
        1058         3724         3644          267          962         1032 
TCGA-21-5787 TCGA-21-A5DI TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 TCGA-22-1011 
         329          979          223         1945          131           53 
TCGA-22-1012 TCGA-22-1016 TCGA-22-4591 TCGA-22-4594 TCGA-22-4595 TCGA-22-4596 
         429          822          623         1470          734           17 
TCGA-22-4599 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-5472 TCGA-22-5473 
        1161          399         1946          587         1964         1933 
TCGA-22-5477 TCGA-22-5478 TCGA-22-5480 TCGA-22-5481 TCGA-22-5483 TCGA-22-5489 
        1346           24         1952         1952          573         1912 
TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4547 TCGA-33-4583 TCGA-33-4586 
        1713          506           29         1311         1941          428 
TCGA-33-4587 TCGA-33-6738 TCGA-34-2600 TCGA-34-2604 TCGA-34-2608 TCGA-34-5231 
        1970          822         1874          958         1000         1528 
TCGA-34-8454 TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4133 TCGA-37-4135 
         166          120           13           12          238          207 
TCGA-37-4141 TCGA-37-5819 TCGA-39-5016 TCGA-39-5024 TCGA-39-5027 TCGA-39-5029 
          12          103         2253         1964         1849          740 
TCGA-39-5030 TCGA-39-5034 TCGA-39-5035 TCGA-39-5040 TCGA-43-2576 TCGA-43-2581 
          59         1107          474         1964         1223         1176 
TCGA-43-3394 TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 TCGA-43-7656 TCGA-43-7658 
         822          349          849          376          212         1970 
TCGA-43-8115 TCGA-43-8116 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V 
         407          358          353          296          432          366 
TCGA-46-6026 TCGA-51-4080 TCGA-52-7622 TCGA-52-7810 TCGA-52-7812 TCGA-56-1622 
         423           12          541          923         1967          881 
TCGA-56-5897 TCGA-56-5898 TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-7822 
           3          555           30           44           40            1 
TCGA-56-8503 TCGA-56-8622 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 
          41           55           36           63           17           16 
TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A5DR 
          34           38           46           30           25            4 
TCGA-58-8388 TCGA-58-8390 TCGA-58-8393 TCGA-58-A46L TCGA-58-A46M TCGA-60-2695 
         378          911         1058         1723         1072          642 
TCGA-60-2696 TCGA-60-2698 TCGA-60-2703 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 
         109          311         1950         1958          661         1963 
TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2719 
        1963         1260          274         1731         1531         1297 
TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 TCGA-60-2725 TCGA-63-6202 
          97          983          908         1092          816         1973 
TCGA-63-7020 TCGA-63-7021 TCGA-63-7023 TCGA-66-2727 TCGA-66-2734 TCGA-66-2742 
        1957         1955         1952         1967         1311          641 
TCGA-66-2753 TCGA-66-2754 TCGA-66-2757 TCGA-66-2759 TCGA-66-2763 TCGA-66-2766 
          31           61           30          762           30           31 
TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 
          61           61         1947          578         1946           61 
TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 
        1956          121         1954          759           60          790 
TCGA-66-2788 TCGA-66-2789 TCGA-66-2791 TCGA-66-2793 TCGA-66-2795 TCGA-68-7757 
         699         1955         1977         1952          122          211 
TCGA-77-6842 TCGA-77-6844 TCGA-77-6845 TCGA-77-7139 TCGA-77-7141 TCGA-77-7335 
        1950         1942         1952         1968           15         1954 
TCGA-77-7337 TCGA-77-7338 TCGA-77-7465 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 
        1942         1952          479         1945         1641         1953 
TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 
        1945         1941         1941         1947         1946         1951 
TCGA-77-8140 TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 TCGA-77-8154 
        1962          833         1943          293         1961         1092 
TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GB 
        1942         1959         1955         1963         1290         1939 
TCGA-77-A5GH TCGA-85-6560 TCGA-85-7696 TCGA-85-7697 TCGA-85-7710 TCGA-85-7844 
         713          364           18           10         1965          911 
TCGA-85-8052 TCGA-85-8070 TCGA-85-8276 TCGA-85-8287 TCGA-85-8288 TCGA-85-8479 
          16          960           13           13           54           22 
TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50Z TCGA-85-A512 
         475           15         1960           25         1973         1987 
TCGA-85-A513 TCGA-85-A53L TCGA-90-7766 TCGA-90-7767 TCGA-90-7964 TCGA-90-A4ED 
          24           13          289           89          428          244 
TCGA-90-A59Q TCGA-92-7341 TCGA-92-8063 TCGA-92-8065 TCGA-94-7033 TCGA-96-7544 
         269          106          122           70           87         1213 
TCGA-96-7545 TCGA-96-8170 TCGA-96-A4JL TCGA-98-8021 TCGA-98-8022 TCGA-L3-A4E7 
        1344          211          183          413          224           35 
TCGA-NC-A5HG TCGA-NC-A5HI 
        1548         1135 

$`17P LOSS WILD-TYPE`
TCGA-18-3408 TCGA-18-3409 TCGA-18-3412 TCGA-18-3417 TCGA-18-4083 TCGA-18-4086 
        2464         2417          345          758          187           85 
TCGA-18-5592 TCGA-18-5595 TCGA-21-1071 TCGA-21-1072 TCGA-21-1076 TCGA-21-1078 
          92          827         1426         3016         1852          474 
TCGA-21-1079 TCGA-21-1081 TCGA-21-5784 TCGA-22-0940 TCGA-22-1005 TCGA-22-1017 
         965          284         1268          608         1952         1485 
TCGA-22-4593 TCGA-22-4601 TCGA-22-4613 TCGA-22-5471 TCGA-22-5474 TCGA-22-5479 
        1067         1057          358          965          445         1651 
TCGA-22-5482 TCGA-22-5485 TCGA-33-4532 TCGA-33-4533 TCGA-33-4538 TCGA-33-4566 
         357          916         2524         1940         2979         5287 
TCGA-33-4582 TCGA-33-4589 TCGA-34-2596 TCGA-34-2605 TCGA-34-2609 TCGA-34-5232 
        1966         1948           80          881          951         2062 
TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 
        1715          707          365          428          941          552 
TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-39-5011 TCGA-39-5019 TCGA-39-5021 
         200          247          227         1454         1361         1947 
TCGA-39-5022 TCGA-39-5028 TCGA-39-5031 TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 
        1996           52          833         1084         1086          544 
TCGA-43-2578 TCGA-43-3920 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-7657 
         684         1007          757          310         1936          236 
TCGA-43-8118 TCGA-46-6025 TCGA-51-4079 TCGA-51-4081 TCGA-52-7809 TCGA-52-7811 
        1971          324           12          911         1948         1958 
TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 TCGA-56-7582 TCGA-56-7730 
          62           26           30           13           26            6 
TCGA-56-7731 TCGA-56-8504 TCGA-56-A4BW TCGA-56-A4ZK TCGA-56-A5DS TCGA-58-8391 
        1961          178            2            4            8         2167 
TCGA-58-A46J TCGA-58-A46N TCGA-60-2704 TCGA-60-2709 TCGA-60-2715 TCGA-60-2716 
        2589          910         1943         1505         1075         1475 
TCGA-60-2724 TCGA-60-2726 TCGA-63-7022 TCGA-66-2737 TCGA-66-2744 TCGA-66-2755 
         717          358         1947           61           30           28 
TCGA-66-2756 TCGA-66-2758 TCGA-66-2765 TCGA-66-2770 TCGA-66-2778 TCGA-66-2787 
          30          639           61          700          578         1217 
TCGA-66-2790 TCGA-66-2792 TCGA-66-2794 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 
         699          913         1645         1492           83          202 
TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-77-6843 TCGA-77-7138 
         244           96          121          104         1941         1959 
TCGA-77-7142 TCGA-77-7463 TCGA-77-8007 TCGA-77-8153 TCGA-77-8156 TCGA-77-A5FZ 
        1286         1954         1960         1684           10         1953 
TCGA-77-A5GA TCGA-77-A5GF TCGA-85-6561 TCGA-85-6798 TCGA-85-7698 TCGA-85-7699 
        1280          839          395           34           49            1 
TCGA-85-7843 TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 TCGA-85-8071 TCGA-85-8072 
          35           60           26           60          428          513 
TCGA-85-8277 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 TCGA-85-8354 
          11           60           55           67           54           61 
TCGA-85-8355 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8664 TCGA-85-A4PA 
          61           21          445          424            3         1972 
TCGA-85-A50M TCGA-85-A510 TCGA-85-A511 TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7769 
          19         1967         1972          111          758          358 
TCGA-90-A4EE TCGA-92-7340 TCGA-92-8064 TCGA-94-7943 TCGA-94-A4VJ TCGA-96-8169 
         331           82          160          356          430          189 
TCGA-96-A4JK TCGA-98-7454 TCGA-98-8023 TCGA-J1-A4AH TCGA-L3-A524 TCGA-LA-A446 
         273          256          308          222          449           36 
TCGA-MF-A522 TCGA-NC-A5HE 
          83         1722 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 1                  1 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              3724               5287 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             749.5              493.5 
[1] "1.0 - 3724.0 (749.5)" "1.0 - 5287.0 (493.5)"
[1] "hr=" "1.1"
D70V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  17P LOSS MUTATED         1       43       74        0        30        39
  17P LOSS WILD-TYPE       0       29       63        1        22        32
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  17P LOSS MUTATED           37         12        4
  17P LOSS WILD-TYPE         20          8        2
D70V3, multiclass
            clus
vv           17P LOSS MUTATED 17P LOSS WILD-TYPE
  STAGE I                   1                  0
  STAGE IA                 43                 29
  STAGE IB                 74                 63
  STAGE II                  0                  1
  STAGE IIA                30                 22
  STAGE IIB                39                 32
  STAGE IIIA               37                 20
  STAGE IIIB               12                  8
  STAGE IV                  4                  2
[1] 9 2
[1] 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    60 141  30   9
  17P LOSS WILD-TYPE  38 113  18  11
D70V4, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  T1               60                 38
  T2              141                113
  T3               30                 18
  T4                9                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  17P LOSS MUTATED   145  60  27   4
  17P LOSS WILD-TYPE 116  53   8   1
D70V5, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  N0              145                116
  N1               60                 53
  N2               27                  8
  N3                4                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A  MX
  17P LOSS MUTATED   205   3   1  28
  17P LOSS WILD-TYPE 153   2   0  22
D70V6, multiclass
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  M0               205                153
  M1                 3                  2
  M1A                1                  0
  MX                28                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V7, binary
                    cls
clus                   0   1
  17P LOSS MUTATED    61 179
  17P LOSS WILD-TYPE  46 134
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     61  179
  17P LOSS WILD-TYPE   46  134
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE               61                 46
  MALE                179                134
[1] 2 2
[1] FALSE
D70V8, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  17P LOSS MUTATED                                       7
  17P LOSS WILD-TYPE                                     5
                    vv
clus                 LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  17P LOSS MUTATED                                        2
  17P LOSS WILD-TYPE                                      4
                    vv
clus                 LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  17P LOSS MUTATED                                         1
  17P LOSS WILD-TYPE                                       0
                    vv
clus                 LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  17P LOSS MUTATED                                                           230
  17P LOSS WILD-TYPE                                                         171
D70V9, multiclass
                                                             clus
vv                                                            17P LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      7
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              230
                                                             clus
vv                                                            17P LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                        5
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                171
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V10, binary
                    cls
clus                   0   1
  17P LOSS MUTATED    10 230
  17P LOSS WILD-TYPE   3 177
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     10  230
  17P LOSS WILD-TYPE    3  177
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  NO                10                  3
  YES              230                177
[1] 2 2
[1] FALSE
D70V11, continuous
                    vv
clus                  R0  R1  R2  RX
  17P LOSS MUTATED   206   5   2   8
  17P LOSS WILD-TYPE 136   3   2  10
D70V12, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  R0              206                136
  R1                5                  3
  R2                2                  2
  RX                8                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17P LOSS MUTATED       6                         7   163
  17P LOSS WILD-TYPE     3                        10   135
D70V13, multiclass
                           clus
vv                          17P LOSS MUTATED 17P LOSS WILD-TYPE
  ASIAN                                    6                  3
  BLACK OR AFRICAN AMERICAN                7                 10
  WHITE                                  163                135
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V14, binary
                    cls
clus                   0   1
  17P LOSS MUTATED     4 144
  17P LOSS WILD-TYPE   4 123
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      4  144
  17P LOSS WILD-TYPE    4  123
                        clus
vv                       17P LOSS MUTATED 17P LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  4
  NOT HISPANIC OR LATINO              144                123
[1] 2 2
[1] FALSE

Clustering(71) Variable = 17Q LOSS MUTATION ANALYSIS
D71V1, survival
                    sevent
clus2                  0   1
  17Q LOSS MUTATED    52  25
  17Q LOSS WILD-TYPE 213  98
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                77                311 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                25                 98 
$`17Q LOSS MUTATED`
TCGA-18-3410 TCGA-18-3414 TCGA-21-1070 TCGA-21-A5DI TCGA-22-1011 TCGA-22-1016 
         146          396         3636          979           53          822 
TCGA-22-4595 TCGA-22-4596 TCGA-22-4605 TCGA-22-5472 TCGA-22-5478 TCGA-22-5492 
         734           17         1946         1964           24          506 
TCGA-33-4583 TCGA-33-4587 TCGA-34-2600 TCGA-34-5241 TCGA-37-4141 TCGA-39-5029 
        1941         1970         1874          428           12          740 
TCGA-39-5035 TCGA-39-5040 TCGA-43-2581 TCGA-43-3394 TCGA-43-5670 TCGA-43-7656 
         474         1964         1176          822          849          212 
TCGA-43-A56U TCGA-43-A56V TCGA-52-7622 TCGA-52-7810 TCGA-56-5897 TCGA-56-5898 
         432          366          541          923            3          555 
TCGA-56-7580 TCGA-56-7822 TCGA-56-8503 TCGA-56-8624 TCGA-56-8628 TCGA-56-A4ZJ 
          40            1           41           36           16           25 
TCGA-58-8393 TCGA-60-2695 TCGA-60-2696 TCGA-60-2708 TCGA-60-2711 TCGA-60-2714 
        1058          642          109         1963         1260         1531 
TCGA-60-2719 TCGA-60-2720 TCGA-60-2723 TCGA-63-7020 TCGA-66-2769 TCGA-66-2771 
        1297           97         1092         1957         1947          578 
TCGA-66-2780 TCGA-66-2782 TCGA-66-2786 TCGA-77-7139 TCGA-77-8008 TCGA-77-8009 
        1956         1954          790         1968         1945         1641 
TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8138 TCGA-77-8144 TCGA-77-8150 
        1945         1941         1941         1946          833         1961 
TCGA-77-A5G1 TCGA-77-A5GB TCGA-77-A5GH TCGA-85-7696 TCGA-85-7697 TCGA-85-7950 
        1942         1939          713           18           10           60 
TCGA-85-8479 TCGA-85-A4QQ TCGA-85-A50Z TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 
          22         1960         1973           24           13          111 
TCGA-92-8063 TCGA-92-8065 TCGA-96-A4JL TCGA-98-8021 TCGA-L3-A4E7 
         122           70          183          413           35 

$`17Q LOSS WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3411 TCGA-18-3412 
         370          136         2464         2417         1415          345 
TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4083 
        1810          862          758           50         1331          187 
TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1071 TCGA-21-1072 
          85         2754           92          827         1426         3016 
TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 
        2134         1852         1058          474          965         3724 
TCGA-21-1081 TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 
         284         3644          267          962         1268         1032 
TCGA-21-5787 TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 
         329          608          223         1945          131         1952 
TCGA-22-1012 TCGA-22-1017 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4599 
         429         1485          623         1067         1470         1161 
TCGA-22-4601 TCGA-22-4604 TCGA-22-4607 TCGA-22-4613 TCGA-22-5471 TCGA-22-5473 
        1057          399          587          358          965         1933 
TCGA-22-5474 TCGA-22-5477 TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 
         445         1346         1651         1952         1952          357 
TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-A5C4 TCGA-33-4532 
         573          916         1912         1713           29         2524 
TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4586 
        1940         2979         1311         5287         1966          428 
TCGA-33-4589 TCGA-33-6738 TCGA-34-2596 TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 
        1948          822           80          958          881         1000 
TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 
         951         1528         2062         1715          707          365 
TCGA-34-5927 TCGA-34-5928 TCGA-34-8454 TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 
         941          552          166          120           13           12 
TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-5819 
         200          247          227          238          207          103 
TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 
        1454         2253         1361         1947         1996         1964 
TCGA-39-5027 TCGA-39-5028 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5036 
        1849           52           59          833         1107         1084 
TCGA-39-5037 TCGA-39-5039 TCGA-43-2576 TCGA-43-2578 TCGA-43-3920 TCGA-43-5668 
        1086          544         1223          684         1007          349 
TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-7657 TCGA-43-7658 
         376          757          310         1936          236         1970 
TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 TCGA-46-6025 
         407          358         1971          353          296          324 
TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7809 TCGA-52-7811 
         423           12           12          911         1948         1958 
TCGA-52-7812 TCGA-56-1622 TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 
        1967          881           62           26           30           13 
TCGA-56-7223 TCGA-56-7579 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-8504 
          30           44           26            6         1961          178 
TCGA-56-8622 TCGA-56-8625 TCGA-56-8626 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW 
          55           63           17           34           38            2 
TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8388 
          46           30            4            4            8          378 
TCGA-58-8390 TCGA-58-8391 TCGA-58-A46J TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N 
         911         2167         2589         1723         1072          910 
TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2709 
         311         1950         1943         1958          661         1505 
TCGA-60-2710 TCGA-60-2712 TCGA-60-2713 TCGA-60-2715 TCGA-60-2716 TCGA-60-2721 
        1963          274         1731         1075         1475          983 
TCGA-60-2722 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 TCGA-63-7021 
         908          717          816          358         1973         1955 
TCGA-63-7022 TCGA-63-7023 TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 
        1947         1952         1967         1311           61          641 
TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 
          30           31           61           28           30           30 
TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 
         639          762           30           61           31           61 
TCGA-66-2768 TCGA-66-2770 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2781 
          61          700         1946           61          578          121 
TCGA-66-2783 TCGA-66-2785 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 
         759           60         1217          699         1955          699 
TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 
        1977          913         1952         1645          122         1492 
TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I 
          83          202          211          244           96          121 
TCGA-68-A59J TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 
         104         1950         1941         1942         1952         1959 
TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 
          15         1286         1954         1942         1952         1954 
TCGA-77-7465 TCGA-77-8007 TCGA-77-8128 TCGA-77-8136 TCGA-77-8139 TCGA-77-8140 
         479         1960         1953         1947         1951         1962 
TCGA-77-8145 TCGA-77-8148 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ 
        1943          293         1684         1092           10         1953 
TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GF 
        1959         1955         1963         1290         1280          839 
TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 
         364          395           34           49            1         1965 
TCGA-85-7843 TCGA-85-7844 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 
          35          911           26           60           16          960 
TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 
         428          513           13           11           13           54 
TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 
          60           55           67           54           61           61 
TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL 
          21          445          424            3          475           15 
TCGA-85-A4PA TCGA-85-A4QR TCGA-85-A50M TCGA-85-A510 TCGA-85-A511 TCGA-85-A512 
        1972           25           19         1967         1972         1987 
TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 TCGA-90-7964 TCGA-90-A4ED 
         758          289           89          358          428          244 
TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-92-8064 TCGA-94-7033 
         331          269           82          106          160           87 
TCGA-94-7943 TCGA-94-A4VJ TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 
         356          430         1213         1344          189          211 
TCGA-96-A4JK TCGA-98-7454 TCGA-98-8022 TCGA-98-8023 TCGA-J1-A4AH TCGA-L3-A524 
         273          256          224          308          222          449 
TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HE TCGA-NC-A5HG TCGA-NC-A5HI 
          36           83         1722         1548         1135 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 1                  1 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              3636               5287 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
               734                623 
[1] "1.0 - 3636.0 (734.0)" "1.0 - 5287.0 (623.0)"
[1] "hr=" "1"  
D71V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  17Q LOSS MUTATED         1       17       28        0         7        14
  17Q LOSS WILD-TYPE       0       55      109        1        45        57
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  17Q LOSS MUTATED           11          1        2
  17Q LOSS WILD-TYPE         46         19        4
D71V3, multiclass
            clus
vv           17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  STAGE I                   1                  0
  STAGE IA                 17                 55
  STAGE IB                 28                109
  STAGE II                  0                  1
  STAGE IIA                 7                 45
  STAGE IIB                14                 57
  STAGE IIIA               11                 46
  STAGE IIIB                1                 19
  STAGE IV                  2                  4
[1] 9 2
[1] 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    23  42  13   3
  17Q LOSS WILD-TYPE  75 212  35  17
D71V4, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  T1               23                 75
  T2               42                212
  T3               13                 35
  T4                3                 17
[1] 4 2
[1] 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    58  14   6   0
  17Q LOSS WILD-TYPE 203  99  29   5
D71V5, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  N0               58                203
  N1               14                 99
  N2                6                 29
  N3                0                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A  MX
  17Q LOSS MUTATED    70   1   1   8
  17Q LOSS WILD-TYPE 288   4   0  42
D71V6, multiclass
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  M0                70                288
  M1                 1                  4
  M1A                1                  0
  MX                 8                 42
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V7, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    29  52
  17Q LOSS WILD-TYPE  78 261
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     29   52
  17Q LOSS WILD-TYPE   78  261
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE               29                 78
  MALE                 52                261
[1] 2 2
[1] FALSE
D71V8, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  17Q LOSS MUTATED                                       1
  17Q LOSS WILD-TYPE                                    11
                    vv
clus                 LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  17Q LOSS MUTATED                                        1
  17Q LOSS WILD-TYPE                                      5
                    vv
clus                 LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  17Q LOSS MUTATED                                         1
  17Q LOSS WILD-TYPE                                       0
                    vv
clus                 LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  17Q LOSS MUTATED                                                            78
  17Q LOSS WILD-TYPE                                                         323
D71V9, multiclass
                                                             clus
vv                                                            17Q LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               78
                                                             clus
vv                                                            17Q LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       11
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                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"
D71V10, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     5  76
  17Q LOSS WILD-TYPE   8 331
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      5   76
  17Q LOSS WILD-TYPE    8  331
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  NO                 5                  8
  YES               76                331
[1] 2 2
[1] FALSE
D71V11, continuous
                    vv
clus                  R0  R1  R2  RX
  17Q LOSS MUTATED    69   1   0   4
  17Q LOSS WILD-TYPE 273   7   4  14
D71V12, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  R0               69                273
  R1                1                  7
  R2                0                  4
  RX                4                 14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17Q LOSS MUTATED       4                         6    50
  17Q LOSS WILD-TYPE     5                        11   248
D71V13, multiclass
                           clus
vv                          17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  ASIAN                                    4                  5
  BLACK OR AFRICAN AMERICAN                6                 11
  WHITE                                   50                248
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V14, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     2  55
  17Q LOSS WILD-TYPE   6 212
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      2   55
  17Q LOSS WILD-TYPE    6  212
                        clus
vv                       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  6
  NOT HISPANIC OR LATINO               55                212
[1] 2 2
[1] FALSE

Clustering(72) Variable = 18P LOSS MUTATION ANALYSIS
D72V1, survival
                    sevent
clus2                  0   1
  18P LOSS MUTATED    72  30
  18P LOSS WILD-TYPE 193  93
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               102                286 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                30                 93 
$`18P LOSS MUTATED`
TCGA-18-3414 TCGA-18-3415 TCGA-18-3417 TCGA-18-3421 TCGA-21-1070 TCGA-21-1071 
         396         1810          758         1331         3636         1426 
TCGA-21-1080 TCGA-21-5787 TCGA-21-A5DI TCGA-22-1000 TCGA-22-1012 TCGA-22-1016 
        3724          329          979         1945          429          822 
TCGA-22-1017 TCGA-22-4593 TCGA-22-4594 TCGA-22-4601 TCGA-22-5478 TCGA-22-5482 
        1485         1067         1470         1057           24          357 
TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 TCGA-33-4582 TCGA-33-4589 TCGA-33-6738 
        1940         2979         1311         1966         1948          822 
TCGA-34-2608 TCGA-34-2609 TCGA-34-5241 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 
        1000          951          428          247          227          238 
TCGA-39-5011 TCGA-39-5028 TCGA-39-5036 TCGA-43-3394 TCGA-43-6647 TCGA-43-7656 
        1454           52         1084          822          757          212 
TCGA-43-8115 TCGA-46-6025 TCGA-51-4079 TCGA-52-7810 TCGA-56-1622 TCGA-56-5897 
         407          324           12          923          881            3 
TCGA-56-6545 TCGA-56-7221 TCGA-56-7222 TCGA-56-8503 TCGA-56-8624 TCGA-56-8626 
          62           30           13           41           36           17 
TCGA-56-8629 TCGA-56-A4BW TCGA-56-A4ZK TCGA-58-A46M TCGA-60-2706 TCGA-60-2707 
          34            2            4         1072         1958          661 
TCGA-60-2708 TCGA-60-2720 TCGA-66-2744 TCGA-66-2753 TCGA-66-2755 TCGA-66-2766 
        1963           97           30           31           28           31 
TCGA-66-2773 TCGA-66-2780 TCGA-66-2781 TCGA-66-2785 TCGA-66-2786 TCGA-66-2790 
        1946         1956          121           60          790          699 
TCGA-66-2791 TCGA-66-2792 TCGA-66-2795 TCGA-68-7757 TCGA-68-8250 TCGA-77-6842 
        1977          913          122          211          244         1950 
TCGA-77-8007 TCGA-77-8131 TCGA-77-8136 TCGA-77-8139 TCGA-77-8140 TCGA-77-8144 
        1960         1941         1947         1951         1962          833 
TCGA-77-A5G1 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GH TCGA-85-6560 TCGA-85-7697 
        1942         1963         1290          713          364           10 
TCGA-85-7950 TCGA-85-8287 TCGA-85-8355 TCGA-85-8481 TCGA-85-A4QR TCGA-85-A511 
          60           13           61           21           25         1972 
TCGA-85-A53L TCGA-90-7766 TCGA-90-7767 TCGA-90-A4ED TCGA-92-7341 TCGA-94-7943 
          13          289           89          244          106          356 
TCGA-96-8170 TCGA-96-A4JK TCGA-98-8023 TCGA-MF-A522 TCGA-NC-A5HE TCGA-NC-A5HG 
         211          273          308           83         1722         1548 

$`18P LOSS WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 
         370          136         2464         2417          146         1415 
TCGA-18-3412 TCGA-18-3416 TCGA-18-3419 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 
         345          862           50          187           85         2754 
TCGA-18-5592 TCGA-18-5595 TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 
          92          827         3016         2134         1852         1058 
TCGA-21-1078 TCGA-21-1079 TCGA-21-1081 TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 
         474          965          284         3644          267          962 
TCGA-21-5784 TCGA-21-5786 TCGA-22-0940 TCGA-22-0944 TCGA-22-1002 TCGA-22-1005 
        1268         1032          608          223          131         1952 
TCGA-22-1011 TCGA-22-4591 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4604 
          53          623          734           17         1161          399 
TCGA-22-4605 TCGA-22-4607 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 
        1946          587          358          965         1964         1933 
TCGA-22-5474 TCGA-22-5477 TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 TCGA-22-5483 
         445         1346         1651         1952         1952          573 
TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4532 
         916         1912         1713          506           29         2524 
TCGA-33-4566 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-34-2596 TCGA-34-2600 
        5287         1941          428         1970           80         1874 
TCGA-34-2604 TCGA-34-2605 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 
         958          881         1528         2062         1715          707 
TCGA-34-5240 TCGA-34-5927 TCGA-34-5928 TCGA-34-8454 TCGA-37-3783 TCGA-37-3789 
         365          941          552          166          120           13 
TCGA-37-3792 TCGA-37-4129 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5016 
          12          200          207           12          103         2253 
TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5029 
        1361         1947         1996         1964         1849          740 
TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5037 TCGA-39-5039 
          59          833         1107          474         1086          544 
TCGA-39-5040 TCGA-43-2576 TCGA-43-2578 TCGA-43-2581 TCGA-43-3920 TCGA-43-5668 
        1964         1223          684         1176         1007          349 
TCGA-43-5670 TCGA-43-6143 TCGA-43-6770 TCGA-43-6771 TCGA-43-7657 TCGA-43-7658 
         849          376          310         1936          236         1970 
TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V 
         358         1971          353          296          432          366 
TCGA-46-6026 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 TCGA-52-7811 
         423           12          911          541         1948         1958 
TCGA-52-7812 TCGA-56-5898 TCGA-56-6546 TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 
        1967          555           26           30           44           40 
TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-8504 TCGA-56-8622 
          26            6         1961            1          178           55 
TCGA-56-8625 TCGA-56-8628 TCGA-56-A49D TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ 
          63           16           38           46           30           25 
TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-8393 
           4            8          378          911         2167         1058 
TCGA-58-A46J TCGA-58-A46L TCGA-58-A46N TCGA-60-2695 TCGA-60-2696 TCGA-60-2698 
        2589         1723          910          642          109          311 
TCGA-60-2703 TCGA-60-2704 TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 
        1950         1943         1505         1963         1260          274 
TCGA-60-2713 TCGA-60-2714 TCGA-60-2715 TCGA-60-2716 TCGA-60-2719 TCGA-60-2721 
        1731         1531         1075         1475         1297          983 
TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 
         908         1092          717          816          358         1973 
TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 TCGA-66-2727 TCGA-66-2734 
        1957         1955         1947         1952         1967         1311 
TCGA-66-2737 TCGA-66-2742 TCGA-66-2754 TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 
          61          641           61           30           30          639 
TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 
         762           30           61           61           61         1947 
TCGA-66-2770 TCGA-66-2771 TCGA-66-2777 TCGA-66-2778 TCGA-66-2782 TCGA-66-2783 
         700          578           61          578         1954          759 
TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2793 TCGA-66-2794 TCGA-66-2800 
        1217          699         1955         1952         1645         1492 
TCGA-68-7755 TCGA-68-7756 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-77-6843 
          83          202           96          121          104         1941 
TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 
        1942         1952         1959         1968           15         1286 
TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8008 
        1954         1942         1952         1954          479         1945 
TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8133 TCGA-77-8138 TCGA-77-8145 
        1641         1953         1945         1941         1946         1943 
TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ 
         293         1961         1684         1092           10         1953 
TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF TCGA-85-6561 
        1959         1955         1280         1939          839          395 
TCGA-85-6798 TCGA-85-7696 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 
          34           18           49            1         1965           35 
TCGA-85-7844 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 
         911           26           60           16          960          428 
TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 
         513           13           11           54           60           55 
TCGA-85-8352 TCGA-85-8353 TCGA-85-8354 TCGA-85-8479 TCGA-85-8580 TCGA-85-8582 
          67           54           61           22          445          424 
TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50M 
           3          475           15         1972         1960           19 
TCGA-85-A50Z TCGA-85-A510 TCGA-85-A512 TCGA-85-A513 TCGA-85-A5B5 TCGA-90-6837 
        1973         1967         1987           24          111          758 
TCGA-90-7769 TCGA-90-7964 TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-8063 
         358          428          331          269           82          122 
TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 TCGA-94-A4VJ TCGA-96-7544 TCGA-96-7545 
         160           70           87          430         1213         1344 
TCGA-96-8169 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-J1-A4AH 
         189          183          256          413          224          222 
TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-NC-A5HI 
          35          449           36         1135 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 2                  1 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              3724               5287 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             545.0              641.5 
[1] "2.0 - 3724.0 (545.0)" "1.0 - 5287.0 (641.5)"
[1] "hr=" "1.1"
D72V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  18P LOSS MUTATED         1       15       37        1        11        23
  18P LOSS WILD-TYPE       0       57      100        0        41        48
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  18P LOSS MUTATED           15          3        4
  18P LOSS WILD-TYPE         42         17        2
D72V3, multiclass
            clus
vv           18P LOSS MUTATED 18P LOSS WILD-TYPE
  STAGE I                   1                  0
  STAGE IA                 15                 57
  STAGE IB                 37                100
  STAGE II                  1                  0
  STAGE IIA                11                 41
  STAGE IIB                23                 48
  STAGE IIIA               15                 42
  STAGE IIIB                3                 17
  STAGE IV                  4                  2
[1] 9 2
[1] 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    20  73  13   6
  18P LOSS WILD-TYPE  78 181  35  14
D72V4, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  T1               20                 78
  T2               73                181
  T3               13                 35
  T4                6                 14
[1] 4 2
[1] 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    71  29   9   1
  18P LOSS WILD-TYPE 190  84  26   4
D72V5, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  N0               71                190
  N1               29                 84
  N2                9                 26
  N3                1                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A  MX
  18P LOSS MUTATED    89   3   1  16
  18P LOSS WILD-TYPE 269   2   0  34
D72V6, multiclass
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  M0                89                269
  M1                 3                  2
  M1A                1                  0
  MX                16                 34
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V7, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    24  88
  18P LOSS WILD-TYPE  83 225
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     24   88
  18P LOSS WILD-TYPE   83  225
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE               24                 83
  MALE                 88                225
[1] 2 2
[1] FALSE
D72V8, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  18P LOSS MUTATED                                       2
  18P LOSS WILD-TYPE                                    10
                    vv
clus                 LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  18P LOSS MUTATED                                        2
  18P LOSS WILD-TYPE                                      4
                    vv
clus                 LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  18P LOSS MUTATED                                         0
  18P LOSS WILD-TYPE                                       1
                    vv
clus                 LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  18P LOSS MUTATED                                                           108
  18P LOSS WILD-TYPE                                                         293
D72V9, multiclass
                                                             clus
vv                                                            18P LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      2
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              108
                                                             clus
vv                                                            18P LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       10
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                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"
D72V10, binary
                    cls
clus                   0   1
  18P LOSS MUTATED     1 111
  18P LOSS WILD-TYPE  12 296
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      1  111
  18P LOSS WILD-TYPE   12  296
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  NO                 1                 12
  YES              111                296
[1] 2 2
[1] FALSE
D72V11, continuous
                    vv
clus                  R0  R1  R2  RX
  18P LOSS MUTATED    89   2   0   4
  18P LOSS WILD-TYPE 253   6   4  14
D72V12, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  R0               89                253
  R1                2                  6
  R2                0                  4
  RX                4                 14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18P LOSS MUTATED       2                         9    72
  18P LOSS WILD-TYPE     7                         8   226
D72V13, multiclass
                           clus
vv                          18P LOSS MUTATED 18P LOSS WILD-TYPE
  ASIAN                                    2                  7
  BLACK OR AFRICAN AMERICAN                9                  8
  WHITE                                   72                226
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V14, binary
                    cls
clus                   0   1
  18P LOSS MUTATED     3  70
  18P LOSS WILD-TYPE   5 197
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      3   70
  18P LOSS WILD-TYPE    5  197
                        clus
vv                       18P LOSS MUTATED 18P LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  5
  NOT HISPANIC OR LATINO               70                197
[1] 2 2
[1] FALSE

Clustering(73) Variable = 18Q LOSS MUTATION ANALYSIS
D73V1, survival
                    sevent
clus2                  0   1
  18Q LOSS MUTATED   103  36
  18Q LOSS WILD-TYPE 162  87
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               139                249 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                36                 87 
$`18Q LOSS MUTATED`
TCGA-18-3412 TCGA-18-3414 TCGA-18-3416 TCGA-18-3417 TCGA-18-3421 TCGA-21-1070 
         345          396          862          758         1331         3636 
TCGA-21-1071 TCGA-21-1079 TCGA-21-1080 TCGA-21-5782 TCGA-21-5786 TCGA-21-5787 
        1426          965         3724          962         1032          329 
TCGA-21-A5DI TCGA-22-1000 TCGA-22-1016 TCGA-22-1017 TCGA-22-4593 TCGA-22-4599 
         979         1945          822         1485         1067         1161 
TCGA-22-4601 TCGA-22-5473 TCGA-22-A5C4 TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 
        1057         1933           29         1940         2979         1311 
TCGA-33-4583 TCGA-33-4589 TCGA-33-6738 TCGA-34-2608 TCGA-34-5231 TCGA-34-5241 
        1941         1948          822         1000         1528          428 
TCGA-34-8454 TCGA-37-3789 TCGA-37-3792 TCGA-37-4130 TCGA-37-4133 TCGA-39-5011 
         166           13           12          247          238         1454 
TCGA-39-5016 TCGA-39-5027 TCGA-39-5028 TCGA-39-5036 TCGA-43-2576 TCGA-43-3394 
        2253         1849           52         1084         1223          822 
TCGA-43-5668 TCGA-43-6647 TCGA-43-7656 TCGA-46-6025 TCGA-51-4079 TCGA-52-7810 
         349          757          212          324           12          923 
TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-6545 TCGA-56-7221 TCGA-56-7222 
        1967          881            3           62           30           13 
TCGA-56-7223 TCGA-56-8503 TCGA-56-8624 TCGA-56-8626 TCGA-56-8629 TCGA-56-A4BW 
          30           41           36           17           34            2 
TCGA-56-A4BY TCGA-56-A4ZK TCGA-56-A5DR TCGA-58-A46M TCGA-60-2696 TCGA-60-2698 
          30            4            4         1072          109          311 
TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2714 TCGA-60-2720 TCGA-60-2726 
        1958          661         1963         1531           97          358 
TCGA-66-2734 TCGA-66-2744 TCGA-66-2753 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 
        1311           30           31           30           61           31 
TCGA-66-2768 TCGA-66-2773 TCGA-66-2780 TCGA-66-2781 TCGA-66-2785 TCGA-66-2786 
          61         1946         1956          121           60          790 
TCGA-66-2790 TCGA-66-2791 TCGA-66-2792 TCGA-66-2795 TCGA-68-7757 TCGA-68-8250 
         699         1977          913          122          211          244 
TCGA-68-A59J TCGA-77-6842 TCGA-77-7337 TCGA-77-8007 TCGA-77-8130 TCGA-77-8131 
         104         1950         1942         1960         1945         1941 
TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8144 TCGA-77-8148 
        1947         1946         1951         1962          833          293 
TCGA-77-A5G1 TCGA-77-A5G8 TCGA-77-A5GH TCGA-85-6560 TCGA-85-7697 TCGA-85-7698 
        1942         1290          713          364           10           49 
TCGA-85-7844 TCGA-85-8049 TCGA-85-8072 TCGA-85-8276 TCGA-85-8287 TCGA-85-8352 
         911           60          513           13           13           67 
TCGA-85-8353 TCGA-85-8355 TCGA-85-8481 TCGA-85-A4QQ TCGA-85-A50Z TCGA-85-A510 
          54           61           21         1960         1973         1967 
TCGA-85-A511 TCGA-85-A512 TCGA-85-A53L TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 
        1972         1987           13          289           89          358 
TCGA-90-A4ED TCGA-92-7341 TCGA-92-8063 TCGA-94-7033 TCGA-94-7943 TCGA-96-8169 
         244          106          122           87          356          189 
TCGA-96-8170 TCGA-96-A4JK TCGA-98-8023 TCGA-L3-A524 TCGA-NC-A5HE TCGA-NC-A5HG 
         211          273          308          449         1722         1548 
TCGA-NC-A5HI 
        1135 

$`18Q LOSS WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 
         370          136         2464         2417          146         1415 
TCGA-18-3415 TCGA-18-3419 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 
        1810           50          187           85         2754           92 
TCGA-18-5595 TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 
         827         3016         2134         1852         1058          474 
TCGA-21-1081 TCGA-21-1082 TCGA-21-1083 TCGA-21-5784 TCGA-22-0940 TCGA-22-0944 
         284         3644          267         1268          608          223 
TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-4591 TCGA-22-4594 
         131         1952           53          429          623         1470 
TCGA-22-4595 TCGA-22-4596 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-4613 
         734           17          399         1946          587          358 
TCGA-22-5471 TCGA-22-5472 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 
         965         1964          445         1346           24         1651 
TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 
        1952         1952          357          573          916         1912 
TCGA-22-5491 TCGA-22-5492 TCGA-33-4532 TCGA-33-4566 TCGA-33-4582 TCGA-33-4586 
        1713          506         2524         5287         1966          428 
TCGA-33-4587 TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 TCGA-34-2609 
        1970           80         1874          958          881          951 
TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 TCGA-34-5927 TCGA-34-5928 
        2062         1715          707          365          941          552 
TCGA-37-3783 TCGA-37-4129 TCGA-37-4132 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 
         120          200          227          207           12          103 
TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5029 TCGA-39-5030 
        1361         1947         1996         1964          740           59 
TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5037 TCGA-39-5039 TCGA-39-5040 
         833         1107          474         1086          544         1964 
TCGA-43-2578 TCGA-43-2581 TCGA-43-3920 TCGA-43-5670 TCGA-43-6143 TCGA-43-6770 
         684         1176         1007          849          376          310 
TCGA-43-6771 TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 
        1936          236         1970          407          358         1971 
TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V TCGA-46-6026 TCGA-51-4080 
         353          296          432          366          423           12 
TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 TCGA-52-7811 TCGA-56-5898 TCGA-56-6546 
         911          541         1948         1958          555           26 
TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 
          44           40           26            6         1961            1 
TCGA-56-8504 TCGA-56-8622 TCGA-56-8625 TCGA-56-8628 TCGA-56-A49D TCGA-56-A4BX 
         178           55           63           16           38           46 
TCGA-56-A4ZJ TCGA-56-A5DS TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-8393 
          25            8          378          911         2167         1058 
TCGA-58-A46J TCGA-58-A46L TCGA-58-A46N TCGA-60-2695 TCGA-60-2703 TCGA-60-2704 
        2589         1723          910          642         1950         1943 
TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2715 
        1505         1963         1260          274         1731         1075 
TCGA-60-2716 TCGA-60-2719 TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 
        1475         1297          983          908         1092          717 
TCGA-60-2725 TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 
         816         1973         1957         1955         1947         1952 
TCGA-66-2727 TCGA-66-2737 TCGA-66-2742 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 
        1967           61          641           61           28           30 
TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 TCGA-66-2767 TCGA-66-2769 TCGA-66-2770 
          30          639          762           61         1947          700 
TCGA-66-2771 TCGA-66-2777 TCGA-66-2778 TCGA-66-2782 TCGA-66-2783 TCGA-66-2787 
         578           61          578         1954          759         1217 
TCGA-66-2788 TCGA-66-2789 TCGA-66-2793 TCGA-66-2794 TCGA-66-2800 TCGA-68-7755 
         699         1955         1952         1645         1492           83 
TCGA-68-7756 TCGA-68-8251 TCGA-68-A59I TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 
         202           96          121         1941         1942         1952 
TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7338 
        1959         1968           15         1286         1954         1952 
TCGA-77-7463 TCGA-77-7465 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8133 
        1954          479         1945         1641         1953         1941 
TCGA-77-8145 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ 
        1943         1961         1684         1092           10         1953 
TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF 
        1959         1955         1963         1280         1939          839 
TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 
         395           34           18            1         1965           35 
TCGA-85-7950 TCGA-85-8048 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8277 
          60           26           16          960          428           11 
TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8354 TCGA-85-8479 TCGA-85-8580 
          54           60           55           61           22          445 
TCGA-85-8582 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A4QR 
         424            3          475           15         1972           25 
TCGA-85-A50M TCGA-85-A513 TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7964 TCGA-90-A4EE 
          19           24          111          758          428          331 
TCGA-90-A59Q TCGA-92-7340 TCGA-92-8064 TCGA-92-8065 TCGA-94-A4VJ TCGA-96-7544 
         269           82          160           70          430         1213 
TCGA-96-7545 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-J1-A4AH 
        1344          183          256          413          224          222 
TCGA-L3-A4E7 TCGA-LA-A446 TCGA-MF-A522 
          35           36           83 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 2                  1 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              3724               5287 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               513                642 
[1] "2.0 - 3724.0 (513.0)" "1.0 - 5287.0 (642.0)"
[1] "hr=" "1.1"
D73V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  18Q LOSS MUTATED         1       18       49        0        20        31
  18Q LOSS WILD-TYPE       0       54       88        1        32        40
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  18Q LOSS MUTATED           22          3        4
  18Q LOSS WILD-TYPE         35         17        2
D73V3, multiclass
            clus
vv           18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  STAGE I                   1                  0
  STAGE IA                 18                 54
  STAGE IB                 49                 88
  STAGE II                  0                  1
  STAGE IIA                20                 32
  STAGE IIB                31                 40
  STAGE IIIA               22                 35
  STAGE IIIB                3                 17
  STAGE IV                  4                  2
[1] 9 2
[1] 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    27  95  22   6
  18Q LOSS WILD-TYPE  71 159  26  14
D73V4, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T1               27                 71
  T2               95                159
  T3               22                 26
  T4                6                 14
[1] 4 2
[1] 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    90  45  11   1
  18Q LOSS WILD-TYPE 171  68  24   4
D73V5, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  N0               90                171
  N1               45                 68
  N2               11                 24
  N3                1                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A  MX
  18Q LOSS MUTATED   121   3   1  21
  18Q LOSS WILD-TYPE 237   2   0  29
D73V6, multiclass
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  M0               121                237
  M1                 3                  2
  M1A                1                  0
  MX                21                 29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V7, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED    33 117
  18Q LOSS WILD-TYPE  74 196
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     33  117
  18Q LOSS WILD-TYPE   74  196
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE               33                 74
  MALE                117                196
[1] 2 2
[1] FALSE
D73V8, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  18Q LOSS MUTATED                                       3
  18Q LOSS WILD-TYPE                                     9
                    vv
clus                 LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  18Q LOSS MUTATED                                        3
  18Q LOSS WILD-TYPE                                      3
                    vv
clus                 LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  18Q LOSS MUTATED                                         0
  18Q LOSS WILD-TYPE                                       1
                    vv
clus                 LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  18Q LOSS MUTATED                                                           144
  18Q LOSS WILD-TYPE                                                         257
D73V9, multiclass
                                                             clus
vv                                                            18Q LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      3
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              144
                                                             clus
vv                                                            18Q LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                        9
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                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"
D73V10, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED     3 147
  18Q LOSS WILD-TYPE  10 260
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      3  147
  18Q LOSS WILD-TYPE   10  260
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  NO                 3                 10
  YES              147                260
[1] 2 2
[1] FALSE
D73V11, continuous
                    vv
clus                  R0  R1  R2  RX
  18Q LOSS MUTATED   122   2   0   8
  18Q LOSS WILD-TYPE 220   6   4  10
D73V12, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  R0              122                220
  R1                2                  6
  R2                0                  4
  RX                8                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18Q LOSS MUTATED       3                         9   105
  18Q LOSS WILD-TYPE     6                         8   193
D73V13, multiclass
                           clus
vv                          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  ASIAN                                    3                  6
  BLACK OR AFRICAN AMERICAN                9                  8
  WHITE                                  105                193
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V14, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED     4 100
  18Q LOSS WILD-TYPE   4 167
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      4  100
  18Q LOSS WILD-TYPE    4  167
                        clus
vv                       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  4
  NOT HISPANIC OR LATINO              100                167
[1] 2 2
[1] FALSE

Clustering(74) Variable = 19P LOSS MUTATION ANALYSIS
D74V1, survival
                    sevent
clus2                  0   1
  19P LOSS MUTATED    86  40
  19P LOSS WILD-TYPE 179  83
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
               126                262 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                40                 83 
$`19P LOSS MUTATED`
TCGA-18-3409 TCGA-18-3412 TCGA-18-3417 TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 
        2417          345          758           92         3636         1426 
TCGA-21-1077 TCGA-21-1081 TCGA-21-1083 TCGA-21-5786 TCGA-21-A5DI TCGA-22-0940 
        1058          284          267         1032          979          608 
TCGA-22-1002 TCGA-22-1005 TCGA-22-4594 TCGA-22-4601 TCGA-22-4605 TCGA-22-4607 
         131         1952         1470         1057         1946          587 
TCGA-22-5478 TCGA-22-5485 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4582 
          24          916          506           29         2524         1966 
TCGA-33-4587 TCGA-33-6738 TCGA-34-2604 TCGA-34-2608 TCGA-34-5241 TCGA-34-5928 
        1970          822          958         1000          428          552 
TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 
          12          200          247          227          238          207 
TCGA-37-4141 TCGA-37-5819 TCGA-39-5011 TCGA-39-5029 TCGA-39-5036 TCGA-43-2576 
          12          103         1454          740         1084         1223 
TCGA-43-2578 TCGA-43-3394 TCGA-43-5668 TCGA-43-5670 TCGA-43-6771 TCGA-43-7656 
         684          822          349          849         1936          212 
TCGA-43-A474 TCGA-43-A56V TCGA-46-6025 TCGA-46-6026 TCGA-51-4081 TCGA-52-7810 
         353          366          324          423          911          923 
TCGA-52-7811 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-7221 TCGA-56-7222 
        1958          881            3          555           30           13 
TCGA-56-7223 TCGA-56-7579 TCGA-56-7730 TCGA-56-7822 TCGA-56-8624 TCGA-56-8629 
          30           44            6            1           36           34 
TCGA-56-A49D TCGA-56-A4BX TCGA-56-A4ZJ TCGA-56-A5DR TCGA-58-8388 TCGA-58-8390 
          38           46           25            4          378          911 
TCGA-58-A46L TCGA-60-2696 TCGA-60-2706 TCGA-60-2707 TCGA-60-2711 TCGA-60-2714 
        1723          109         1958          661         1260         1531 
TCGA-60-2722 TCGA-60-2723 TCGA-63-6202 TCGA-63-7020 TCGA-63-7023 TCGA-66-2727 
         908         1092         1973         1957         1952         1967 
TCGA-66-2753 TCGA-66-2756 TCGA-66-2759 TCGA-66-2769 TCGA-66-2780 TCGA-66-2781 
          31           30          762         1947         1956          121 
TCGA-66-2782 TCGA-66-2786 TCGA-66-2788 TCGA-66-2793 TCGA-68-7755 TCGA-68-7756 
        1954          790          699         1952           83          202 
TCGA-68-8250 TCGA-77-6845 TCGA-77-7138 TCGA-77-7338 TCGA-77-7463 TCGA-77-8136 
         244         1952         1959         1952         1954         1947 
TCGA-77-8138 TCGA-77-8144 TCGA-77-8145 TCGA-77-8156 TCGA-85-6560 TCGA-85-7697 
        1946          833         1943           10          364           10 
TCGA-85-8070 TCGA-85-8072 TCGA-85-8276 TCGA-85-8287 TCGA-85-8351 TCGA-85-A4CL 
         960          513           13           13           55           15 
TCGA-85-A510 TCGA-85-A53L TCGA-90-7964 TCGA-90-A4ED TCGA-92-7341 TCGA-92-8063 
        1967           13          428          244          106          122 
TCGA-94-7943 TCGA-94-A4VJ TCGA-96-8169 TCGA-L3-A524 TCGA-NC-A5HG TCGA-NC-A5HI 
         356          430          189          449         1548         1135 

$`19P LOSS WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3410 TCGA-18-3411 TCGA-18-3414 
         370          136         2464          146         1415          396 
TCGA-18-3415 TCGA-18-3416 TCGA-18-3419 TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 
        1810          862           50         1331          187           85 
TCGA-18-4721 TCGA-18-5595 TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1078 
        2754          827         3016         2134         1852          474 
TCGA-21-1079 TCGA-21-1080 TCGA-21-1082 TCGA-21-5782 TCGA-21-5784 TCGA-21-5787 
         965         3724         3644          962         1268          329 
TCGA-22-0944 TCGA-22-1000 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-1017 
         223         1945           53          429          822         1485 
TCGA-22-4591 TCGA-22-4593 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4604 
         623         1067          734           17         1161          399 
TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 
         358          965         1964         1933          445         1346 
TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 TCGA-22-5489 
        1651         1952         1952          357          573         1912 
TCGA-22-5491 TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4583 
        1713         1940         2979         1311         5287         1941 
TCGA-33-4586 TCGA-33-4589 TCGA-34-2596 TCGA-34-2600 TCGA-34-2605 TCGA-34-2609 
         428         1948           80         1874          881          951 
TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 TCGA-34-5927 
        1528         2062         1715          707          365          941 
TCGA-34-8454 TCGA-37-3783 TCGA-37-3789 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 
         166          120           13         2253         1361         1947 
TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5030 TCGA-39-5031 
        1996         1964         1849           52           59          833 
TCGA-39-5034 TCGA-39-5035 TCGA-39-5037 TCGA-39-5039 TCGA-39-5040 TCGA-43-2581 
        1107          474         1086          544         1964         1176 
TCGA-43-3920 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-7657 TCGA-43-7658 
        1007          376          757          310          236         1970 
TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 TCGA-43-A475 TCGA-43-A56U TCGA-51-4079 
         407          358         1971          296          432           12 
TCGA-51-4080 TCGA-52-7622 TCGA-52-7809 TCGA-52-7812 TCGA-56-6545 TCGA-56-6546 
          12          541         1948         1967           62           26 
TCGA-56-7580 TCGA-56-7582 TCGA-56-7731 TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 
          40           26         1961           41          178           55 
TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-A4BW TCGA-56-A4BY TCGA-56-A4ZK 
          63           17           16            2           30            4 
TCGA-56-A5DS TCGA-58-8391 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46M TCGA-58-A46N 
           8         2167         1058         2589         1072          910 
TCGA-60-2695 TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2708 TCGA-60-2709 
         642          311         1950         1943         1963         1505 
TCGA-60-2710 TCGA-60-2712 TCGA-60-2713 TCGA-60-2715 TCGA-60-2716 TCGA-60-2719 
        1963          274         1731         1075         1475         1297 
TCGA-60-2720 TCGA-60-2721 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-7021 
          97          983          717          816          358         1955 
TCGA-63-7022 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 TCGA-66-2754 
        1947         1311           61          641           30           61 
TCGA-66-2755 TCGA-66-2757 TCGA-66-2758 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 
          28           30          639           30           61           31 
TCGA-66-2767 TCGA-66-2768 TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 
          61           61          700          578         1946           61 
TCGA-66-2778 TCGA-66-2783 TCGA-66-2785 TCGA-66-2787 TCGA-66-2789 TCGA-66-2790 
         578          759           60         1217         1955          699 
TCGA-66-2791 TCGA-66-2792 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-68-7757 
        1977          913         1645          122         1492          211 
TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 
          96          121          104         1950         1941         1942 
TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7465 
        1968           15         1286         1954         1942          479 
TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 
        1960         1945         1641         1953         1945         1941 
TCGA-77-8133 TCGA-77-8139 TCGA-77-8140 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 
        1941         1951         1962          293         1961         1684 
TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 
        1092         1953         1942         1959         1955         1963 
TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6561 
        1290         1280         1939          839          713          395 
TCGA-85-6798 TCGA-85-7696 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 
          34           18           49            1         1965           35 
TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8071 
         911           60           26           60           16          428 
TCGA-85-8277 TCGA-85-8288 TCGA-85-8350 TCGA-85-8352 TCGA-85-8353 TCGA-85-8354 
          11           54           60           67           54           61 
TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8664 
          61           22           21          445          424            3 
TCGA-85-8666 TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z 
         475         1972         1960           25           19         1973 
TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7766 
        1972         1987           24          111          758          289 
TCGA-90-7767 TCGA-90-7769 TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-8064 
          89          358          331          269           82          160 
TCGA-92-8065 TCGA-94-7033 TCGA-96-7544 TCGA-96-7545 TCGA-96-8170 TCGA-96-A4JK 
          70           87         1213         1344          211          273 
TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-J1-A4AH 
         183          256          413          224          308          222 
TCGA-L3-A4E7 TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HE 
          35           36           83         1722 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 1                  1 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              3636               5287 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             571.0              699.5 
[1] "1.0 - 3636.0 (571.0)" "1.0 - 5287.0 (699.5)"
[1] "hr=" "1.2"
D74V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  19P LOSS MUTATED         1       23       42        0        21        19
  19P LOSS WILD-TYPE       0       49       95        1        31        52
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  19P LOSS MUTATED           19          6        3
  19P LOSS WILD-TYPE         38         14        3
D74V3, multiclass
            clus
vv           19P LOSS MUTATED 19P LOSS WILD-TYPE
  STAGE I                   1                  0
  STAGE IA                 23                 49
  STAGE IB                 42                 95
  STAGE II                  0                  1
  STAGE IIA                21                 31
  STAGE IIB                19                 52
  STAGE IIIA               19                 38
  STAGE IIIB                6                 14
  STAGE IV                  3                  3
[1] 9 2
[1] 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    35  80  14   8
  19P LOSS WILD-TYPE  63 174  34  12
D74V4, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  T1               35                 63
  T2               80                174
  T3               14                 34
  T4                8                 12
[1] 4 2
[1] 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    96  25  14   0
  19P LOSS WILD-TYPE 165  88  21   5
D74V5, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  N0               96                165
  N1               25                 88
  N2               14                 21
  N3                0                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A  MX
  19P LOSS MUTATED   114   3   0  18
  19P LOSS WILD-TYPE 244   2   1  32
D74V6, multiclass
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  M0               114                244
  M1                 3                  2
  M1A                0                  1
  MX                18                 32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V7, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    31 106
  19P LOSS WILD-TYPE  76 207
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     31  106
  19P LOSS WILD-TYPE   76  207
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE               31                 76
  MALE                106                207
[1] 2 2
[1] FALSE
D74V8, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  19P LOSS MUTATED                                       4
  19P LOSS WILD-TYPE                                     8
                    vv
clus                 LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  19P LOSS MUTATED                                        2
  19P LOSS WILD-TYPE                                      4
                    vv
clus                 LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  19P LOSS MUTATED                                         1
  19P LOSS WILD-TYPE                                       0
                    vv
clus                 LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  19P LOSS MUTATED                                                           130
  19P LOSS WILD-TYPE                                                         271
D74V9, multiclass
                                                             clus
vv                                                            19P LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      4
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              130
                                                             clus
vv                                                            19P LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                        8
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                271
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V10, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     6 131
  19P LOSS WILD-TYPE   7 276
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      6  131
  19P LOSS WILD-TYPE    7  276
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  NO                 6                  7
  YES              131                276
[1] 2 2
[1] FALSE
D74V11, continuous
                    vv
clus                  R0  R1  R2  RX
  19P LOSS MUTATED   105   4   1   5
  19P LOSS WILD-TYPE 237   4   3  13
D74V12, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  R0              105                237
  R1                4                  4
  R2                1                  3
  RX                5                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19P LOSS MUTATED       2                         7    98
  19P LOSS WILD-TYPE     7                        10   200
D74V13, multiclass
                           clus
vv                          19P LOSS MUTATED 19P LOSS WILD-TYPE
  ASIAN                                    2                  7
  BLACK OR AFRICAN AMERICAN                7                 10
  WHITE                                   98                200
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V14, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     3  91
  19P LOSS WILD-TYPE   5 176
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      3   91
  19P LOSS WILD-TYPE    5  176
                        clus
vv                       19P LOSS MUTATED 19P LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  5
  NOT HISPANIC OR LATINO               91                176
[1] 2 2
[1] FALSE

Clustering(75) Variable = 19Q LOSS MUTATION ANALYSIS
D75V1, survival
                    sevent
clus2                  0   1
  19Q LOSS MUTATED    63  20
  19Q LOSS WILD-TYPE 202 103
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                83                305 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                20                103 
$`19Q LOSS MUTATED`
TCGA-18-3409 TCGA-18-3412 TCGA-18-3416 TCGA-18-5592 TCGA-21-1077 TCGA-21-A5DI 
        2417          345          862           92         1058          979 
TCGA-22-0940 TCGA-22-0944 TCGA-22-1005 TCGA-22-4594 TCGA-22-4607 TCGA-22-4613 
         608          223         1952         1470          587          358 
TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4586 TCGA-33-4587 TCGA-37-4129 TCGA-37-4133 
          29         2524          428         1970          200          238 
TCGA-37-4135 TCGA-37-4141 TCGA-39-5036 TCGA-43-3394 TCGA-43-6771 TCGA-43-7656 
         207           12         1084          822         1936          212 
TCGA-43-A474 TCGA-46-6025 TCGA-46-6026 TCGA-51-4081 TCGA-52-7810 TCGA-52-7811 
         353          324          423          911          923         1958 
TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-7221 TCGA-56-7222 TCGA-56-7579 
         881            3          555           30           13           44 
TCGA-56-7822 TCGA-56-A4BX TCGA-58-A46L TCGA-60-2696 TCGA-60-2706 TCGA-60-2707 
           1           46         1723          109         1958          661 
TCGA-60-2711 TCGA-60-2714 TCGA-63-6202 TCGA-63-7023 TCGA-66-2727 TCGA-66-2753 
        1260         1531         1973         1952         1967           31 
TCGA-66-2756 TCGA-66-2759 TCGA-66-2781 TCGA-66-2782 TCGA-66-2794 TCGA-68-7755 
          30          762          121         1954         1645           83 
TCGA-68-7756 TCGA-68-8250 TCGA-77-6845 TCGA-77-7338 TCGA-77-7463 TCGA-77-8136 
         202          244         1952         1952         1954         1947 
TCGA-77-8144 TCGA-77-8156 TCGA-85-6560 TCGA-85-6561 TCGA-85-7697 TCGA-85-7843 
         833           10          364          395           10           35 
TCGA-85-7950 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 TCGA-85-8287 
          60          960          428          513           13           13 
TCGA-85-8351 TCGA-85-A4CL TCGA-85-A512 TCGA-90-A4ED TCGA-92-8063 TCGA-94-7943 
          55           15         1987          244          122          356 
TCGA-94-A4VJ TCGA-L3-A524 TCGA-MF-A522 TCGA-NC-A5HG TCGA-NC-A5HI 
         430          449           83         1548         1135 

$`19Q LOSS WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3410 TCGA-18-3411 TCGA-18-3414 
         370          136         2464          146         1415          396 
TCGA-18-3415 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 
        1810          758           50         1331          187           85 
TCGA-18-4721 TCGA-18-5595 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 
        2754          827         3636         1426         3016         2134 
TCGA-21-1076 TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 
        1852          474          965         3724          284         3644 
TCGA-21-1083 TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-22-1000 
         267          962         1268         1032          329         1945 
TCGA-22-1002 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 
         131           53          429          822         1485          623 
TCGA-22-4593 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 
        1067          734           17         1161         1057          399 
TCGA-22-4605 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 
        1946          965         1964         1933          445         1346 
TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 
          24         1651         1952         1952          357          573 
TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-33-4533 TCGA-33-4538 
         916         1912         1713          506         1940         2979 
TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-33-4589 TCGA-33-6738 
        1311         5287         1966         1941         1948          822 
TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 
          80         1874          958          881         1000          951 
TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 
        1528         2062         1715          707          365          428 
TCGA-34-5927 TCGA-34-5928 TCGA-34-8454 TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 
         941          552          166          120           13           12 
TCGA-37-4130 TCGA-37-4132 TCGA-37-5819 TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 
         247          227          103         1454         2253         1361 
TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 
        1947         1996         1964         1849           52          740 
TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5037 TCGA-39-5039 
          59          833         1107          474         1086          544 
TCGA-39-5040 TCGA-43-2576 TCGA-43-2578 TCGA-43-2581 TCGA-43-3920 TCGA-43-5668 
        1964         1223          684         1176         1007          349 
TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-7657 TCGA-43-7658 
         849          376          757          310          236         1970 
TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V 
         407          358         1971          296          432          366 
TCGA-51-4079 TCGA-51-4080 TCGA-52-7622 TCGA-52-7809 TCGA-52-7812 TCGA-56-6545 
          12           12          541         1948         1967           62 
TCGA-56-6546 TCGA-56-7223 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 
          26           30           40           26            6         1961 
TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 
          41          178           55           36           63           17 
TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BY TCGA-56-A4ZJ 
          16           34           38            2           30           25 
TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 
           4            4            8          378          911         2167 
TCGA-58-8393 TCGA-58-A46J TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 TCGA-60-2698 
        1058         2589         1072          910          642          311 
TCGA-60-2703 TCGA-60-2704 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2712 
        1950         1943         1963         1505         1963          274 
TCGA-60-2713 TCGA-60-2715 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 
        1731         1075         1475         1297           97          983 
TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-7020 
         908         1092          717          816          358         1957 
TCGA-63-7021 TCGA-63-7022 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 
        1955         1947         1311           61          641           30 
TCGA-66-2754 TCGA-66-2755 TCGA-66-2757 TCGA-66-2758 TCGA-66-2763 TCGA-66-2765 
          61           28           30          639           30           61 
TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 
          31           61           61         1947          700          578 
TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2783 TCGA-66-2785 
        1946           61          578         1956          759           60 
TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 
         790         1217          699         1955          699         1977 
TCGA-66-2792 TCGA-66-2793 TCGA-66-2795 TCGA-66-2800 TCGA-68-7757 TCGA-68-8251 
         913         1952          122         1492          211           96 
TCGA-68-A59I TCGA-68-A59J TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-7138 
         121          104         1950         1941         1942         1959 
TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7465 
        1968           15         1286         1954         1942          479 
TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 
        1960         1945         1641         1953         1945         1941 
TCGA-77-8133 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8145 TCGA-77-8148 
        1941         1946         1951         1962         1943          293 
TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 
        1961         1684         1092         1953         1942         1959 
TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF 
        1955         1963         1290         1280         1939          839 
TCGA-77-A5GH TCGA-85-6798 TCGA-85-7696 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 
         713           34           18           49            1         1965 
TCGA-85-7844 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8277 TCGA-85-8288 
         911           26           60           16           11           54 
TCGA-85-8350 TCGA-85-8352 TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 
          60           67           54           61           61           22 
TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4PA 
          21          445          424            3          475         1972 
TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 
        1960           25           19         1973         1967         1972 
TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 
          24           13          111          758          289           89 
TCGA-90-7769 TCGA-90-7964 TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 
         358          428          331          269           82          106 
TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 
         160           70           87         1213         1344          189 
TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 
         211          273          183          256          413          224 
TCGA-98-8023 TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-LA-A446 TCGA-NC-A5HE 
         308          222           35           36         1722 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 1                  1 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              2524               5287 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
               428                713 
[1] "1.0 - 2524.0 (428.0)" "1.0 - 5287.0 (713.0)"
[1] "hr=" "1.2"
D75V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  19Q LOSS MUTATED         1       14       27        0        17        14
  19Q LOSS WILD-TYPE       0       58      110        1        35        57
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  19Q LOSS MUTATED            9          4        1
  19Q LOSS WILD-TYPE         48         16        5
D75V3, multiclass
            clus
vv           19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  STAGE I                   1                  0
  STAGE IA                 14                 58
  STAGE IB                 27                110
  STAGE II                  0                  1
  STAGE IIA                17                 35
  STAGE IIB                14                 57
  STAGE IIIA                9                 48
  STAGE IIIB                4                 16
  STAGE IV                  1                  5
[1] 9 2
[1] 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    23  52  10   5
  19Q LOSS WILD-TYPE  75 202  38  15
D75V4, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  T1               23                 75
  T2               52                202
  T3               10                 38
  T4                5                 15
[1] 4 2
[1] 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    59  20   8   0
  19Q LOSS WILD-TYPE 202  93  27   5
D75V5, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  N0               59                202
  N1               20                 93
  N2                8                 27
  N3                0                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A  MX
  19Q LOSS MUTATED    76   1   0  11
  19Q LOSS WILD-TYPE 282   4   1  39
D75V6, multiclass
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  M0                76                282
  M1                 1                  4
  M1A                0                  1
  MX                11                 39
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V7, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    16  74
  19Q LOSS WILD-TYPE  91 239
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     16   74
  19Q LOSS WILD-TYPE   91  239
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE               16                 91
  MALE                 74                239
[1] 2 2
[1] FALSE
D75V8, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  19Q LOSS MUTATED                                       3
  19Q LOSS WILD-TYPE                                     9
                    vv
clus                 LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  19Q LOSS MUTATED                                        2
  19Q LOSS WILD-TYPE                                      4
                    vv
clus                 LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  19Q LOSS MUTATED                                         1
  19Q LOSS WILD-TYPE                                       0
                    vv
clus                 LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  19Q LOSS MUTATED                                                            84
  19Q LOSS WILD-TYPE                                                         317
D75V9, multiclass
                                                             clus
vv                                                            19Q LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      3
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               84
                                                             clus
vv                                                            19Q LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                        9
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                317
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V10, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     5  85
  19Q LOSS WILD-TYPE   8 322
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      5   85
  19Q LOSS WILD-TYPE    8  322
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  NO                 5                  8
  YES               85                322
[1] 2 2
[1] FALSE
D75V11, continuous
                    vv
clus                  R0  R1  R2  RX
  19Q LOSS MUTATED    67   2   1   6
  19Q LOSS WILD-TYPE 275   6   3  12
D75V12, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  R0               67                275
  R1                2                  6
  R2                1                  3
  RX                6                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19Q LOSS MUTATED       1                         4    66
  19Q LOSS WILD-TYPE     8                        13   232
D75V13, multiclass
                           clus
vv                          19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  ASIAN                                    1                  8
  BLACK OR AFRICAN AMERICAN                4                 13
  WHITE                                   66                232
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V14, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     2  59
  19Q LOSS WILD-TYPE   6 208
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      2   59
  19Q LOSS WILD-TYPE    6  208
                        clus
vv                       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  6
  NOT HISPANIC OR LATINO               59                208
[1] 2 2
[1] FALSE

Clustering(76) Variable = 20P LOSS MUTATION ANALYSIS
D76V1, survival
                    sevent
clus2                  0   1
  20P LOSS MUTATED    26  11
  20P LOSS WILD-TYPE 239 112
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                37                351 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                11                112 
$`20P LOSS MUTATED`
TCGA-18-3416 TCGA-18-4721 TCGA-21-1078 TCGA-21-5787 TCGA-22-4593 TCGA-22-5478 
         862         2754          474          329         1067           24 
TCGA-33-4583 TCGA-33-4586 TCGA-37-3792 TCGA-37-4135 TCGA-39-5034 TCGA-43-3394 
        1941          428           12          207         1107          822 
TCGA-43-6771 TCGA-52-7810 TCGA-60-2706 TCGA-60-2712 TCGA-60-2714 TCGA-66-2755 
        1936          923         1958          274         1531           28 
TCGA-66-2766 TCGA-66-2768 TCGA-66-2790 TCGA-66-2791 TCGA-68-A59J TCGA-77-7337 
          31           61          699         1977          104         1942 
TCGA-77-7463 TCGA-77-7465 TCGA-77-8144 TCGA-85-6560 TCGA-85-7950 TCGA-85-8071 
        1954          479          833          364           60          428 
TCGA-85-8352 TCGA-85-A4QR TCGA-85-A50Z TCGA-92-8065 TCGA-96-7544 TCGA-96-8169 
          67           25         1973           70         1213          189 
TCGA-NC-A5HG 
        1548 

$`20P LOSS WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 
         370          136         2464         2417          146         1415 
TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 
         345          396         1810          758           50         1331 
TCGA-18-4083 TCGA-18-4086 TCGA-18-5592 TCGA-18-5595 TCGA-21-1070 TCGA-21-1071 
         187           85           92          827         3636         1426 
TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1079 TCGA-21-1080 
        3016         2134         1852         1058          965         3724 
TCGA-21-1081 TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 
         284         3644          267          962         1268         1032 
TCGA-21-A5DI TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 
         979          608          223         1945          131         1952 
TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 TCGA-22-4594 
          53          429          822         1485          623         1470 
TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 
         734           17         1161         1057          399         1946 
TCGA-22-4607 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 
         587          358          965         1964         1933          445 
TCGA-22-5477 TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 
        1346         1651         1952         1952          357          573 
TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4532 
         916         1912         1713          506           29         2524 
TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4587 
        1940         2979         1311         5287         1966         1970 
TCGA-33-4589 TCGA-33-6738 TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 
        1948          822           80         1874          958          881 
TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 
        1000          951         1528         2062         1715          707 
TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-8454 TCGA-37-3783 
         365          428          941          552          166          120 
TCGA-37-3789 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4141 
          13          200          247          227          238           12 
TCGA-37-5819 TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 
         103         1454         2253         1361         1947         1996 
TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 
        1964         1849           52          740           59          833 
TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 
         474         1084         1086          544         1964         1223 
TCGA-43-2578 TCGA-43-2581 TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 
         684         1176         1007          349          849          376 
TCGA-43-6647 TCGA-43-6770 TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 
         757          310          212          236         1970          407 
TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V 
         358         1971          353          296          432          366 
TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 
         324          423           12           12          911          541 
TCGA-52-7809 TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 
        1948         1958         1967          881            3          555 
TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 
          62           26           30           13           30           44 
TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-8503 
          40           26            6         1961            1           41 
TCGA-56-8504 TCGA-56-8622 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 
         178           55           36           63           17           16 
TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ 
          34           38            2           46           30           25 
TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 
           4            4            8          378          911         2167 
TCGA-58-8393 TCGA-58-A46J TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 
        1058         2589         1723         1072          910          642 
TCGA-60-2696 TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2707 TCGA-60-2708 
         109          311         1950         1943          661         1963 
TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 TCGA-60-2713 TCGA-60-2715 TCGA-60-2716 
        1505         1963         1260         1731         1075         1475 
TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 
        1297           97          983          908         1092          717 
TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 
         816          358         1973         1957         1955         1947 
TCGA-63-7023 TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 
        1952         1967         1311           61          641           30 
TCGA-66-2753 TCGA-66-2754 TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 
          31           61           30           30          639          762 
TCGA-66-2763 TCGA-66-2765 TCGA-66-2767 TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 
          30           61           61         1947          700          578 
TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 
        1946           61          578         1956          121         1954 
TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 
         759           60          790         1217          699         1955 
TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 
         913         1952         1645          122         1492           83 
TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-77-6842 
         202          211          244           96          121         1950 
TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 
        1941         1942         1952         1959         1968           15 
TCGA-77-7142 TCGA-77-7335 TCGA-77-7338 TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 
        1286         1954         1952         1960         1945         1641 
TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 
        1953         1945         1941         1941         1947         1946 
TCGA-77-8139 TCGA-77-8140 TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 
        1951         1962         1943          293         1961         1684 
TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 
        1092           10         1953         1942         1959         1955 
TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF TCGA-77-A5GH 
        1963         1290         1280         1939          839          713 
TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 
         395           34           18           10           49            1 
TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 
        1965           35          911           26           60           16 
TCGA-85-8070 TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 
         960          513           13           11           13           54 
TCGA-85-8350 TCGA-85-8351 TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 
          60           55           54           61           61           22 
TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL 
          21          445          424            3          475           15 
TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50M TCGA-85-A510 TCGA-85-A511 TCGA-85-A512 
        1972         1960           19         1967         1972         1987 
TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 
          24           13          111          758          289           89 
TCGA-90-7769 TCGA-90-7964 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 
         358          428          244          331          269           82 
TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 TCGA-94-7033 TCGA-94-7943 TCGA-94-A4VJ 
         106          122          160           87          356          430 
TCGA-96-7545 TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 
        1344          211          273          183          256          413 
TCGA-98-8022 TCGA-98-8023 TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 
         224          308          222           35          449           36 
TCGA-MF-A522 TCGA-NC-A5HE TCGA-NC-A5HI 
          83         1722         1135 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                12                  1 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
              2754               5287 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
               479                642 
[1] "12.0 - 2754.0 (479.0)" "1.0 - 5287.0 (642.0)" 
[1] "hr=" "1"  
D76V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  20P LOSS MUTATED         0        5       11        0         4        10
  20P LOSS WILD-TYPE       1       67      126        1        48        61
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  20P LOSS MUTATED            5          2        0
  20P LOSS WILD-TYPE         52         18        6
D76V3, multiclass
            clus
vv           20P LOSS MUTATED 20P LOSS WILD-TYPE
  STAGE I                   0                  1
  STAGE IA                  5                 67
  STAGE IB                 11                126
  STAGE II                  0                  1
  STAGE IIA                 4                 48
  STAGE IIB                10                 61
  STAGE IIIA                5                 52
  STAGE IIIB                2                 18
  STAGE IV                  0                  6
[1] 9 2
[1] 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     6  27   4   0
  20P LOSS WILD-TYPE  92 227  44  20
D76V4, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  T1                6                 92
  T2               27                227
  T3                4                 44
  T4                0                 20
[1] 4 2
[1] 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    21  11   4   1
  20P LOSS WILD-TYPE 240 102  31   4
D76V5, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  N0               21                240
  N1               11                102
  N2                4                 31
  N3                1                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A  MX
  20P LOSS MUTATED    33   0   0   4
  20P LOSS WILD-TYPE 325   5   1  46
D76V6, multiclass
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  M0                33                325
  M1                 0                  5
  M1A                0                  1
  MX                 4                 46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V7, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     7  30
  20P LOSS WILD-TYPE 100 283
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      7   30
  20P LOSS WILD-TYPE  100  283
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE                7                100
  MALE                 30                283
[1] 2 2
[1] FALSE
D76V8, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  20P LOSS MUTATED                                       1
  20P LOSS WILD-TYPE                                    11
                    vv
clus                 LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  20P LOSS MUTATED                                        0
  20P LOSS WILD-TYPE                                      6
                    vv
clus                 LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  20P LOSS MUTATED                                         0
  20P LOSS WILD-TYPE                                       1
                    vv
clus                 LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  20P LOSS MUTATED                                                            36
  20P LOSS WILD-TYPE                                                         365
D76V9, multiclass
                                                             clus
vv                                                            20P LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     0
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               36
                                                             clus
vv                                                            20P LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       11
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                365
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V10, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     1  36
  20P LOSS WILD-TYPE  12 371
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      1   36
  20P LOSS WILD-TYPE   12  371
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  NO                 1                 12
  YES               36                371
[1] 2 2
[1] FALSE
D76V11, continuous
                    vv
clus                  R0  R1  R2  RX
  20P LOSS MUTATED    28   1   0   3
  20P LOSS WILD-TYPE 314   7   4  15
D76V12, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  R0               28                314
  R1                1                  7
  R2                0                  4
  RX                3                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20P LOSS MUTATED       0                         2    27
  20P LOSS WILD-TYPE     9                        15   271
D76V13, multiclass
                           clus
vv                          20P LOSS MUTATED 20P LOSS WILD-TYPE
  ASIAN                                    0                  9
  BLACK OR AFRICAN AMERICAN                2                 15
  WHITE                                   27                271
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V14, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     0  23
  20P LOSS WILD-TYPE   8 244
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      0   23
  20P LOSS WILD-TYPE    8  244
                        clus
vv                       20P LOSS MUTATED 20P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  8
  NOT HISPANIC OR LATINO               23                244
[1] 2 2
[1] FALSE

Clustering(77) Variable = 20Q LOSS MUTATION ANALYSIS
D77V1, survival
                    sevent
clus2                  0   1
  20Q LOSS MUTATED    25  10
  20Q LOSS WILD-TYPE 240 113
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                35                353 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                10                113 
$`20Q LOSS MUTATED`
TCGA-18-3411 TCGA-18-3415 TCGA-18-3416 TCGA-18-4721 TCGA-21-1078 TCGA-22-4604 
        1415         1810          862         2754          474          399 
TCGA-22-5478 TCGA-33-4583 TCGA-33-4586 TCGA-34-2600 TCGA-39-5021 TCGA-39-5034 
          24         1941          428         1874         1947         1107 
TCGA-43-3394 TCGA-46-6025 TCGA-52-7622 TCGA-56-7580 TCGA-56-A49D TCGA-60-2698 
         822          324          541           40           38          311 
TCGA-60-2712 TCGA-60-2723 TCGA-66-2755 TCGA-66-2766 TCGA-66-2791 TCGA-68-A59J 
         274         1092           28           31         1977          104 
TCGA-77-7142 TCGA-77-8144 TCGA-77-8153 TCGA-77-8156 TCGA-85-7698 TCGA-85-7950 
        1286          833         1684           10           49           60 
TCGA-85-8071 TCGA-85-8352 TCGA-92-8065 TCGA-96-A4JK TCGA-L3-A524 
         428           67           70          273          449 

$`20Q LOSS WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3412 
         370          136         2464         2417          146          345 
TCGA-18-3414 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 
         396          758           50         1331          187           85 
TCGA-18-5592 TCGA-18-5595 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 
          92          827         3636         1426         3016         2134 
TCGA-21-1076 TCGA-21-1077 TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 
        1852         1058          965         3724          284         3644 
TCGA-21-1083 TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-21-A5DI 
         267          962         1268         1032          329          979 
TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 
         608          223         1945          131         1952           53 
TCGA-22-1012 TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 
         429          822         1485          623         1067         1470 
TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 TCGA-22-4605 TCGA-22-4607 
         734           17         1161         1057         1946          587 
TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 
         358          965         1964         1933          445         1346 
TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 
        1651         1952         1952          357          573          916 
TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4533 
        1912         1713          506           29         2524         1940 
TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4587 TCGA-33-4589 
        2979         1311         5287         1966         1970         1948 
TCGA-33-6738 TCGA-34-2596 TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 
         822           80          958          881         1000          951 
TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 
        1528         2062         1715          707          365          428 
TCGA-34-5927 TCGA-34-5928 TCGA-34-8454 TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 
         941          552          166          120           13           12 
TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 
         200          247          227          238          207           12 
TCGA-37-5819 TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5022 TCGA-39-5024 
         103         1454         2253         1361         1996         1964 
TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5035 
        1849           52          740           59          833          474 
TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 TCGA-43-2578 
        1084         1086          544         1964         1223          684 
TCGA-43-2581 TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 
        1176         1007          349          849          376          757 
TCGA-43-6770 TCGA-43-6771 TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 
         310         1936          212          236         1970          407 
TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V 
         358         1971          353          296          432          366 
TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7809 TCGA-52-7810 
         423           12           12          911         1948          923 
TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 
        1958         1967          881            3          555           62 
TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7582 
          26           30           13           30           44           26 
TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 
           6         1961            1           41          178           55 
TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A4BW 
          36           63           17           16           34            2 
TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS 
          46           30           25            4            4            8 
TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46L 
         378          911         2167         1058         2589         1723 
TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 TCGA-60-2696 TCGA-60-2703 TCGA-60-2704 
        1072          910          642          109         1950         1943 
TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 
        1958          661         1963         1505         1963         1260 
TCGA-60-2713 TCGA-60-2714 TCGA-60-2715 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 
        1731         1531         1075         1475         1297           97 
TCGA-60-2721 TCGA-60-2722 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 
         983          908          717          816          358         1973 
TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 TCGA-66-2727 TCGA-66-2734 
        1957         1955         1947         1952         1967         1311 
TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2756 
          61          641           30           31           61           30 
TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2767 
          30          639          762           30           61           61 
TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 
          61         1947          700          578         1946           61 
TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 
         578         1956          121         1954          759           60 
TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2792 
         790         1217          699         1955          699          913 
TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 
        1952         1645          122         1492           83          202 
TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-77-6842 TCGA-77-6843 
         211          244           96          121         1950         1941 
TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 TCGA-77-7335 
        1942         1952         1959         1968           15         1954 
TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 
        1942         1952         1954          479         1960         1945 
TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 
        1641         1953         1945         1941         1941         1947 
TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 
        1946         1951         1962         1943          293         1961 
TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 
        1092         1953         1942         1959         1955         1963 
TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6560 
        1290         1280         1939          839          713          364 
TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7699 TCGA-85-7710 
         395           34           18           10            1         1965 
TCGA-85-7843 TCGA-85-7844 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 
          35          911           26           60           16          960 
TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 
         513           13           11           13           54           60 
TCGA-85-8351 TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 
          55           54           61           61           22           21 
TCGA-85-8580 TCGA-85-8582 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4PA 
         445          424            3          475           15         1972 
TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 
        1960           25           19         1973         1967         1972 
TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7766 
        1987           24           13          111          758          289 
TCGA-90-7767 TCGA-90-7769 TCGA-90-7964 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q 
          89          358          428          244          331          269 
TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 TCGA-94-7033 TCGA-94-7943 
          82          106          122          160           87          356 
TCGA-94-A4VJ TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL 
         430         1213         1344          189          211          183 
TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-J1-A4AH TCGA-L3-A4E7 
         256          413          224          308          222           35 
TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HE TCGA-NC-A5HG TCGA-NC-A5HI 
          36           83         1722         1548         1135 

  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                10                  1 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
              2754               5287 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
               428                699 
[1] "10.0 - 2754.0 (428.0)" "1.0 - 5287.0 (699.0)" 
[1] "hr=" "1.3"
D77V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  20Q LOSS MUTATED         0        5       17        1         2         8
  20Q LOSS WILD-TYPE       1       67      120        0        50        63
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  20Q LOSS MUTATED            5          1        0
  20Q LOSS WILD-TYPE         52         19        6
D77V3, multiclass
            clus
vv           20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  STAGE I                   0                  1
  STAGE IA                  5                 67
  STAGE IB                 17                120
  STAGE II                  1                  0
  STAGE IIA                 2                 50
  STAGE IIB                 8                 63
  STAGE IIIA                5                 52
  STAGE IIIB                1                 19
  STAGE IV                  0                  6
[1] 9 2
[1] 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     6  29   4   0
  20Q LOSS WILD-TYPE  92 225  44  20
D77V4, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  T1                6                 92
  T2               29                225
  T3                4                 44
  T4                0                 20
[1] 4 2
[1] 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    25   9   4   1
  20Q LOSS WILD-TYPE 236 104  31   4
D77V5, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  N0               25                236
  N1                9                104
  N2                4                 31
  N3                1                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A  MX
  20Q LOSS MUTATED    36   0   0   3
  20Q LOSS WILD-TYPE 322   5   1  47
D77V6, multiclass
     clus
vv    20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  M0                36                322
  M1                 0                  5
  M1A                0                  1
  MX                 3                 47
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V7, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED    12  27
  20Q LOSS WILD-TYPE  95 286
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED     12   27
  20Q LOSS WILD-TYPE   95  286
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  FEMALE               12                 95
  MALE                 27                286
[1] 2 2
[1] FALSE
D77V8, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  20Q LOSS MUTATED                                       0
  20Q LOSS WILD-TYPE                                    12
                    vv
clus                 LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  20Q LOSS MUTATED                                        0
  20Q LOSS WILD-TYPE                                      6
                    vv
clus                 LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  20Q LOSS MUTATED                                         0
  20Q LOSS WILD-TYPE                                       1
                    vv
clus                 LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  20Q LOSS MUTATED                                                            39
  20Q LOSS WILD-TYPE                                                         362
D77V9, multiclass
                                                             clus
vv                                                            20Q LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     0
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               39
                                                             clus
vv                                                            20Q LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       12
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                362
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V10, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     0  39
  20Q LOSS WILD-TYPE  13 368
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      0   39
  20Q LOSS WILD-TYPE   13  368
     clus
vv    20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  NO                 0                 13
  YES               39                368
[1] 2 2
[1] FALSE
D77V11, continuous
                    vv
clus                  R0  R1  R2  RX
  20Q LOSS MUTATED    33   1   0   3
  20Q LOSS WILD-TYPE 309   7   4  15
D77V12, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  R0               33                309
  R1                1                  7
  R2                0                  4
  RX                3                 15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20Q LOSS MUTATED       0                         1    27
  20Q LOSS WILD-TYPE     9                        16   271
D77V13, multiclass
                           clus
vv                          20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  ASIAN                                    0                  9
  BLACK OR AFRICAN AMERICAN                1                 16
  WHITE                                   27                271
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V14, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     1  23
  20Q LOSS WILD-TYPE   7 244
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      1   23
  20Q LOSS WILD-TYPE    7  244
                        clus
vv                       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  7
  NOT HISPANIC OR LATINO               23                244
[1] 2 2
[1] FALSE

Clustering(78) Variable = 21Q LOSS MUTATION ANALYSIS
D78V1, survival
                    sevent
clus2                  0   1
  21Q LOSS MUTATED   143  63
  21Q LOSS WILD-TYPE 122  60
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               206                182 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                63                 60 
$`21Q LOSS MUTATED`
TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3416 
        2464         1415          345          396         1810          862 
TCGA-18-3417 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-21-1070 TCGA-21-1072 
         758          187           85         2754         3636         3016 
TCGA-21-1075 TCGA-21-1076 TCGA-21-1079 TCGA-21-1083 TCGA-21-5786 TCGA-21-5787 
        2134         1852          965          267         1032          329 
TCGA-22-0944 TCGA-22-1002 TCGA-22-1012 TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 
         223          131          429          822         1485          623 
TCGA-22-4593 TCGA-22-4594 TCGA-22-4599 TCGA-22-4604 TCGA-22-4613 TCGA-22-5471 
        1067         1470         1161          399          358          965 
TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 
        1933          445         1346           24         1651         1952 
TCGA-22-5482 TCGA-22-5483 TCGA-22-5491 TCGA-33-4532 TCGA-33-4538 TCGA-33-4547 
         357          573         1713         2524         2979         1311 
TCGA-33-4582 TCGA-33-4586 TCGA-33-4589 TCGA-34-2604 TCGA-34-2608 TCGA-34-5231 
        1966          428         1948          958         1000         1528 
TCGA-34-5241 TCGA-34-5927 TCGA-37-3789 TCGA-37-3792 TCGA-37-4130 TCGA-37-4133 
         428          941           13           12          247          238 
TCGA-37-4135 TCGA-37-5819 TCGA-39-5016 TCGA-39-5019 TCGA-39-5027 TCGA-39-5029 
         207          103         2253         1361         1849          740 
TCGA-39-5031 TCGA-39-5034 TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 TCGA-43-2576 
         833         1107         1084         1086          544         1223 
TCGA-43-2578 TCGA-43-3920 TCGA-43-5668 TCGA-43-6771 TCGA-43-7656 TCGA-43-8116 
         684         1007          349         1936          212          358 
TCGA-43-8118 TCGA-43-A56V TCGA-46-6025 TCGA-46-6026 TCGA-51-4080 TCGA-51-4081 
        1971          366          324          423           12          911 
TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 
         541         1948          923          881            3          555 
TCGA-56-6545 TCGA-56-6546 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 
          62           26           13           30           44           40 
TCGA-56-7582 TCGA-56-7730 TCGA-56-7822 TCGA-56-8503 TCGA-56-8629 TCGA-56-A49D 
          26            6            1           41           34           38 
TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4ZJ TCGA-58-8388 TCGA-58-8390 TCGA-60-2698 
           2           46           25          378          911          311 
TCGA-60-2703 TCGA-60-2707 TCGA-60-2708 TCGA-60-2711 TCGA-60-2712 TCGA-60-2715 
        1950          661         1963         1260          274         1075 
TCGA-60-2719 TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 TCGA-60-2725 TCGA-60-2726 
        1297          983          908         1092          816          358 
TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 TCGA-63-7023 TCGA-66-2734 TCGA-66-2742 
        1973         1957         1955         1952         1311          641 
TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 
          31           61           28           30          639          762 
TCGA-66-2765 TCGA-66-2766 TCGA-66-2771 TCGA-66-2777 TCGA-66-2780 TCGA-66-2781 
          61           31          578           61         1956          121 
TCGA-66-2782 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2791 
        1954           60          790         1217          699         1977 
TCGA-66-2792 TCGA-66-2793 TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 
         913         1952          122         1492           83          202 
TCGA-68-8250 TCGA-68-8251 TCGA-77-6842 TCGA-77-7141 TCGA-77-7335 TCGA-77-7463 
         244           96         1950           15         1954         1954 
TCGA-77-7465 TCGA-77-8008 TCGA-77-8009 TCGA-77-8136 TCGA-77-8145 TCGA-77-8148 
         479         1945         1641         1947         1943          293 
TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5G3 TCGA-77-A5G6 
        1961         1684         1092           10         1959         1955 
TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7698 
         839          713          395           34           18           49 
TCGA-85-7843 TCGA-85-8048 TCGA-85-8049 TCGA-85-8070 TCGA-85-8071 TCGA-85-8276 
          35           26           60          960          428           13 
TCGA-85-8287 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8354 TCGA-85-8355 
          13           60           55           67           61           61 
TCGA-85-8481 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4QR TCGA-85-A50Z 
          21            3          475           15           25         1973 
TCGA-85-A510 TCGA-85-A511 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-7766 TCGA-90-7769 
        1967         1972           13          111          289          358 
TCGA-90-A4ED TCGA-90-A4EE TCGA-92-7341 TCGA-92-8064 TCGA-94-7943 TCGA-94-A4VJ 
         244          331          106          160          356          430 
TCGA-96-A4JK TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-L3-A4E7 TCGA-LA-A446 
         273          413          224          308           35           36 
TCGA-MF-A522 TCGA-NC-A5HE 
          83         1722 

$`21Q LOSS WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3419 TCGA-18-3421 
         370          136         2417          146           50         1331 
TCGA-18-5592 TCGA-18-5595 TCGA-21-1071 TCGA-21-1077 TCGA-21-1078 TCGA-21-1080 
          92          827         1426         1058          474         3724 
TCGA-21-1081 TCGA-21-1082 TCGA-21-5782 TCGA-21-5784 TCGA-21-A5DI TCGA-22-0940 
         284         3644          962         1268          979          608 
TCGA-22-1000 TCGA-22-1005 TCGA-22-1011 TCGA-22-4595 TCGA-22-4596 TCGA-22-4601 
        1945         1952           53          734           17         1057 
TCGA-22-4605 TCGA-22-4607 TCGA-22-5472 TCGA-22-5481 TCGA-22-5485 TCGA-22-5489 
        1946          587         1964         1952          916         1912 
TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4533 TCGA-33-4566 TCGA-33-4583 TCGA-33-4587 
         506           29         1940         5287         1941         1970 
TCGA-33-6738 TCGA-34-2596 TCGA-34-2600 TCGA-34-2605 TCGA-34-2609 TCGA-34-5232 
         822           80         1874          881          951         2062 
TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 TCGA-34-5928 TCGA-34-8454 TCGA-37-3783 
        1715          707          365          552          166          120 
TCGA-37-4129 TCGA-37-4132 TCGA-37-4141 TCGA-39-5011 TCGA-39-5021 TCGA-39-5022 
         200          227           12         1454         1947         1996 
TCGA-39-5024 TCGA-39-5028 TCGA-39-5030 TCGA-39-5035 TCGA-39-5040 TCGA-43-2581 
        1964           52           59          474         1964         1176 
TCGA-43-3394 TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-7657 
         822          849          376          757          310          236 
TCGA-43-7658 TCGA-43-8115 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U TCGA-51-4079 
        1970          407          353          296          432           12 
TCGA-52-7811 TCGA-52-7812 TCGA-56-7221 TCGA-56-7731 TCGA-56-8504 TCGA-56-8622 
        1958         1967           30         1961          178           55 
TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-A4BY TCGA-56-A4ZK 
          36           63           17           16           30            4 
TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8391 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46L 
           4            8         2167         1058         2589         1723 
TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 TCGA-60-2696 TCGA-60-2704 TCGA-60-2706 
        1072          910          642          109         1943         1958 
TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 TCGA-60-2714 TCGA-60-2716 TCGA-60-2720 
        1505         1963         1731         1531         1475           97 
TCGA-60-2724 TCGA-63-7022 TCGA-66-2727 TCGA-66-2737 TCGA-66-2744 TCGA-66-2756 
         717         1947         1967           61           30           30 
TCGA-66-2763 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 TCGA-66-2773 
          30           61           61         1947          700         1946 
TCGA-66-2778 TCGA-66-2783 TCGA-66-2789 TCGA-66-2790 TCGA-66-2794 TCGA-68-7757 
         578          759         1955          699         1645          211 
TCGA-68-A59I TCGA-68-A59J TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 
         121          104         1941         1942         1952         1959 
TCGA-77-7139 TCGA-77-7142 TCGA-77-7337 TCGA-77-7338 TCGA-77-8007 TCGA-77-8128 
        1968         1286         1942         1952         1960         1953 
TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 
        1945         1941         1941         1946         1951         1962 
TCGA-77-8144 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA 
         833         1953         1942         1963         1290         1280 
TCGA-77-A5GB TCGA-85-6560 TCGA-85-7697 TCGA-85-7699 TCGA-85-7710 TCGA-85-7844 
        1939          364           10            1         1965          911 
TCGA-85-7950 TCGA-85-8052 TCGA-85-8072 TCGA-85-8277 TCGA-85-8288 TCGA-85-8353 
          60           16          513           11           54           54 
TCGA-85-8479 TCGA-85-8580 TCGA-85-8582 TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50M 
          22          445          424         1972         1960           19 
TCGA-85-A512 TCGA-85-A513 TCGA-90-6837 TCGA-90-7767 TCGA-90-7964 TCGA-90-A59Q 
        1987           24          758           89          428          269 
TCGA-92-7340 TCGA-92-8063 TCGA-92-8065 TCGA-94-7033 TCGA-96-7544 TCGA-96-7545 
          82          122           70           87         1213         1344 
TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-J1-A4AH TCGA-L3-A524 
         189          211          183          256          222          449 
TCGA-NC-A5HG TCGA-NC-A5HI 
        1548         1135 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 1                  1 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              3636               5287 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             477.0              790.5 
[1] "1.0 - 3636.0 (477.0)" "1.0 - 5287.0 (790.5)"
[1] "hr=" "1.2"
D78V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  21Q LOSS MUTATED         0       42       74        1        29        33
  21Q LOSS WILD-TYPE       1       30       63        0        23        38
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  21Q LOSS MUTATED           27         10        5
  21Q LOSS WILD-TYPE         30         10        1
D78V3, multiclass
            clus
vv           21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  STAGE I                   0                  1
  STAGE IA                 42                 30
  STAGE IB                 74                 63
  STAGE II                  1                  0
  STAGE IIA                29                 23
  STAGE IIB                33                 38
  STAGE IIIA               27                 30
  STAGE IIIB               10                 10
  STAGE IV                  5                  1
[1] 9 2
[1] 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    53 136  22  11
  21Q LOSS WILD-TYPE  45 118  26   9
D78V4, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  T1               53                 45
  T2              136                118
  T3               22                 26
  T4               11                  9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  21Q LOSS MUTATED   141  60  17   1
  21Q LOSS WILD-TYPE 120  53  18   4
D78V5, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  N0              141                120
  N1               60                 53
  N2               17                 18
  N3                1                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A  MX
  21Q LOSS MUTATED   195   4   1  19
  21Q LOSS WILD-TYPE 163   1   0  31
D78V6, multiclass
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  M0               195                163
  M1                 4                  1
  M1A                1                  0
  MX                19                 31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V7, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    40 182
  21Q LOSS WILD-TYPE  67 131
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     40  182
  21Q LOSS WILD-TYPE   67  131
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE               40                 67
  MALE                182                131
[1] 2 2
[1] FALSE
D78V8, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  21Q LOSS MUTATED                                       5
  21Q LOSS WILD-TYPE                                     7
                    vv
clus                 LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  21Q LOSS MUTATED                                        2
  21Q LOSS WILD-TYPE                                      4
                    vv
clus                 LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  21Q LOSS MUTATED                                         0
  21Q LOSS WILD-TYPE                                       1
                    vv
clus                 LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  21Q LOSS MUTATED                                                           215
  21Q LOSS WILD-TYPE                                                         186
D78V9, multiclass
                                                             clus
vv                                                            21Q LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      5
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              215
                                                             clus
vv                                                            21Q LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                        7
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                186
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V10, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     7 215
  21Q LOSS WILD-TYPE   6 192
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      7  215
  21Q LOSS WILD-TYPE    6  192
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  NO                 7                  6
  YES              215                192
[1] 2 2
[1] FALSE
D78V11, continuous
                    vv
clus                  R0  R1  R2  RX
  21Q LOSS MUTATED   184   3   2   7
  21Q LOSS WILD-TYPE 158   5   2  11
D78V12, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  R0              184                158
  R1                3                  5
  R2                2                  2
  RX                7                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  21Q LOSS MUTATED       3                         7   158
  21Q LOSS WILD-TYPE     6                        10   140
D78V13, multiclass
                           clus
vv                          21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  ASIAN                                    3                  6
  BLACK OR AFRICAN AMERICAN                7                 10
  WHITE                                  158                140
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V14, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     6 137
  21Q LOSS WILD-TYPE   2 130
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      6  137
  21Q LOSS WILD-TYPE    2  130
                        clus
vv                       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    6                  2
  NOT HISPANIC OR LATINO              137                130
[1] 2 2
[1] FALSE

Clustering(79) Variable = 22Q LOSS MUTATION ANALYSIS
D79V1, survival
                    sevent
clus2                  0   1
  22Q LOSS MUTATED    46  26
  22Q LOSS WILD-TYPE 219  97
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                72                316 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                26                 97 
$`22Q LOSS MUTATED`
TCGA-18-3407 TCGA-18-3417 TCGA-18-4083 TCGA-21-1070 TCGA-21-1071 TCGA-21-1080 
         136          758          187         3636         1426         3724 
TCGA-21-5787 TCGA-21-A5DI TCGA-22-0940 TCGA-22-1016 TCGA-22-4594 TCGA-22-5480 
         329          979          608          822         1470         1952 
TCGA-22-5483 TCGA-33-4582 TCGA-33-4583 TCGA-33-4587 TCGA-34-5928 TCGA-37-3792 
         573         1966         1941         1970          552           12 
TCGA-37-4129 TCGA-37-4132 TCGA-37-5819 TCGA-39-5011 TCGA-39-5016 TCGA-39-5029 
         200          227          103         1454         2253          740 
TCGA-39-5040 TCGA-43-2578 TCGA-43-2581 TCGA-43-6771 TCGA-43-7658 TCGA-52-7812 
        1964          684         1176         1936         1970         1967 
TCGA-56-6546 TCGA-56-7222 TCGA-60-2695 TCGA-63-6202 TCGA-66-2727 TCGA-66-2753 
          26           13          642         1973         1967           31 
TCGA-66-2754 TCGA-66-2757 TCGA-66-2759 TCGA-66-2766 TCGA-66-2771 TCGA-66-2778 
          61           30          762           31          578          578 
TCGA-66-2782 TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 TCGA-66-2793 TCGA-68-8250 
        1954         1955          699         1977         1952          244 
TCGA-68-A59I TCGA-77-7138 TCGA-77-7337 TCGA-77-7465 TCGA-77-8139 TCGA-77-8150 
         121         1959         1942          479         1951         1961 
TCGA-77-A5G6 TCGA-85-6560 TCGA-85-7697 TCGA-85-8048 TCGA-85-8049 TCGA-85-8072 
        1955          364           10           26           60          513 
TCGA-85-8664 TCGA-85-8666 TCGA-85-A510 TCGA-85-A53L TCGA-90-A4ED TCGA-90-A4EE 
           3          475         1967           13          244          331 
TCGA-90-A59Q TCGA-92-8063 TCGA-92-8065 TCGA-98-7454 TCGA-MF-A522 TCGA-NC-A5HE 
         269          122           70          256           83         1722 

$`22Q LOSS WILD-TYPE`
TCGA-18-3406 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 TCGA-18-3412 
         370         2464         2417          146         1415          345 
TCGA-18-3414 TCGA-18-3415 TCGA-18-3416 TCGA-18-3419 TCGA-18-3421 TCGA-18-4086 
         396         1810          862           50         1331           85 
TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 
        2754           92          827         3016         2134         1852 
TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 TCGA-21-1081 TCGA-21-1082 TCGA-21-1083 
        1058          474          965          284         3644          267 
TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 
         962         1268         1032          223         1945          131 
TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1017 TCGA-22-4591 TCGA-22-4593 
        1952           53          429         1485          623         1067 
TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 
         734           17         1161         1057          399         1946 
TCGA-22-4607 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 
         587          358          965         1964         1933          445 
TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5481 TCGA-22-5482 TCGA-22-5485 
        1346           24         1651         1952          357          916 
TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4533 
        1912         1713          506           29         2524         1940 
TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4586 TCGA-33-4589 TCGA-33-6738 
        2979         1311         5287          428         1948          822 
TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 
          80         1874          958          881         1000          951 
TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 
        1528         2062         1715          707          365          428 
TCGA-34-5927 TCGA-34-8454 TCGA-37-3783 TCGA-37-3789 TCGA-37-4130 TCGA-37-4133 
         941          166          120           13          247          238 
TCGA-37-4135 TCGA-37-4141 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 
         207           12         1361         1947         1996         1964 
TCGA-39-5027 TCGA-39-5028 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 
        1849           52           59          833         1107          474 
TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 TCGA-43-2576 TCGA-43-3394 TCGA-43-3920 
        1084         1086          544         1223          822         1007 
TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-7656 
         349          849          376          757          310          212 
TCGA-43-7657 TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 
         236          407          358         1971          353          296 
TCGA-43-A56U TCGA-43-A56V TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 
         432          366          324          423           12           12 
TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 TCGA-56-1622 
         911          541         1948          923         1958          881 
TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-7221 TCGA-56-7223 TCGA-56-7579 
           3          555           62           30           30           44 
TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-8503 
          40           26            6         1961            1           41 
TCGA-56-8504 TCGA-56-8622 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 
         178           55           36           63           17           16 
TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ 
          34           38            2           46           30           25 
TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 
           4            4            8          378          911         2167 
TCGA-58-8393 TCGA-58-A46J TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2696 
        1058         2589         1723         1072          910          109 
TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 
         311         1950         1943         1958          661         1963 
TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 
        1505         1963         1260          274         1731         1531 
TCGA-60-2715 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 
        1075         1475         1297           97          983          908 
TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-7020 TCGA-63-7021 
        1092          717          816          358         1957         1955 
TCGA-63-7022 TCGA-63-7023 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 
        1947         1952         1311           61          641           30 
TCGA-66-2755 TCGA-66-2756 TCGA-66-2758 TCGA-66-2763 TCGA-66-2765 TCGA-66-2767 
          28           30          639           30           61           61 
TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 TCGA-66-2773 TCGA-66-2777 TCGA-66-2780 
          61         1947          700         1946           61         1956 
TCGA-66-2781 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 
         121          759           60          790         1217          699 
TCGA-66-2792 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 
         913         1645          122         1492           83          202 
TCGA-68-7757 TCGA-68-8251 TCGA-68-A59J TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 
         211           96          104         1950         1941         1942 
TCGA-77-6845 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7338 
        1952         1968           15         1286         1954         1952 
TCGA-77-7463 TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 
        1954         1960         1945         1641         1953         1945 
TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8140 TCGA-77-8144 
        1941         1941         1947         1946         1962          833 
TCGA-77-8145 TCGA-77-8148 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ 
        1943          293         1684         1092           10         1953 
TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB 
        1942         1959         1963         1290         1280         1939 
TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7698 
         839          713          395           34           18           49 
TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 TCGA-85-8052 
           1         1965           35          911           60           16 
TCGA-85-8070 TCGA-85-8071 TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 
         960          428           13           11           13           54 
TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 
          60           55           67           54           61           61 
TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-A4CL TCGA-85-A4PA 
          22           21          445          424           15         1972 
TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A511 TCGA-85-A512 
        1960           25           19         1973         1972         1987 
TCGA-85-A513 TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 
          24          111          758          289           89          358 
TCGA-90-7964 TCGA-92-7340 TCGA-92-7341 TCGA-92-8064 TCGA-94-7033 TCGA-94-7943 
         428           82          106          160           87          356 
TCGA-94-A4VJ TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK 
         430         1213         1344          189          211          273 
TCGA-96-A4JL TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-J1-A4AH TCGA-L3-A4E7 
         183          413          224          308          222           35 
TCGA-L3-A524 TCGA-LA-A446 TCGA-NC-A5HG TCGA-NC-A5HI 
         449           36         1548         1135 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 3                  1 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              3724               5287 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               625                651 
[1] "3.0 - 3724.0 (625.0)" "1.0 - 5287.0 (651.0)"
[1] "hr=" "1.1"
D79V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  22Q LOSS MUTATED         1       10       18        0        14        12
  22Q LOSS WILD-TYPE       0       62      119        1        38        59
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IV
  22Q LOSS MUTATED           15          4        2
  22Q LOSS WILD-TYPE         42         16        4
D79V3, multiclass
            clus
vv           22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  STAGE I                   1                  0
  STAGE IA                 10                 62
  STAGE IB                 18                119
  STAGE II                  0                  1
  STAGE IIA                14                 38
  STAGE IIB                12                 59
  STAGE IIIA               15                 42
  STAGE IIIB                4                 16
  STAGE IV                  2                  4
[1] 9 2
[1] 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    17  48  10   2
  22Q LOSS WILD-TYPE  81 206  38  18
D79V4, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T1               17                 81
  T2               48                206
  T3               10                 38
  T4                2                 18
[1] 4 2
[1] 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    41  21  12   3
  22Q LOSS WILD-TYPE 220  92  23   2
D79V5, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  N0               41                220
  N1               21                 92
  N2               12                 23
  N3                3                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A  MX
  22Q LOSS MUTATED    64   2   0  10
  22Q LOSS WILD-TYPE 294   3   1  40
D79V6, multiclass
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  M0                64                294
  M1                 2                  3
  M1A                0                  1
  MX                10                 40
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V7, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    19  58
  22Q LOSS WILD-TYPE  88 255
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     19   58
  22Q LOSS WILD-TYPE   88  255
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE               19                 88
  MALE                 58                255
[1] 2 2
[1] FALSE
D79V8, continuous
                    vv
clus                 LUNG BASALOID SQUAMOUS CELL CARCINOMA
  22Q LOSS MUTATED                                       2
  22Q LOSS WILD-TYPE                                    10
                    vv
clus                 LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  22Q LOSS MUTATED                                        2
  22Q LOSS WILD-TYPE                                      4
                    vv
clus                 LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  22Q LOSS MUTATED                                         1
  22Q LOSS WILD-TYPE                                       0
                    vv
clus                 LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  22Q LOSS MUTATED                                                            72
  22Q LOSS WILD-TYPE                                                         329
D79V9, multiclass
                                                             clus
vv                                                            22Q LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                      2
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                     2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                    1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               72
                                                             clus
vv                                                            22Q LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       10
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                       4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                      0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                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"
D79V10, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED     3  74
  22Q LOSS WILD-TYPE  10 333
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      3   74
  22Q LOSS WILD-TYPE   10  333
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  NO                 3                 10
  YES               74                333
[1] 2 2
[1] FALSE
D79V11, continuous
                    vv
clus                  R0  R1  R2  RX
  22Q LOSS MUTATED    60   2   1   4
  22Q LOSS WILD-TYPE 282   6   3  14
D79V12, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  R0               60                282
  R1                2                  6
  R2                1                  3
  RX                4                 14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  22Q LOSS MUTATED       3                         4    50
  22Q LOSS WILD-TYPE     6                        13   248
D79V13, multiclass
                           clus
vv                          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  ASIAN                                    3                  6
  BLACK OR AFRICAN AMERICAN                4                 13
  WHITE                                   50                248
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V14, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED     2  46
  22Q LOSS WILD-TYPE   6 221
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      2   46
  22Q LOSS WILD-TYPE    6  221
                        clus
vv                       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  6
  NOT HISPANIC OR LATINO               46                221
[1] 2 2
[1] FALSE

Clustering(80) Variable = XQ LOSS MUTATION ANALYSIS
D80V1, survival
                   sevent
clus2                 0   1
  XQ LOSS MUTATED    51  31
  XQ LOSS WILD-TYPE 214  92
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               82               306 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               31                92 
$`XQ LOSS MUTATED`
TCGA-18-3408 TCGA-18-3416 TCGA-18-4086 TCGA-18-5592 TCGA-18-5595 TCGA-21-1072 
        2464          862           85           92          827         3016 
TCGA-21-1080 TCGA-21-1082 TCGA-21-1083 TCGA-22-0940 TCGA-22-4591 TCGA-22-4607 
        3724         3644          267          608          623          587 
TCGA-22-4613 TCGA-22-5473 TCGA-22-5477 TCGA-22-5481 TCGA-22-5485 TCGA-22-5491 
         358         1933         1346         1952          916         1713 
TCGA-22-A5C4 TCGA-33-4582 TCGA-33-4587 TCGA-34-2600 TCGA-34-2605 TCGA-37-4135 
          29         1966         1970         1874          881          207 
TCGA-37-4141 TCGA-39-5027 TCGA-39-5028 TCGA-39-5037 TCGA-43-5668 TCGA-43-7656 
          12         1849           52         1086          349          212 
TCGA-43-8116 TCGA-46-6025 TCGA-51-4080 TCGA-52-7810 TCGA-56-7221 TCGA-56-7222 
         358          324           12          923           30           13 
TCGA-56-8625 TCGA-56-A5DR TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-60-2696 
          63            4          378          911         2167          109 
TCGA-60-2712 TCGA-60-2713 TCGA-60-2721 TCGA-60-2726 TCGA-63-7023 TCGA-66-2727 
         274         1731          983          358         1952         1967 
TCGA-66-2757 TCGA-66-2763 TCGA-66-2773 TCGA-66-2780 TCGA-66-2782 TCGA-66-2786 
          30           30         1946         1956         1954          790 
TCGA-66-2789 TCGA-66-2790 TCGA-66-2795 TCGA-68-7755 TCGA-68-7756 TCGA-77-6845 
        1955          699          122           83          202         1952 
TCGA-77-7142 TCGA-77-8136 TCGA-77-8140 TCGA-77-8144 TCGA-77-8153 TCGA-77-8154 
        1286         1947         1962          833         1684         1092 
TCGA-77-A5G3 TCGA-85-7699 TCGA-85-8071 TCGA-85-8288 TCGA-85-8352 TCGA-85-8479 
        1959            1          428           54           67           22 
TCGA-85-8580 TCGA-85-A4QR TCGA-85-A512 TCGA-90-7766 TCGA-92-8063 TCGA-96-7544 
         445           25         1987          289          122         1213 
TCGA-98-8022 TCGA-LA-A446 TCGA-NC-A5HG TCGA-NC-A5HI 
         224           36         1548         1135 

$`XQ LOSS WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 TCGA-18-3412 
         370          136         2417          146         1415          345 
TCGA-18-3414 TCGA-18-3415 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4083 
         396         1810          758           50         1331          187 
TCGA-18-4721 TCGA-21-1070 TCGA-21-1071 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 
        2754         3636         1426         2134         1852         1058 
TCGA-21-1078 TCGA-21-1079 TCGA-21-1081 TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 
         474          965          284          962         1268         1032 
TCGA-21-5787 TCGA-21-A5DI TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 
         329          979          223         1945          131         1952 
TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-1017 TCGA-22-4593 TCGA-22-4594 
          53          429          822         1485         1067         1470 
TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 
         734           17         1161         1057          399         1946 
TCGA-22-5471 TCGA-22-5472 TCGA-22-5474 TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 
         965         1964          445           24         1651         1952 
TCGA-22-5482 TCGA-22-5483 TCGA-22-5489 TCGA-22-5492 TCGA-33-4532 TCGA-33-4533 
         357          573         1912          506         2524         1940 
TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4583 TCGA-33-4586 TCGA-33-4589 
        2979         1311         5287         1941          428         1948 
TCGA-33-6738 TCGA-34-2596 TCGA-34-2604 TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 
         822           80          958         1000          951         1528 
TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 
        2062         1715          707          365          428          941 
TCGA-34-5928 TCGA-34-8454 TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 
         552          166          120           13           12          200 
TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-5819 TCGA-39-5011 TCGA-39-5016 
         247          227          238          103         1454         2253 
TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5029 TCGA-39-5030 
        1361         1947         1996         1964          740           59 
TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5039 TCGA-39-5040 
         833         1107          474         1084          544         1964 
TCGA-43-2576 TCGA-43-2578 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-5670 
        1223          684         1176          822         1007          849 
TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-7657 TCGA-43-7658 
         376          757          310         1936          236         1970 
TCGA-43-8115 TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V 
         407         1971          353          296          432          366 
TCGA-46-6026 TCGA-51-4079 TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 TCGA-52-7811 
         423           12          911          541         1948         1958 
TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 
        1967          881            3          555           62           26 
TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 
          30           44           40           26            6         1961 
TCGA-56-7822 TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 TCGA-56-8624 TCGA-56-8626 
           1           41          178           55           36           17 
TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY 
          16           34           38            2           46           30 
TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DS TCGA-58-8393 TCGA-58-A46J TCGA-58-A46L 
          25            4            8         1058         2589         1723 
TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 
        1072          910          642          311         1950         1943 
TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 
        1958          661         1963         1505         1963         1260 
TCGA-60-2714 TCGA-60-2715 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2722 
        1531         1075         1475         1297           97          908 
TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 
        1092          717          816         1973         1957         1955 
TCGA-63-7022 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 TCGA-66-2753 
        1947         1311           61          641           30           31 
TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2758 TCGA-66-2759 TCGA-66-2765 
          61           28           30          639          762           61 
TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 
          31           61           61         1947          700          578 
TCGA-66-2777 TCGA-66-2778 TCGA-66-2781 TCGA-66-2783 TCGA-66-2785 TCGA-66-2787 
          61          578          121          759           60         1217 
TCGA-66-2788 TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 TCGA-66-2800 
         699         1977          913         1952         1645         1492 
TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-77-6842 
         211          244           96          121          104         1950 
TCGA-77-6843 TCGA-77-6844 TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 TCGA-77-7335 
        1941         1942         1959         1968           15         1954 
TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 
        1942         1952         1954          479         1960         1945 
TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8138 
        1641         1953         1945         1941         1941         1946 
TCGA-77-8139 TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 TCGA-77-8156 TCGA-77-A5FZ 
        1951         1943          293         1961           10         1953 
TCGA-77-A5G1 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB 
        1942         1955         1963         1290         1280         1939 
TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 
         839          713          364          395           34           18 
TCGA-85-7697 TCGA-85-7698 TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 
          10           49         1965           35          911           60 
TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8072 TCGA-85-8276 
          26           60           16          960          513           13 
TCGA-85-8277 TCGA-85-8287 TCGA-85-8350 TCGA-85-8351 TCGA-85-8353 TCGA-85-8354 
          11           13           60           55           54           61 
TCGA-85-8355 TCGA-85-8481 TCGA-85-8582 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL 
          61           21          424            3          475           15 
TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 
        1972         1960           19         1973         1967         1972 
TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7767 TCGA-90-7769 
          24           13          111          758           89          358 
TCGA-90-7964 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 
         428          244          331          269           82          106 
TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 TCGA-94-7943 TCGA-94-A4VJ TCGA-96-7545 
         160           70           87          356          430         1344 
TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 
         189          211          273          183          256          413 
TCGA-98-8023 TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 TCGA-MF-A522 TCGA-NC-A5HE 
         308          222           35          449           83         1722 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                1                 1 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             3724              5287 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            744.5             640.0 
[1] "1.0 - 3724.0 (744.5)" "1.0 - 5287.0 (640.0)"
[1] "hr=" "1.1"
D80V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  XQ LOSS MUTATED         0       19       25        0        11        15
  XQ LOSS WILD-TYPE       1       53      112        1        41        56
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IV
  XQ LOSS MUTATED           10          5        0
  XQ LOSS WILD-TYPE         47         15        6
D80V3, multiclass
            clus
vv           XQ LOSS MUTATED XQ LOSS WILD-TYPE
  STAGE I                  0                 1
  STAGE IA                19                53
  STAGE IB                25               112
  STAGE II                 0                 1
  STAGE IIA               11                41
  STAGE IIB               15                56
  STAGE IIIA              10                47
  STAGE IIIB               5                15
  STAGE IV                 0                 6
[1] 9 2
[1] 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    27  43  10   7
  XQ LOSS WILD-TYPE  71 211  38  13
D80V4, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T1              27                71
  T2              43               211
  T3              10                38
  T4               7                13
[1] 4 2
[1] 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    56  26   4   1
  XQ LOSS WILD-TYPE 205  87  31   4
D80V5, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  N0              56               205
  N1              26                87
  N2               4                31
  N3               1                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A  MX
  XQ LOSS MUTATED    75   0   0   9
  XQ LOSS WILD-TYPE 283   5   1  41
D80V6, multiclass
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  M0               75               283
  M1                0                 5
  M1A               0                 1
  MX                9                41
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V7, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    26  61
  XQ LOSS WILD-TYPE  81 252
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     26   61
  XQ LOSS WILD-TYPE   81  252
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE              26                81
  MALE                61               252
[1] 2 2
[1] FALSE
D80V8, continuous
                   vv
clus                LUNG BASALOID SQUAMOUS CELL CARCINOMA
  XQ LOSS MUTATED                                       3
  XQ LOSS WILD-TYPE                                     9
                   vv
clus                LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  XQ LOSS MUTATED                                        1
  XQ LOSS WILD-TYPE                                      5
                   vv
clus                LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  XQ LOSS MUTATED                                         1
  XQ LOSS WILD-TYPE                                       0
                   vv
clus                LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  XQ LOSS MUTATED                                                            82
  XQ LOSS WILD-TYPE                                                         319
D80V9, multiclass
                                                             clus
vv                                                            XQ LOSS MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                     3
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                    1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                   1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)              82
                                                             clus
vv                                                            XQ LOSS WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                       9
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                      5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                     0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)               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"
D80V10, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     3  84
  XQ LOSS WILD-TYPE  10 323
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      3   84
  XQ LOSS WILD-TYPE   10  323
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  NO                3                10
  YES              84               323
[1] 2 2
[1] FALSE
D80V11, continuous
                   vv
clus                 R0  R1  R2  RX
  XQ LOSS MUTATED    73   1   0   3
  XQ LOSS WILD-TYPE 269   7   4  15
D80V12, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  R0              73               269
  R1               1                 7
  R2               0                 4
  RX               3                15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XQ LOSS MUTATED       0                         2    63
  XQ LOSS WILD-TYPE     9                        15   235
D80V13, multiclass
                           clus
vv                          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  ASIAN                                   0                 9
  BLACK OR AFRICAN AMERICAN               2                15
  WHITE                                  63               235
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V14, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     0  53
  XQ LOSS WILD-TYPE   8 214
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      0   53
  XQ LOSS WILD-TYPE    8  214
                        clus
vv                       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 8
  NOT HISPANIC OR LATINO              53               214
[1] 2 2
[1] FALSE
